State Water Resources Control Board Cases (136 Cal. App. 4th 674, 2006)

Opinion

ROBIE, J.

The history of California is written on its waters—from the Eel River, to the Saltón Sea, to the Colorado River, to Lake Tahoe. But no area has been more critical than the Sacramento and San Joaquin Rivers and their great Delta and San Francisco Bay estuary.

Before us are eight appeals and three cross-appeals in seven coordinated cases known collectively as the SWRCB Cases, Judicial Council Coordinated Proceeding No. 4118. These cases arose out of an omnibus water rights proceeding before the State Water Resources Control Board (the Board) that ostensibly began with notices issued in July 1995, and ostensibly ended in March 2000 with Revised Water Right Decision 1641 (Decision 1641).

In truth, however, the water rights proceeding from which these appeals arose is but a small part of a process that has been ongoing for more than four decades to solve the problems of water quality in the San Francisco Bay/Sacramento-San Joaquin Delta Estuary. In the water rights proceeding, the Board sought to allocate responsibility among various water rights holders for meeting the flow-dependent water quality objectives in the Water Quality Control Plan for the Bay-Delta, which the Board had approved in May 1995 (the 1995 Bay-Delta Plan). As will be seen, Decision 1641 assigned much of that responsibility to the two great water projects in the state—the Central Valley Project (CVP), operated by the United States Bureau of Reclamation (the Bureau), and the State Water Project (SWP), operated by the Department of Water Resources (the Department)—which, in normal water years, export about 30 percent of the water that reaches the Delta. Many of the issues on appeal involve this allocation of responsibility.

The water rights proceeding giving rise to these appeals also dealt with two other long-standing issues: first, a petition filed by the Bureau and the Department in 1995 to use each other’s points of diversion in the southern Delta (the joint points of diversion petition), which had its origin in a similar petition filed by the Bureau in 1981; and second, a petition filed by the Bureau in 1985 (and thereafter amended) to change the places of use and conform the purposes of use in many of its CVP permits (the change petition).

On the joint points of diversion petition, the Board, in Decision 1641, conditionally granted the Bureau and the Department the right to use each other’s pumping plants in the southern Delta to export water to the south and west. On the change petition, the Board took two actions. Decision 1641 approved the Bureau’s request to conform the purposes of use in its CVP permits, which had the effect of adding fish and wildlife enhancement as an authorized purpose of use for water appropriated under 14 of those permits. Decision 1641 also approved the Bureau’s request to change the places of use in its CVP permits, but only in part. The Board authorized the addition of lands that were previously outside the permits’ authorized places of use but were already being served by CVP water, subject to mitigation requirements imposed on the Bureau for all of that land first converted to irrigated agricultural use by the delivery of that water. The Board did not, however, authorize the addition of lands that were not already being served by CVP water but were within the service districts of various CVP contractors. Instead, the Board determined those lands could be added later on a case-by-case basis.

Not surprisingly, given that water from the Delta is diverted to meet the needs of two-thirds of the population of California and to irrigate 4.5 million acres, many individuals and entities interested in Delta water appeared before the Board in the water rights proceeding at issue here. Again not surprisingly, not all of those parties were satisfied with the Board’s Decision 1641, which is what brings us here today. Originally, four cases challenging different aspects of the Board’s decision were coordinated and assigned to Judge Roland L. Candee. Ultimately, seven more cases were added, and three were dismissed, leaving eight.

In May 2003, Judge Candee issued his statement of decision in the coordinated cases, upholding Decision 1641 with two exceptions. First, Judge Candee concluded the Board erred when it failed to allocate responsibility for meeting all of the flow objectives in the 1995 Bay-Delta Plan. Second, he concluded the Board erred as to the change petition, when it refused to include all of the lands within the service area of Westlands Water District (Westlands) for authorized place of use in the Bureau’s CVP permits without any mitigation requirement. This latter conclusion rested on Judge Candee’s determination that a 1965 statute that merged Westlands with another water district “effectuated a statutory authorization for the delivery of federal CVP water to all of the lands of the combined . . . district.”

From the resulting judgments, eight timely notices of appeal and three timely notices of cross-appeal were filed in seven of the coordinated cases. The Board and two other groups of parties challenge Judge Candee’s ruling that Decision 1641 failed to implement all of the flow objectives in the 1995 Bay-Delta Plan. The Board also challenges Judge Candee’s mling that it must expand the authorized place of use in the Bureau’s CVP permits to include all of the Westlands service area without any mitigation requirement. Various other parties challenge other aspects of Judge Candee’s ruling, in which he upheld the remainder of Decision 1641. These challenges raise numerous issues regarding the law of water rights, as well as issues regarding the California Environmental Quality Act (CEQA; Pub. Resources Code, § 21000 et seq.).

Following this introduction, we will begin by setting forth the factual and procedural background of the coordinated cases, starting with brief descriptions of the CVP and SWP and continuing with a summary of the efforts to address the problems of water quality in the Delta, which led to the Board’s adoption of the 1995 Bay-Delta Plan. From there, we will summarize the underlying water rights proceeding in which the Board sought to allocate responsibility for meeting the flow-dependent objectives in the 1995 Bay-Delta Plan among the various water rights holders with interests in water that flows into the Delta. We will also describe the joint points of diversion petition and the change petition, the reasons behind those petitions, and the Board’s actions on them. We then will turn to the trial court proceedings.

The discussion section of our opinion will first address arguments on appeal relating to the Board’s implementation of the 1995 Bay-Delta Plan in the water rights proceeding. We will then address challenges relating to the joint points of diversion petition. Following this, we will address challenges to the environmental impact report (EIR) the Board prepared for the implementation of the 1995 Bay-Delta Plan and for the joint points of diversion petition. After addressing challenges relating to the change petition and to the EIR the Board prepared for that petition, we will conclude by addressing challenges to the Board’s impartiality.

We agree with Judge Candee in most respects, but disagree with him in a few instances. Most significantly, we agree with Judge Candee that the Board erred when it failed to allocate responsibility for meeting all of the flow objectives in the 1995 Bay-Delta Plan. As will be seen, we conclude the Board was not entitled to implement alternate flow objectives agreed to by various interested parties in lieu of the flow objectives actually provided for in the 1995 Bay-Delta Plan. We also conclude that the Board failed to adequately implement certain salinity objectives in the 1995 Bay-Delta Plan and failed to implement the minimum flows necessary to achieve the narrative objective for salmon protection in the 1995 Bay-Delta Plan.

Unlike Judge Candee, however, we conclude the Merger Law did not impose a ministerial duty on the Board to augment the authorized place of use in the Bureau’s CVP permits to include all of the lands within the Westlands service area without mitigation. We also reject all of the alternate arguments for upholding this aspect of Judge Candee’s decision.

Based on our conclusions, we will affirm, modify, and reverse the judgments in the seven coordinated cases as appropriate.

FACTUAL AND PROCEDURAL BACKGROUND

I

The CVP and the SWP

Nearly 20 years ago, in an opinion authored by former Presiding Justice John T. Racanelli that is often identified simply as Racanelli, the Court of Appeal, First Appellate District, Division One, addressed an earlier attempt by the Board to adopt water quality objectives for the Delta. (United States v. State Water Resources Control Bd. (1986) 182 Cal.App.3d 82 [227 Cal.Rptr. 161].) Rather than reinvent the wheel, we will draw on that opinion extensively, particularly in setting forth the background necessary to understand the issues in these coordinated cases.

We begin with Justice Racanelli’s description of the two great California water projects—the CVP and the SWP.

A

The CVP

“The history of California water development and distribution is a story of supply and demand. California’s critical water problem is not a lack of water but uneven distribution of water resources. The state is endowed with flowing rivers, countless lakes and streams and abundant winter rains and snowfall. But while over 70 percent of the stream flow lies north of Sacramento, nearly 80 percent of the demand for water supplies originates in the southern regions of the state. And because of the semiarid climate, rainfall is at a seasonal low during the summer and fall when the demand for water is greatest; conversely, rainfall and runoff from the northern snowpacks occur in late winter and early spring when user demand is lower. [Citation.] Largely to remedy such seasonal and geographic maldistribution, while simultaneously providing relief from devastating floods and droughts, the California water projects were ultimately conceived and formed.

“In 1933 the California Legislature adopted a plan for transfer of surplus water from the Sacramento River and its northern tributaries to the water-deficient areas of the San Joaquin Valley through construction of a ‘Central Valley Project’: Shasta Dam, the central feature, to store and regulate waters of the Sacramento River; Friant Dam, on the western edge of the Sierra, to divert water from the San Joaquin River to southern regions of the valley; and various other units designed to transfer water from the Sacramento River system to the San Joaquin Valley. (Wat. Code, § 11100 et seq.) However, due to the pervasive unfavorable economic conditions during the Great Depression, the state turned to the federal government to finance and construct the massive project.

“Construction of the CVP began in 1937. It is now one of the world’s most extensive water transport systems.[] As noted, Shasta Dam on the upper Sacramento River is the focal point of the CVP. Shasta Dam was completed in 1945 but began storing water and generating electric power in 1944. The waters of the Sacramento River which flow past the Shasta Dam are augmented by additional water supplies brought through a tunnel from the Trinity River and from reservoirs formed by Folsom and Nimbus Dams on the American River. About 30 miles south of Sacramento, the Delta Cross Channel regulates the passage of Sacramento River water through the Delta to the Tracy Pumping Plant.

“At Rock Slough, a portion of the water is pumped into the Contra Costa Canal for municipal uses in Contra Costa County. At the Tracy Pumping Plant, the water is lifted nearly 200 feet above sea level into the Delta[-]Mendota Canal and flows 117 miles southward to the Mendota Pool. Here, the waters from the north replace the natural flow of the San Joaquin River. At Friant Dam, the flow of the San Joaquin River is impounded and diverted through the Friant-Kem Canal 152 miles south to the southern reaches of the San Joaquin Valley.” (United States v. State Water Resources Control Bd., supra, 182 Cal.App.3d at pp. 98-99, fn. omitted.)

In addition to providing water to replace the flow of the San Joaquin River at the Mendota Pool, the Delta-Mendota Canal also supplies water for agricultural users on the west side of the San Joaquin Valley and conveys water for storage in San Luis Reservoir. That reservoir provides water to CVP contractors in the San Joaquin Valley as well as to Santa Clara and San Benito Counties through the Pacheco Tunnel.

Another part of the CVP significant to this proceeding is New Melones Dam on the Stanislaus River, which joins the San Joaquin River near Vemalis. Completed in 1979, New Melones provides flood control and maintains water quality conditions in the Stanislaus and San Joaquin Rivers. Water from New Melones is also delivered to local CVP contractors.

The CVP supplies water to over 250 long-term water contractors under contracts with the Bureau. Most of those contractors put the water to agricultural use; as of 1999, CVP water was used to irrigate approximately 19,000 farms covering three million acres. The CVP also supplies water to many urban areas in Northern and Central California, including Redding, Sacramento, most of Santa Clara County, Stockton, and Fresno.

“Under section 8 of the Reclamation Act of 1902 (43 U.S.C. § 383), the . . . Bureau is required to comply with state law and to acquire water rights for diversion and storage of water by the CVP.” (United States v. State Water Resources Control Bd., supra, 182 Cal.App.3d at p. 106; see also California v. United States (1978) 438 U.S. 645 [57 L.Ed.2d 1018, 98 S.Ct. 2985] [a state may impose any condition on control, appropriation, use or distribution of water in a federal reclamation project which is not inconsistent with clear congressional directives respecting the project].) Permit applications to appropriate water for the CVP, initially filed on behalf of the state, were assigned to the Bureau when the federal government assumed responsibility for constructing the CVP. (United States v. State Water Resources Control Bd., supra, 182 Cal.App.3d at p. 106.) “The CVP was actually completed and in operation before permits [to appropriate water for the project] were issued; the first permits were issued to the . . . Bureau in 1958 . . . and the principal permits were issued in 1961 . . . .” (Ibid.)

B

The SWP

“Following World War II, state authorities renewed their efforts to develop a comprehensive statewide water plan. In 1951 the Legislature authorized the Feather River and Sacramento-San Joaquin Delta Diversion Project. (§ 11260.) This project—referred to as the SWP—began operations in 1967 under management of the [Department].[] Water from the Feather River is stored behind Oroville Dam and is released into the Feather River and its eventual confluence with the Sacramento River.” (United States v. State Water Resources Control Bd., supra, 182 Cal.App.3d at pp. 99-100, fn. omitted.) In the northern Delta, water is diverted from Barker Slough into the North Bay Aqueduct for municipal use in Solano and Napa Counties. “The water flow continues through the Delta to the Clifton Court Forebay [in the southern Delta] where a portion of it enters the South Bay Aqueduct for delivery to [urban and agricultural areas in Alameda and Santa Clara Counties], A much greater portion is lifted [at the Harvey O. Banks Delta Pumping Plant] into the [Edmund G. Brown] California Aqueduct for transport through the San Joaquin Valley [and for use by contractors in the southern San Joaquin Valley] and eventually again lifted by a series of pumping stations over the Tehachapi Mountains for delivery and use in the Southern California region.” (Id. at p. 100.)

SWP water is delivered to 29 long-term contractors, including agricultural users in the San Joaquin Valley, with Kern County Water Agency having the contract for the greatest amount of water. SWP water transported to Southern California is used primarily for municipal and industrial purposes; the Metropolitan Water District of Southern California is the SWP’s largest contractor.

The permits to appropriate water for operation of the SWP were issued to the Department in 1967. (United States v. State Water Resources Control Bd., supra, 182 Cal.App.3d at p. 106.)

II

Water Quality in the Delta

Obviously, the Delta plays a major role in both of California’s great water projects, as water exported by both projects to the San Francisco Bay Area, the San Joaquin Valley, and Southern California is diverted from the southern Delta for transportation to the west and south. Thus, the quality of water in the Delta is important to the projects and their contractors, as well as to other water users in and around the Delta, and to the maintenance and enhancement of fish and wildlife in the Delta.

Once again, we turn to Justice Racanelli’s opinion:

“The Delta generally describes a large lowland area with a labyrinth of natural channels in and around the confluence of the Sacramento and San Joaquin Rivers. The combined river water passes through the Delta into Suisun Bay and then into San Francisco Bay. In 1959, the legal boundaries of the Delta were fixed by the Legislature. (§ 12220.) The bounded area is roughly triangular, with Sacramento at the north, Vemalis at the south and Pittsburg at the west.

“The major factor affecting water quality in the Delta is saltwater intrusion. Delta lands, situated at or below sea level, are constantly subject to ocean tidal action. Salt water entering from San Francisco Bay extends well into the Delta, and intrusion of the saline tidal waters is checked only by the natural barrier formed by fresh water flowing out from the Delta.

“But as fresh water was increasingly diverted from the Delta for agricultural, industrial and municipal development, salinity intrusion intensified, particularly during the dry summer months and in years of low precipitation and runoff into the river systems. One of the major purposes of the projects was containment of maximum salinity intrusion into the Delta. By storing waters during periods of heavy flow and releasing water during times of low flow, the freshwater barrier could be maintained at a constant level.” (United States v. State Water Resources Control Bd., supra, 182 Cal.App.3d at p. 107.)

A

Before the 1995 Bay-Delta Plan

Efforts to address water quality problems in the Delta date back more than 40 years. In 1961, the State Water Rights Board (the Water Rights Board) adopted Decision 990, which approved the Bureau’s applications for permits to appropriate water from the Sacramento River and the Delta for the CVP. In that decision, the Water Rights Board recognized the problem of salinity incursion into the Delta, but the Water Rights Board did not attach any specific water quality standards as terms and conditions of the CVP permits. Instead, the Water Rights Board reserved jurisdiction to impose such requirements later, allowing the Bureau, the state, and water users in the Delta an opportunity to reach agreement on salinity control for the Delta in the interim.

In 1965, various interested parties reached agreement on water quality criteria for the Delta—the so-called Tracy standards. (See United States v. State Water Resources Control Bd., supra, 182 Cal.App.3d at p. 110.) Two years later, the Water Rights Board issued Decision 1275, which approved the Department’s applications for permits to appropriate water from the Feather River and the Delta to operate the SWP. In that decision, the Water Rights Board noted that “both federal and state agencies are conducting extensive studies regarding the problem of water quality in the San Francisco Bay and the Delta for the purpose of determining what standards of water quality should be maintained and recommending how this is to be accomplished.” Because it lacked “sufficient information ... to finally determine the terms and conditions regarding water quality in the Delta which will reasonably protect vested rights without resulting in waste of water,” the Water Rights Board reserved jurisdiction to impose terms and conditions on the SWP permits for water quality control. In the interim, the Water Rights Board limited the Department’s diversion and storage of water from April 1 through June 30 in certain circumstances and conditioned the permits on compliance with the Tracy standards.

Meanwhile, in 1966, a proposal was made to consolidate the then existing State Water Quality Control Board with the Water Rights Board into a new agency—the State Water Resources Control Board. (See generally Assem. Interim Com. on Water, A Proposed Water Resources Control Board for Cal.: A Staff Study, supra.) The purpose of this consolidation was “to provide for the orderly and efficient administration of the water resources of the state [by] establishing] a control board which shall exercise the adjudicatory and regulatory functions of the state in the field of water resources” and “to combine the water rights and the water pollution and water quality functions of state government to provide for consideration of water pollution and water quality, and availability of unappropriated water whenever applications for appropriation of water are granted or waste discharge requirements or water quality objectives are established.” (§ 174.) Legislation creating the consolidated Board was enacted in 1967, and the Board came into existence on December 1, 1967. (Stats. 1967, ch. 284, § 2, p. 1442.)

In 1969, the Legislature enacted a new water quality control law—the Porter-Cologne Water Quality Control Act (Porter-Cologne Act; § 13000 et seq.). (Stats. 1969, ch. 482, § 18, p. 1051; see also Robie, Water Pollution: An Affirmative Response by the California Legislature (1970) 1 Pacific L.J. 2.) A summary of some of the provisions of that act will assist in understanding the efforts to address water quality in the Delta that followed.

“[T]he Porter-Cologne Water Quality Control Act . . . establishes a comprehensive statewide program for water quality control administered by nine regional boards and coordinated by the state Board. The regional boards are primarily responsible for formulation and adoption of water quality control plans covering the state’s 16 planning basins (§ 13240) subject to the Board’s review and approval (§ 13245). But the Board alone is responsible for setting statewide policy concerning water quality control (§§ 13140-13147).

“And in its capacity as the designated state water pollution control agency for purposes of the Federal Water Pollution Control Act (§ 13160), the Board is empowered to formulate its own water quality control plans which supersede conflicting regional basin plans. (§ 13170.)” (United States v. State Water Resources Control Bd., supra, 182 Cal.App.3d at p. 109.)

Under the Porter-Cologne Act, “ ‘[w]ater quality control’ means the regulation of any activity or factor which may affect the quality of the waters of the state . . . .” (§ 13050, subd. (i).) “ ‘Quality of the water’ . . . refers to chemical, physical, biological, bacteriological, radiological, and other properties and characteristics of water which affect its use.” (Id., subd. (g).) A water quality control plan “consists of a designation or establishment for the waters within a specified area of all of the following: [][] (1) Beneficial uses to be protected, [f] (2) Water quality objectives, [f] (3) A program of implementation needed for achieving water quality objectives.” (Id., subd. (j).) “ ‘Water quality objectives’ means the limits or levels of water quality constituents or characteristics which are established for the reasonable protection of beneficial uses of water or the prevention of nuisance within a specific area.” (Id., subd. (h).)

“In formulating a water quality control plan, the Board is invested with wide authority ‘to attain the highest water quality which is reasonable, considering all demands being made and to be made on those waters and the total values involved, beneficial and detrimental, economic and social, tangible and intangible.’ (§ 13000.) In fulfilling its statutory imperative, the Board is required to ‘establish such water quality objectives ... as in its judgment will ensure the reasonable protection of beneficial uses . . .’ (§ 13241), a conceptual classification far-reaching in scope.[] ‘ “Beneficial uses” of the waters of the state that may be protected against quality degradation include, but are not necessarily limited to, domestic, municipal, agricultural and industrial supply; power generation; recreation; aesthetic enjoyment; navigation; and preservation and enhancement of fish, wildlife, and other aquatic resources or preserves.’ (§ 13050, subd. (f).) Thus, in carrying out its water quality planning function, the Board possesses broad powers and responsibilities in setting water quality [objectives].” (United States v. State Water Resources Control Bd., supra, 182 Cal.App.3d at pp. 109-110.)

The program of implementation that must be included in every water quality control plan must “include, but not be limited to: [][] (a) A description of the nature of actions which are necessary to achieve the objectives, including recommendations for appropriate action by any entity, public or private. [][] (b) A time schedule for the actions to be taken, [f] (c) A description of surveillance to be undertaken to determine compliance with objectives.” (§ 13242.) Also, the Board may “not adopt any water quality control plan unless a public hearing is first held, after the giving of notice . . . .” (§ 13244.)

“In performing its regulatory function of ensuring water quality by establishing water quality objectives, the Board acts in a legislative capacity.” (United States v. State Water Resources Control Bd., supra, 182 Cal.App.3d at p. 112.) “[W]ater quality control plans ... are quasi-legislative.” (State Water Resources Control Bd. v. Office of Admin. Law (1993) 12 Cal.App.4th 697, 701-702 [16 Cal.Rptr.2d 25].)

In 1971, following the enactment of the Porter-Cologne Act, “the Board issued Decision 1379 establishing new water quality [objectives] purportedly applicable to both the CVP and the SWP. The decision was stayed as a result of litigation challenging the Board’s authority to impose conditions on permits held by a federal agency.[]

“At about the same time, the regional water quality control boards (see § 13240) formulated plans for the 16 ‘basins’ of the state, including the Delta and the Suisun Marsh. The Basin 5B Plan, setting water quality [objectives] for the Delta, and the Basin 2 Plan, setting [objectives] for the San Francisco Bay Basin, were finally approved by the Board in 1975.

“In approving the Basin 5B Plan, the Board indicated its intention to convene hearings no later than July 1, 1978, for the purpose of receiving further evidence relating to salinity control and protection of fish and wildlife. [Over an 11-month period], the Board held an extended evidentiary hearing culminating in [August 1978 with the] adoption of the 1978 Water Quality Control Plan for the Sacramento-San Joaquin Delta and Suisun Marsh. The Plan [wa]s intended to remain in effect for 10 years with new hearings to be scheduled in 1986 to reevaluate the Delta [objectives],

“In conducting the 1978 proceedings, the Board for the first time acted pursuant to its combined authority to determine water rights and to establish water quality [objectives]. (§ 174.) In discharging its dual functions, the Board reconsidered existing water quality [objectives] in light of current data concerning the effects on the Delta of the operations of the two water projects—the users with the greatest impact. The Board also undertook to modify the existing water rights permits of the projects—the water rights holders with the lowest seniority—in order to implement the enacted water quality [objectives].

“The final product of the Board’s efforts was the Water Quality Control Plan for the Sacramento-San Joaquin Delta and Suisun Marsh and Water Right Decision 1485. In the Plan, the Board set new water quality [objectives] to protect fish and wildlife and to protect agricultural, industrial and municipal uses of Delta waters. In the Decision, the Board modified the permits held by the . . . Bureau and the [Department] to compel the projects to release enough water into the Delta or to reduce their exports from the Delta so as to maintain the water quality [objectives] set in the Plan.” (United States v. State Water Resources Control Bd., supra, 182 Cal.App.3d at pp. 110-111.)

A number of parties filed mandamus petitions seeking to invalidate the water quality control plan and Decision 1485. (United States v. State Water Resources Control Bd., supra, 182 Cal.App.3d at p. 111.) In the coordinated proceeding on those petitions, the trial court rejected the Board’s water quality objectives as inadequate and issued a writ of mandate commanding the Board to set aside the plan and the decision and to reconsider the plan. (Id. at pp. 111, 120.)

On appeal, in the 1986 opinion authored by Justice Racanelli, the appellate court concluded “that the modification of the projects’ permits in order to implement the water quality [objectives] was a proper exercise of the Board’s water rights authority,” but “in establishing only such water quality [objectives] as will protect Delta water users against the effects of project activities, the Board misconceived the scope of its water quality planning function.” (United States v. State Water Resources Control Bd., supra, 182 Cal.App.3d at p. 98.) According to the court, “the Board has the power and duty to provide water quality protection to the fish and wildlife that make up the delicate ecosystem within the Delta.” (Ibid.) The appellate court also concluded that “the procedure followed—combining the water quality and water rights functions in a single proceeding—was unwise” because in doing so “the Board compromised its important water quality role by defining its scope too narrowly in terms of enforceable water rights.” (Id. at pp. 119, 120.)

Because the Board had already announced its “intention to conduct hearings during 1986 to establish new and revised” water quality objectives, the appellate court determined that “remand to the Board could serve no useful purpose.” (United States v. State Water Resources Control Bd., supra, 182 Cal.App.3d at p. 120.) Accordingly, the court reversed the judgment commanding the Board to reconsider the water quality control plan and instead simply expressed its expectation that “the renewed proceedings [would] be conducted in light of the principles and views expressed in [the court’s] opinion.” (Ibid.) As a result, Decision 1485 remained in effect.

A description of the next phase in the history of water quality control in the Delta can be found in the 1995 Bay-Delta Plan:

“In July 1987, the [Board] began proceedings to reexamine water quality objectives for the Bay-Delta Estuary and consider how water right permits would be modified to meet the new objectives. In May 1991, the [Board] adopted the 1991 Bay-Delta Plan with objectives for salinity, dissolved oxygen, and temperature. The 1991 Bay-Delta Plan was subsequently submitted to the U.S. Environmental Protection Agency (USEPA) for approval. In September 1991, the USEPA approved all of the salinity objectives for municipal, industrial, and agricultural beneficial uses, and the dissolved oxygen objective for fish and wildlife beneficial uses. The USEPA stated that the other fish and wildlife objectives were disapproved because of their failure to protect estuarine habitat and other fish and wildlife beneficial uses. As required under federal regulations [citation] when a state does not adopt changes in standards recommended by the USEPA upon notification of approval or disapproval of a state’s standards, the USEPA initiated promulgation of water quality standards for the Bay-Delta Estuary. In January 1994, the USEPA published draft standards for the Estuary in the Federal Register [citation].

“To coordinate the parallel State and federal Bay-Delta resource management activities, the Governor’s Water Policy Council of the State of California (Council) and the Federal Ecosystem Directorate (FED), comprised of State and federal resource agencies collectively known as CALFED, entered into a Framework Agreement in June 1994. The purpose of the agreement is to establish a comprehensive program for coordination and communication between the Council and the FED regarding environmental protection and water supply dependability in the Bay-Delta Estuary and its watershed. The CALFED agreement identifies three areas where both State and federal interests and responsibilities are interrelated, and coordination and cooperation are particularly important: (1) formulation of water quality standards for the Estuary; (2) improved coordination of federal and State water project operations with regulatory requirements; and (3) development of a long-term solution to fish and wildlife, water supply reliability, flood control, and water quality problems in the Bay-Delta Estuary. In accordance with the Framework Agreement, the administrator of the USEPA signed final federal standards for the Estuary on December 14, 1994.” (1995 Bay-Delta Plan, pp. 5-6, fn. omitted.)

Meanwhile, in March 1994, the Board commenced a proceeding to revise the water quality objectives for the Bay-Delta. During public workshops, the Board encouraged interested parties to develop alternatives for revising the objectives. Eventually, various representatives of the state and federal governments and certain urban, agricultural, and environmental interests reached agreement on recommendations to the Board for the revised objectives. This agreement is embodied in a document entitled “Principles for Agreement on Bay-Delta Standards between the State of California and the Federal Government” (principles for agreement), which was signed on December 15, 1994. Among the signatories were the Secretary of the California Resources Agency and the Secretary for the California Environmental Protection Agency.

The same day the principles for agreement were signed, the Board released the first draft of its new water quality control plan for the Bay-Delta. The Board used several elements of the principles for agreement, as well other recommendations from interested parties, in preparing the draft plan.

B

The 1995 Bay-Delta Water Quality Control Plan

The Board adopted the new water quality control plan for the Bay-Delta in May 1995. The 1995 Bay-Delta Plan identified 17 beneficial uses, both within the Delta and throughout the state, to be served by the waters of the Delta. These uses fall into three broad categories: municipal and industrial, agricultural, and fish and wildlife. The 1995 Bay-Delta Plan then identified water quality objectives with respect to each of these categories of uses “to attain the highest water quality which is reasonable, considering all demands being made on the waters of the Estuary.” (1995 Bay-Delta Plan, p. 14.) The Board established various salinity objectives “for the reasonable protection of [agriculture as a beneficial use] from the effects of salinity intrusion and agricultural drainage in the western, interior, and southern Delta.” To protect fish and wildlife uses, the Board’s plan established objectives for six parameters: dissolved oxygen, salinity, amounts of Delta outflow, river flows, export limits, and Delta cross-channel gate operation. The plan also included a narrative objective for salmon protection. The objectives at issue in these coordinated cases are described below.

1. The Southern Delta Salinity Objectives

The Board adopted various salinity objectives in the plan (expressed as electrical conductivity or EC) to protect agricultural uses in the western, interior, and southern Delta. To protect agricultural uses in the southern Delta, the Board adopted salinity objectives to be met at four different locations: (1) San Joaquin River at Airport Way Bridge, Vemalis (the Vemalis salinity objective); (2) San Joaquin River at Brandt Bridge; (3) Old River near Middle River; and (4) Old River at Tracy Road Bridge. The 1995 Bay-Delta Plan specified the objectives as 0.7 EC from April through August and 1.0 EC from September through March at all four locations, but specified in a footnote that the objectives were to be met at the two Old River locations by December 31, 1997. (1995 Bay-Delta Plan, p. 17.)

2. The Delta Outflow Objective

Water flow can be regulated as a water quality objective because, as the Board explained in the 1995 Bay-Delta Plan, “the rate and quantity of flow ... are physical properties or characteristics of the water” which “have an impact on the beneficial uses of’ water in the Bay-Delta. (See § 13050, subd. (g).) Thus, a flow objective sets the amount of water that must be flowing in a watercourse at a given time “for the reasonable protection of beneficial uses of [the] water.” (Id., subd. (h).) Obviously, meeting such an objective may be achieved, among other ways, by reducing the amount of water that upstream water right holders divert from the watercourse or by increasing the amount of water released into the watercourse.

In the 1995 Bay-Delta Plan, the Board explained that “Delta outflow objectives are included for the protection of estuarine habitat for anadromous fishes and other estuarine-dependent species.” The parameter for those objectives was the net Delta outflow index (outflow index). The outflow index was a number representing the net amount of water flowing out of the Delta, which was to be calculated by talcing the amount of water flowing into the Delta and subtracting from that figure the amount of water being consumed in the Delta and the amount of water being exported from the Delta. For example, every year in September, the 1995 Bay-Delta Plan required a minimum monthly average outflow index of 3,000 cubic feet per second (cfs) of water to be flowing out of the Delta to protect estuarine habitat within the Delta. (1995 Bay-Delta Plan, pp. 15, 19, 25.)

3. The Vernalis Flow Objectives

As part of the river flow objectives in the 1995 Bay-Delta Plan, the Board set minimum monthly average flow rates on the San Joaquin River at Vernalis (the Vernalis flow objectives). The Board explained that “Sacramento and San Joaquin river flow objectives are included to provide attraction and transport flows and suitable habitat for various life stages of aquatic organisms, including Delta smelt and chinook salmon.” One part of the Vernalis flow objectives was a “pulse” flow during a 31-day period in April and May of each year (the Vernalis pulse flow objective). The 1995 Bay-Delta Plan called for an average flow rate during that period ranging from 3,110 to 8,620 cfs, depending on the type of water year and on certain salinity measurements. The 1995 Bay-Delta Plan also specified that while the default period for the pulse flow was April 15 to May 15, “[t]his time period may be varied based on real-time monitoring. One pulse, or two separate pulses of combined duration equal to the single pulse, should be scheduled to coincide with fish migration in San Joaquin River tributaries and the Delta. The time period for this 31-day flow requirement will be determined by the operations group established under the Framework Agreement.” (1995 Bay-Delta Plan, p. 21, table " " . [18].)

4. The Salmon Protection Objective

The 1995 Bay-Delta Plan also included a narrative objective for the protection of salmon, which provided: “Water quality conditions shall be maintained, together with [other] measures in the watershed, sufficient to achieve a doubling of natural production of chinook salmon from the average production of 1967-1991, consistent with the provisions of State and federal law.” (1995 Bay-Delta Plan, p. 18, table 3.)

5. The Program of Implementation

In addressing implementation of the objectives in the 1995 Bay-Delta Plan, the Board divided the program of implementation into “four general components: (1) measures within [the Board’s] authority over water diversion and use which implement the water quality objectives; (2) measures requiring a combination of [the Board’s] water quality and water rights authorities and actions by other agencies to implement the objectives; (3) recommendations to other agencies to improve fish and wildlife habitat conditions; and (4) a monitoring and special studies program.” The Board then explained: “The specific actions identified within these components include time schedules for implementation, if appropriate. If no time schedule is included, implementation should be immediate.” (1995 Bay-Delta Plan, p. 27.)

The Board included within the first component of its program of implementation the agricultural salinity objectives (with the exception of those for the protection of the southern Delta), the Delta outflow objectives, and the river flow objectives for the protection of fish and wildlife, including the Vemalis pulse flow objective. In describing “the nature of [the] actions . . . necessary to achieve the[se] objectives” (§ 13242, subd. (a)), the Board explained that it would “initiate a water rights proceeding following adoption of this water quality control plan” that would “address the water supply-related objectives in this plan through the amendment of water rights under the authority of the [Board].” According to the Board, “[t]he water right decision . . . will allocate responsibility for meeting the objectives among water rights holders in the Bay-Delta Estuary watershed and establish terms and conditions in appropriate water rights.” The Board noted that pending adoption of that decision, which the Board anticipated would occur before June 1998, “the [Bureau] intends to meet San Joaquin River flow requirements, in accordance with the March 6, 1995 U.S. Fish and Wildlife Service (USFWS) biological opinion for the threatened Delta smelt, which are consistent with the San Joaquin River flow objectives in this plan. These flows are interim flows and will be reevaluated as to timing and magnitude, up or down, within the next three years. During the three-year period, decisions by the FERC [the Federal Energy Regulatory Commission] or other regulatory orders may increase flows to the Estuary required of upstream water users. These flows will be considered by the [Board] in its allocation of responsibility among the water rights holders in the watershed during the water rights proceeding.” (1995 Bay-Delta Plan, p. 29.)

The Board included within the second component of the program of implementation—“measures requiring a combination of [the Board’s] water quality and water rights authorities and actions by other agencies to implement the objectives”—the agricultural salinity objectives for the southern Delta, including the Vemalis salinity objective. The Board explained: “Elevated salinity in the southern Delta is caused by low flows, salts imported in irrigation water by the State and federal water projects, and discharges of land-derived salts, primarily from agricultural drainage. Implementation of the objectives will be accomplished through the release of adequate flows to the San Joaquin River and control of saline agricultural drainage to the San Joaquin River and its tributaries. Implementation of the agricultural salinity objectives for the two Old River sites shall be phased in so that compliance with the objectives is achieved by December 31, 1997.” (1995 Bay-Delta Plan, pp. 27, 29.)

With respect to the Vemalis salinity objective in particular, the Board explained: “This plan’s objectives, for flows in the San Joaquin River at Vemalis are expected to contribute to achieving the salinity objectives in the southern Delta. Presently, the [Bureau] is responsible for meeting Vemalis salinity objectives through the release of water from New Melones Reservoir, as required under Water Right Decision 1422. Additional releases from other reservoirs for fish and wildlife protection in San Joaquin River tributaries may be required through ongoing FERC proceedings. Implementation of the [Board]’s Nonpoint Source Management Plan, adopted in 1988, and recommended activities of the multi-agency San Joaquin Valley Drainage Program (SJVDP), discussed below, will also contribute to achieving the salinity objectives. Additionally, the Central Valley [Regional Water Quality Control Board] should continue its salt load reduction program, initiated in response to adoption of the 1991 Bay-Delta Plan, to reduce annual salt loads discharged to the San Joaquin River by at least 10 percent and to adjust the timing of such discharges from low flow to high flow periods. These source control and drainage management measures will decrease the need for releases of water from New Melones. The [Board] will evaluate implementation measures for the southern Delta agricultural salinity objectives in the water rights proceeding.” (1995 Bay-Delta Plan, p. 29.)

The plan also included, in the second component of the program of implementation, the narrative objective for salmon protection. The Board explained: “It is uncertain whether implementation of the numeric objectives in this plan alone will result in achieving the narrative objective for salmon protection. Therefore, in addition to the timely completion of a water rights proceeding to implement river flow and operational requirements which will help protect salmon migration through the Bay-Delta Estuary, other measures may be necessary to achieve the objective of doubling the natural production of chinook salmon from average 1967-1991 levels. This narrative objective is consistent with the anadromous fish doubling goals of the [CVP Improvement Act]; thus, prompt and efficient actions taken to implement this [CVP Improvement Act] goal, in concert with other recommended actions in this plan, are important to achieving the narrative salmon protection objective. Monitoring results will be considered in the ongoing review to evaluate achievement of this objective and the development of numeric objectives to replace it.” (1995 Bay-Delta Plan, pp. 28-29.)

In discussing the third component of the program of implementation— “recommendations to other agencies to improve fish and wildlife habitat conditions”—the plan recommended the development of “an experimental study program on the effects of pulse flows on fish eggs and larvae in the Delta.” More specifically, the Board stated: “The [Department] and the [Bureau] should conduct experiments to investigate and evaluate the biological benefits of pulse flows to move planktonic fish eggs and larvae into Suisun Bay. These experiments, which should be conducted as soon as feasible, should: (1) involve flows released from both the Sacramento and San Joaquin rivers; (2) include real-time biological monitoring to determine the most favorable times for the pulse flows and the effects of the pulse flows on the eggs and larvae; (3) determine whether short-term pulse flows have a lasting benefit or whether, when outflows are reduced after a pulse flow, the larval fish are drawn back into interior Delta areas; and (4) take into account base flows and availability of water supplies. If results of the experiments were obtained soon enough, they could be used to refine potential pulse flow requirements in a water right decision implementing this water quality control plan.” (1995 Bay-Delta Plan, p. 38.)

C

The Water Rights Proceeding to Implement the 1995 Bay-Delta Plan

In November 1997, the Board issued a draft environmental impact report for implementation of the 1995 Bay-Delta Plan (the implementation EIR). The following month, the Board issued a notice of public hearing, setting hearing dates for the water rights proceeding in which the Board would allocate responsibility for implementing the flow-dependent objectives of the 1995 Bay-Delta Plan. (As discussed more fully below, this water rights proceeding also encompassed the petitions by the Bureau and the Department for certain changes in their CVP and SWP permits.)

Ultimately, the Board divided the public hearing into eight phases. The hearing convened on July 1, 1998, and continued off and on until July 6, 1999. On December 29, 1999, the Board certified the final implementation EIR and issued Decision 1641. On March 15, 2000, following the filing of various petitions for reconsideration, the Board issued its order denying petitions for reconsideration and amending Decision 1641 (order on reconsideration) and issued the revised decision that we refer to as Decision 1641. ( (as of Feb. 9, 2006).) With respect to its allocation of responsibility for meeting the flow-dependent objectives in the 1995 Bay-Delta Plan, we describe the most pertinent parts of Decision 1641 below.

1. Responsibility for Meeting the Vernalis Flow Objectives—The San Joaquin River Agreement and the Vernalis Adaptive Management Plan

In a revised notice of public hearing issued in May 1998, the Board explained that “[sjeveral agreements have been negotiated among the parties interested in this proceeding, proposing allocations of responsibility to meet the flow-dependent objectives in the 1995 Bay-Delta Plan. The [Board] will receive evidence on these agreements during the hearing and will consider adopting water right terms and conditions consistent with these agreements.” One such agreement was the proposed San Joaquin River Agreement—an agreement between “some, but not all, of the parties who have an interest in the allocation of responsibility to provide the San Joaquin River’s share of water for meeting the Bay-Delta flow objectives.” (Decision 1641, p. 18.)

As the Board explained in Decision 1641: “The [San Joaquin River Agreement] was presented to the [Board] as a settlement agreement proposing an allocation of responsibility for meeting the April-May objective for pulse flows from the San Joaquin River.” “For a twelve-year period, the [San Joaquin River Agreement] proposes to allocate responsibility for meeting the April-May pulse flow objectives in the 1995 Bay-Delta Plan to certain water right holders in the watershed of the San Joaquin River.” Under the San Joaquin River Agreement, “[t]he members of the [San Joaquin River Group Authority] who provide the water will receive $3 million per year from the [Bureau], . . . and $1 million per year from the [Department]... . . The [San Joaquin River Agreement] would assign responsibility to the [Department] and the [Bureau] to meet the flows it specifies during the pulse flow period in the southern Delta.” (Decision 1641, pp. 12, 17, 18.) In addition, “[t]he [Department] and the [Bureau] have committed themselves to provide ‘backup’ during the term of the [San Joaquin River Agreement] for any responsibility that otherwise would be placed on the San Joaquin basin water right holders as a result of an allocation of responsibility in the Bay-Delta Water Rights Hearing.” (Id., p. 18, fn. 26.)

The San Joaquin River Agreement, however, did not provide sufficient flows to meet all of the Vemalis flow objectives in the 1995 Bay-Delta Plan. Nevertheless, to induce the Board to approve the San Joaquin River Agreement as part of Decision 1641, the Bureau and the Department committed to provide additional water, beyond what was required by the agreement, to meet all of the Vemalis flow objectives except the Vemalis pulse flow objective.

The reason the parties to the San Joaquin River Agreement were not proposing to meet the Vemalis pulse flow objective was ostensibly to conduct an experiment known as the Vemalis Adaptive Management Plan, which had been developed “to gather better scientific fisheries information on the lower San Joaquin River”—specifically, “information on the relative effects of flows in the San Joaquin River, CVP and SWP pumping rates, and operation of a fish barrier at the head of Old River on the survival and passage of salmon smolts through the Delta.” According to the San Joaquin River Agreement, the flows and pumping regimen provided for in the agreement would not only allow the conduct of the Vemalis Adaptive Management Plan but would “provide environmental benefits in the lower San Joaquin River and Delta at a level of protection equivalent to the San Joaquin River Portion of the” 1995 Bay-Delta Plan. (San Joaquin River Agreement, § 2.1.)

To implement the San Joaquin River Agreement, four petitions were filed for long-term changes in licenses held by Merced, Turlock, Modesto, Oakdale, and South San Joaquin Irrigation Districts (the irrigation districts). The petitions proposed to add the San Joaquin River upstream of Vemalis as a place of use and add fish and wildlife enhancement as a purpose of use. These changes would allow these irrigation districts to contribute water toward the Vemalis pulse flow.

As Decision 1641 explained: “Pursuant to the [San Joaquin River Agreement], [the irrigation districts] along with the [San Joaquin River Exchange Contractors Water Authority] would provide up to 110 taf [thousand acre-feet] per year during a 31-day pulse flow period in April and May of each year, for instream flows in the lower San Joaquin River above Vemalis. . . . The [irrigation districts] and the Exchange Contractors would decide each year how to allocate the water required during the pulse flow period.” (Decision 1641, p. 14, fn. omitted.)

In evaluating the Vemalis Adaptive Management Plan, the Board concluded it provided “a unique opportunity for collecting data under controlled conditions because of the commitment of the [Department] and [the Bureau] to control exports and releases from New Melones Reservoir, and operate the head of Old River barrier as needed for the experiment.” (Decision 1641, p. 21.) The Board also noted, however, that “[t]here are differences in the flow targets between the [Vemalis Adaptive Management Plan] and the [San Joaquin River Agreement],” and “the [San Joaquin River Agreement] does not fully provide for conducting the experiment as designed.” (Id., pp. 20, 22.) Among other things, “the [San Joaquin River Agreement] provides flow targets of 2,000 cfs, but the minimum flow targets under the [Vemalis Adaptive Management Plan] are 3,200 cfs.” (Id., p. 20, fn. omitted.) The Board “urges the [Bureau] to supplement the flows provided under the [San Joaquin River Agreement] as needed to ensure that the experiment is completed,” but the Board did not require the Bureau to do so. (Id., p. 22.)

In evaluating the San Joaquin River Agreement, the Board declined a request by its proponents to find that the agreement provided environmental protection equivalent to the Vemalis pulse flow objective in the 1995 Bay-Delta Plan. According to the Board: “A finding of equivalent protection would be premature at this time. The purpose of the [San Joaquin River Agreement] and [the Vemalis Adaptive Management Plan] is to determine through experimentation alternative measures to protect the beneficial uses in the 1995 Bay-Delta Plan designated to be protected by the Vemalis pulse flow objectives. Until the experiment is complete, there will not be adequate information to know whether the measures provide equivalent protection.” (Decision 1641, p. 23.)

The Board went on to note that “the Vemalis flow objectives in the 1995 Bay-Delta Plan do not contain a provision allowing a different set of objectives to be met if it is demonstrated that they provide equivalent protection for the beneficial uses protected by the objectives. In cases where equivalent protection can be provided, the objectives normally so state. Instead of providing for equivalent protection, the 1995 Bay-Delta Plan provides that the Vemalis flow objectives will be reevaluated in a future review of the plan.” (Decision 1641, p. 23.)

The Board candidly acknowledged that “[mjeeting the flows specified in the [Vemalis Adaptive Management Plan] will not meet the pulse flow objectives” in the 1995 Bay-Delta Plan and “it is not certain that the [Vemalis Adaptive Management Plan] will provide protection for the Chinook salmon equivalent to that provided by the objectives.” Nonetheless, the Board “approves the [San Joaquin River Agreement] for the purpose of conducting the [Vemalis Adaptive Management Plan] experiment” on the theory that “[ujnder Water Code section 13242, an objective can be implemented in stages over a period of time” and “[t]he [Vemalis Adaptive Management Plan] experiment . . . will serve as a step toward implementation of the Vemalis pulse flow objectives.” According to the Board, by approving the agreement, it was “authorizing] a staged implementation of the Vemalis pulse flow objectives so that experimental operations can be conducted in lieu of meeting the objectives as the first stage of implementation.” (Decision 1641, pp. 23, 24, 48.)

To allow for performance of the San Joaquin River Agreement, the Board in Decision 1641 amended two of the Bureau’s permits for New Melones storage to require the Bureau to meet the Vemalis flow objectives during the term of the agreement, with the exception of the Vemalis pulse flow objective. In lieu of the Vemalis pulse flow objective, the Bureau was required to meet the alternate pulse flow objectives from the agreement. The Board specifically explained that this was an interim requirement and that it would “consider a permanent allocation of responsibility with respect to the San Joaquin River basin after the [San Joaquin River Agreement] has expired.” The new permit term provided that “[i]f the San Joaquin River Agreement ... is dissolved by the signatory parties before it expires, then Permittee shall meet the San Joaquin River flow objective set forth in [the 1995 Bay-Delta Plan] until the Board establishes alternative implementation of the San Joaquin River flow objective.” (Decision 1641, pp. 132, 162.) The Board also explained that the Bureau was not required to “use water under [the New Melones] permits to meet [the Vemalis flow objectives] if it uses other sources of water or other means to meet these” objectives. (Id., p. 160, fit. 87.)

The Board also approved the petitions by the irrigation districts to add the San Joaquin River upstream of Vemalis as a place of use and add fish and wildlife enhancement as a purpose of use in their licenses during the period of the San Joaquin River Agreement. Consistent with the terms of the San Joaquin River Agreement, the Board required the irrigation districts to contribute up to 110 thousand acre-feet (taf) of water annually toward the alternate pulse flow objectives from the agreement. The Board further specified that “[w]hen the [San Joaquin River Agreement] expires or is terminated, the Board will give notice and will commence a proceeding to determine the responsibility of the [irrigation districts] to meet the objectives.” (Decision 1641, p. 166.)

2. Responsibility for Meeting the Southern Delta Salinity Objectives

In Decision 1641, the Board determined that salinity concentrations at Vemalis are caused by “a combination of upstream water diversions, discharges of saline drainage water to the San Joaquin River and subsurface accretions to the river from groundwater.” The Board further determined “that the actions of the CVP are the principal cause of the salinity concentrations exceeding the objectives at Vemalis.” This is so because “[t]he source of much of the saline discharge to the San Joaquin River is from lands on the west side of the San Joaquin Valley which are irrigated with water provided from the Delta by the CVP,” and “[t]he capacity of the lower San Jo