Full opinion text
OPINION and ORDER BARBARA B. CRABB, District Judge. Plaintiffs Wisconsin Resources Protection Council, Center for Biological Diversity and Laura Gauger bring this action for declaratory and injunctive relief and civil penalties under the citizen suit provision of the Clean Water Act, 33 U.S.C. § 1365(a)(1). Plaintiffs contend that defendant Flambeau Mining Company is violating the Clean Water Act by discharging pollutants without a Wisconsin or National Pollutant Discharge Elimination System permit issued under the Act. Now before the court are plaintiffs’ motion for partial summary judgment; defendant’s motion for summary judgment on all of plaintiffs’ claims; defendant’s motion to dismiss the case for plaintiffs’ failure to join the Wisconsin Department of Natural Resources as an indispensable party; plaintiffs’ motion for leave to file supplemental proposed findings of fact; defendant’s motion to strike plaintiffs’ supplemental facts; and the state of Wisconsin’s motion to file an amicus curiae brief. In their motion for partial summary judgment, plaintiffs seek a declaration that they have standing to bring this suit and a determination that defendant violated the Clean Water Act on 23 days by discharging pollutants without a permit. In its motion for summary judgment, defendant seeks judgment on all of plaintiffs claims, contending that plaintiffs lack standing to bring this suit. On the merits, defendant contends that it did not discharge pollutants into navigable waters that are protected by the Act and that even if it did, it was complying with a permit issued under the Act. Defendant also raises several affirmative defenses, contending that plaintiffs’ claims should be dismissed because plaintiffs failed to exhaust their administrative remedies and waived their claims. Additionally, defendant contends that plaintiffs claims are barred by the statute of limitations, the doctrines of issue and claims preclusion, various forms of estoppel and laches and their failure to exhaust their administrative remedies. With respect to the threshold jurisdictional and procedural questions, I conclude that plaintiffs have Article III standing to bring this suit and that the Department of Natural Resources is not a necessary or indispensable party under Fed.R.Civ.P. 19. Therefore, I am granting plaintiffs’ motion for summary judgment on the issue of standing and am denying defendant’s motion to dismiss the case under Rule 19. I am granting the state’s motion to file an amicus curiae brief. The brief sets forth the state’s interpretation of state statutes and regulations relating to mining and storm water discharge permits and provides useful background on issues relevant to the case. In addition, I am denying defendant’s motion for summary judgment on its contentions that plaintiffs are barred from bringing this suit by their failure to exhaust their administrative remedies, by the running of the statute of limitations, by laches or by the doctrines of issue and claims preclusion. With respect to the merits of plaintiffs’ claims, plaintiffs have shown that defendant discharged pollutants from the biofilter located on its former mine site, that Stream C is a navigable water that is protected by the Clean Water Act and that defendant did not have a permit under the Act authorizing the discharges. Therefore, I am granting plaintiffs’ motion for summary judgment on those issues. However, there are disputed issues of fact regarding whether the discharges from defendant’s biofilter entered Stream C or a grassy wetland. Because plaintiffs have not shown that the grassy wetland qualifies as navigable waters under the Act, I am denying plaintiffs’ motion for summary judgment with respect to defendant’s ultimate liability under the Act for the discharges. Before defendant can be held liable for its unpermitted discharges, plaintiffs must prove that defendant discharged pollutants into Stream C or that the wetland area near the biofilter outlet has a “significant nexus” to the Flambeau River. As for the remaining motions, I am denying plaintiffs’ motion for leave to file supplemental proposed findings of fact because the proposed findings were not necessary to the decisions on the parties’ substantive motions. Consequently, I am denying defendant’s motion to strike the supplemental facts as moot. From the findings of fact proposed by the parties, I find that the following facts are material and undisputed. UNDISPUTED FACTS A. Defendant Flambeau Mining Company From 1993 to 1997, defendant Flambeau Mining Company owned and operated an open pit metallic mine, along with related facilities, on property in Ladysmith, Wisconsin. The mine has been partially reclaimed but several industrial buildings and structures remain in place and in use. One of these remaining structures is a “biofilter” that is used to detain and partially treat runoff from a 32-acre business and industrial park on defendant’s property, known as the “industrial outlot.” The biofilter collects, stores and periodically discharges storm water. The industrial outlot contains various buildings and structures, including an administrative office and laboratory, recreational facilities, defendant’s former wastewater treatment building and a parking area. Defendant still owns the former mine site, including the industrial outlot, which is leased by the Ladysmith Community Industrial Development Corporation. B. Stream C The Flambeau mine site is bordered on the east by State Highway 27 and on the west and southwestern sides by the Flam-beau River. Several intermittent streams flow on the mine site. The only stream relevant to this case is a seasonally-flowing intermittent stream known as Stream C that flows in a generally southwesterly direction on the east side of the property. During various stages of mining and reclamation, defendant manipulated the channel of Stream C by re-routing segments of it, installing culverts underneath the former access road and rail spur and performing significant grading of the lands on its property that drain to Stream C. C. Plaintiffs Plaintiff Wisconsin Resources Protection Council is a Wisconsin nonprofit environmental organization headquartered in La Crosse, Wisconsin, with approximately 225 members in Wisconsin and Minnesota. One of its primary purposes is to educate citizens about the effects of large scale metallic mining on Wisconsin’s water supplies, the tourism and dairy industries and the Native American communities located near potential mine sites. Since at least 1991, the Council has worked with the Wisconsin Department of Natural Resources on issues relating to the Flambeau mine, including the development of defendant’s 1991 mining permit; advocating the passage of Wisconsin’s Metallic Mining Moratorium in 1998; and tracking defendant’s compliance with its mining permit and monitoring requirements. Plaintiff Center for Biological Diversity is a nonprofit environmental membership organization headquartered in Tucson, Arizona, with a regional office in Duluth, Minnesota and approximately 320 members in Wisconsin. The Center’s mission is preservation, protection and restoration of biodiversity, native species, ecosystems and public lands, with an emphasis on protecting the habitats of threatened and endangered species. It also promotes the ability of its members to engage in recreational activities and study the habitat of species that are or may become imperiled. One of the Council’s members, Harold Flater, lives approximately 15 miles downstream from the Flambeau mine site and owns Flater’s Flambeau Point Resort, which provides guided fishing trips on the Flambeau River. Flater enjoys boating and fishing on the river near and downstream from the Flambeau mine. He is familiar with the mine and has attended several public hearings and meetings concerning defendant’s permit applications over the years. Flater knows that both copper and zinc are considered toxic pollutants and can be harmful to human health and aquatic life at elevated concentrations. He is concerned that discharges from defendant’s industrial outlot and biofilter will harm fish and other aquatic wildlife and will decrease his enjoyment of fishing and boating on the river. Plaintiff Laura Gauger lived in Wisconsin from September 1991 to February 2010 and is now a citizen and resident of Duluth, Minnesota. She is a member of plaintiff Center for Biological Diversity and plaintiff Wisconsin Resources Protection Council. Gauger is an outdoor enthusiast who enjoys hiking, bird and animal watching, canoeing, fishing and camping, among other activities. On multiple occasions, she has canoed and hiked near the Flam-beau River and Flambeau mine site. Between May 2007 and October 2011, Gauger visited the Flambeau mine site at least 12 times. She has co-authored a 1,200 page book documenting the history of the Flam-beau Mine and its effects on the surrounding area. Lori Andresen is a member of plaintiffs Center for Biological Diversity and Wisconsin Resource Protection Council and enjoys outdoor activities. She has been involved in mining issues in Minnesota and Wisconsin for many years and has been interested in reclamation of the Flambeau mine since 2006. Andresen visited the Flambeau River for the first time in 2009 with plaintiff Gauger, and has visited twice since then to observe and photograph wildlife and birds. Andresen and plaintiff Gauger are aware that metallic mining can lead to soil contamination and water pollution. They also know that the sediments and soils in the area around the Flambeau mine site contain copper and zinc, that these metals have been listed by the United States Environmental Protection Agency and the State of Wisconsin as toxic pollutants and that at certain concentrations they can be harmful to human health and aquatic life. Gauger and Andresen have read reports and reviewed toxicity data for discharges from defendant’s biofilter, the Flambeau River and Stream C and know that the Wisconsin Department of Natural Resources has recorded concentrations of copper from the defendant’s discharges that exceed Wisconsin’s acute toxicity criteria for copper. Andresen and plaintiff Gauger are concerned that elevated levels of copper and zinc are being carried from defendant’s industrial outlot by Stream C to the Flam-beau River and will cause harm to the aquatic life in the stream and river. They are worried that the discharges will reduce their enjoyment of those waters for canoeing, fishing, wildlife observation and other recreational and aesthetic pursuits and will harm their health by exposing them to toxic pollutants. During Gauger’s most recent canoe trip to the Flambeau River in October 2011, she did not wade in the waters near Stream C because of her concern about exposure to copper, zinc and other pollutants. Her enjoyment of the experience was lessened. Gauger intends to return to the river in the spring or summer of 2012, but is less likely to do so near the mouth of Stream C. D. Defendant’s Permits Defendant operated the mine pursuant to a 1991 mining permit issued by the Wisconsin Department of Natural Resources that governed both active mining operations and the reclamation phase. The mining permit provided the general framework for the operation of the mine, including provisions for storm water management, and required defendant to submit annual chemical monitoring results to the Department, including the results of copper and zinc monitoring. Also, the permit required a surface water management plan, a risk assessment, a contingency plan and a reclamation plan that required defendants to return the site to approximate pre-mining site grades and remove all facilities and infrastructure. The mining permit states that it was issued under Wis. Stat. §§ 144.80-144.94 and 144.43-144.47, which are Wisconsin’s mining laws. 1991 Mining Permit, Part I, Cond. 5, dkt. #40-20. (These statutes were renumbered by 1995 Wis. Act 227 and are now found in Wis. Stat. ch. 293.) The permit also states that “Flambeau shall obtain any and all other permits, licenses and approvals necessary from federal, state and local authorities.” Id. The administrative law judge who approved the 1991 mining permit stated in his decision that: [T]he authority of the Mining Permit issued by the Department is limited to the authority vested in the Department by ss. 144.80 to 144.94, Stats, and 144.43 to 144.47, Stats., relative to mining waste disposal. If another state or federal rule specifically regulates an activity, also regulated under ss. 144.80 to 144.94, Stats., the other statute or rule shall be the controlling standard to the extent applicable. Dkt. # 66-1 at 87. During the active phase of mining, defendant held a wastewater discharge permit issued in 1991 by the Department under the Wisconsin Pollutant Discharge Elimination System program. The 1991 wastewater discharge permit authorized various discharges, including storm water discharges, during the active phases of mining and reclamation. In particular, the permit authorized three discharge points, identified as outfalls 1, 2 and 3. Outfall 1 was the discharge point from the wastewater treatment plant to the Flambeau River; outfall 2 was the discharge point from settling ponds on the mine site to the Flambeau River; and outfall 3 was an alternative discharge point from the settling ponds to nearby wetlands. The wastewater discharge permit was reissued on March 29,1996. E. 1998 Permit Modification In 1997, defendant ceased active mining operations and began the reclamation phase. Before active reclamation began, the City of Ladysmith requested that defendant retain the facilities and infrastructure located in the industrial outlot for future development opportunities. On January 8, 1998, defendant submitted a request for modification of the mining permit. The request was contained in a document titled “Supplement to the Surface Reclamation Plan for the Flambeau Mining Company, Ladysmith, Wisconsin,” dated December 18,1997. In the request, defendant sought, among other things, to modify its original reclamation plan to allow it to (a) retain approximately 32 acres of facilities for reuse as the industrial outlot; (b) establish an 8.5 acre wetland in the northeast corner of the mine site; (c) redirect a portion of intermittent Stream B north of the former mine pit; (d) make adjustments to the success criteria for monitoring of vegetation and wildlife; (e) leave a concrete diaphragm in place as part of the mine pit west wall; and (f) construct a storm water biofilter system for the proposed industrial outlot and the 0.9 acre biofilter. The supplement provided detailed grading plans for routing storm water from nearly all of the industrial outlot through a biofilter located in the area of the former surge pond as follows: Industrial Outlot An approximately 28-acre outlot is proposed to be located west of State Trunk Highway (STH) 27 on the southern portion of the site. Ancillary facilities such as the administration building, wastewater treatment plant, utilities, and railroad spur not underlain with HDPE liner will be left in place to service the planned industrial park. The decision to leave these facilities in-place and incorporate the industrial park into the reclamation plan is based on the desire of local officials. In addition, storm water from the industrial outlot would be directed to a constructed biofilter located in the area of the former surge pond. Flow from the biofilter would be directed to Stream C. Drainage from the future industrial area of the Flambeau Mine property (south of the reclaimed area) will be conveyed to the existing surge pond at the east side of the site. This surge pond will be reconstructed as a biofilter/detention basin, to improve the water quality and decrease the peak flow rates of runoff from the developed area prior to its discharge into Stream C. Dkt. # 60-10. The modification request did not include an application for a discharge permit under the National or Wisconsin Pollutant Discharge Elimination System permit program or make any reference to one. The supplement was reviewed by staff at Wisconsin’s Department of Natural Resources, including Lawrence Lynch. Lynch had worked for the Department’s mine reclamation program since 1980, was the mining team leader beginning in the mid-1990s and had been involved heavily in the review, permitting and monitoring of defendant’s mine. On March 20, 1998, Lynch wrote defendant, stating, in part: Flambeau Mining Company personnel and department staff have recently had several conversations concerning surface water management at the Flambeau mining site. This letter is to clarify how the department intends to regulate surface water management at the site. The current water handling procedures are acceptable to the department and are consistent with the Mining Permit, including the Surface Water Management Plan, and the Wisconsin Pollutant Discharge Elimination System (WPDES) Permit. It is our intent that the WPDES permit will continue to regulate discharges from the site through outfalls 001 and 002 as long as water is being pumped from one location to another on the site. Any discharge through those outfalls must comply with the effluent limits and monitoring requirements specified in the WPDES permit ... as long as the WPDES permit remains in force. Once all permanent water management structures and facilities are in place and pumping is no longer necessary, discharges through outfall 002 will cease to be covered under the WPDES permit. At that time, storm water management will fall under the regulatory authority of the Mining Permit and its associated plans. ... I hope this clarifies the department’s position concerning our regulatory oversight of stormwater management at the Flambeau site. Dkt. # 66-2. The Department determined that defendant’s requested modification of its mining permit constituted a substantial change to the mining permit under Wis. Stat. § 293.55. On March 26, 1998, the Department issued a public notice titled “Notice of Proposed Modification Mining Permit and Reclamation Plan” and noted that interested persons had the right to request a public hearing. The public notice did not mention the Clean Water Act, permitting under the National or Wisconsin Pollutant Discharge Elimination System or discharge of pollutants from the biofilter. The Department received 12 requests for a public hearing regarding the proposed modification, including requests from plaintiff Gauger and other members of plaintiff Wisconsin Resources Protection Council. Thomas Wilson, a long-time member of the Council, also filed a request for a formal hearing regarding defendant’s proposed supplement and modification. Wilson, Gauger and the Council believed that defendant’s proposed modifications were violations of the conditions of the mining permit and state mining laws and regulations and wanted a scientific review of the proposed modifications. On May 9, 1998, Wilson wrote to the Department, stating that he was willing to withdraw his request for a formal hearing if the Department would organize an “informal informational hearing” where he could express his concerns and receive written responses to those concerns. Dkt. # 60-45. On June 2, 1998, Lawrence Lynch wrote to Wilson, confirming that the Department had agreed to proceed with an “informational meeting” to discuss the proposed modifications to defendant’s reclamation plan. Dkt. # 60-46. In preparation for the meeting, Wilson drafted a document titled “Issues of Concern to Petitioners on the Revised Flam-beau Mine Reclamation Plan” and provided a copy to the Department. Dkt. # 60-13. Wilson raised more than 40 issues of concern, including whether the modification had “been reviewed with reference to the original ... [Wisconsin Pollutant Discharge Elimination System] Permit Application”; how “surface and groundwater runoff [would be] monitored before it seeps into the Flambeau River where it will be diluted to a point that it becomes a non-point source”; and how the “revised plan [would] meet the original ... [Wisconsin Pollutant Discharge Elimination System] Permit Application ... and the flow and transport modeling reports.” Id. Approximately one week before the informational meeting was held, plaintiff Gauger and other members of Wisconsin Resources Protection Council held a meeting to discuss defendant’s proposed modification and Wilson’s list of concerns. On June 16, 1998, the Department convened the informational meeting in Ladysmith, Wisconsin, to discuss the proposed modification to defendant’s plan. Plaintiff Gauger and other attendees asked whether defendant’s existing wastewater treatment plant could be decommissioned under the modification. There was no discussion about Clean Water Act permits and requirements, potential overflows from the biofilter, discharges into Stream C or the scope of copper contamination in the industrial outlot. Neither the Department nor any persons attending the meeting called witnesses, offered evidence, made oral arguments or filed legal briefs. No hearing examiner or administrative law judge was present, no administrative record or transcript was prepared and only defendant and the Department were represented by legal counsel. On June 26, 1998, Wilson sent a letter to the Department regarding issues that were raised at the informational meeting, including the wastewater treatment plant. He stated that it would be acceptable to keep the plant, so long as the wastewater treatment system was decommissioned and the discharge pipeline was removed. On July 7, 1998, Lynch responded to Wilson, saying that the Department intended to require defendant to decommission the wastewater treatment plant as a condition of its approval of defendant’s modification. Dkt. # 60-19. After reviewing Lynch’s July 7 letter, plaintiff Gauger and the other petitioners withdrew their request for a formal contested hearing on the proposed modification. On July 30, 1998, the Department formally approved defendant’s supplement, citing Wis. Stat. § 293.55 (modifications to metallic mining permits), and issuing findings of fact, conclusions of law and a “Mining Permit Modification.” Dkt. # 66-7. The modification states that “[a]ll other provisions of the Mining Permit remain in full force. Under this modification, the proposed changes as outlined in the request from January 9, 1998 and the above mentioned supplement are approved with [certain] conditions ...including the dismantling of the wastewater treatment plant. Id. The modification included 13 findings of fact, none related to the biofilter, Stream C, the Flambeau River or defendant’s intent to discharge pollutants from the biofilter. Also, the modification included three conclusions of law, each made under Wis. Stat. § 293.55, the state mining laws and a general notice of appeal rights. The modification did not cite the Clean Water Act, Wis. Stat. ch. 283 (Wisconsin Pollutant Discharge Elimination System permitting program) or Wis. Admin. Code ch. NR 216 (Wisconsin’s storm water permitting program) and was not submitted to the Environmental Protection Agency for review. The Department sent a copy of the modification to all those who had petitioned for a hearing, including plaintiffs Gauger and the Council. No person or entity sought judicial review of the modification. After the modification was approved, defendant completed site grading, constructed the biofilter and decommissioned its wastewater treatment plant. On September 8, 1998, Lynch wrote to defendant, saying: This letter is to acknowledge that surface water management and related discharges through outfall 002 at the Flam-beau mining site are no longer subject to the provisions of the Wisconsin Pollutant Discharge Elimination System (WPDES) Permit. This is consistent with the regulatory approach outlined in my letter to you dated March 20, 1998. With the permanent shutdown of the wastewater treatment plant and related facilities on August 13, 1998 and completion of construction of the permanent stormwater facilities on the site, storm-water management and discharges through outfall 002 will be regulated under the Mining Permit. As such, Flam-beau must continue to exercise a storm-water management and erosion control program that meets or exceeds current best management practices. Particular care should be taken to provide additional protection to the area that flows to the southwest biofilter until the area is completely stabilized. Further, we suggest that, until the drainage area is fully revegetated and stabilized, Flambeau maintains the capability to pump water from the biofilter to the abandoned gravel pit in the event of an extreme precipitation event. Dkt. # 66-8. On September 23,1998, the Department formally terminated defendant’s Wisconsin Pollutant Discharge Elimination System permit by letter, stating: We understand the wastewater treatment system serving the Flambeau Mine in Ladysmith has permanently shut down as of August 13, 1998. Therefore, the Department has decided to close the wastewater permit for the discharge described in the Wisconsin Pollutant Discharge Elimination System Permit No. WI-0047376-2, issued on March 29, 1996. No further discharges to waters of the State of Wisconsin will be allowed under the WPDES permit. All existing waste-water discharge points from the waste-water treatment system must be abandoned, with the exception of Outfall 002 which may discharge storm water runoff through the biofilter overflow regulated under the Mining Permit. Dkt. # 66-9. F. The Biofilter After the modification was approved, defendant created a 0.9 acre storm water detention basin called a “biofilter” in the industrial outlot. The biofilter was created in the area of the former surge pond on the east side of the property and approximately 75 yards from Copper Park Lane. It was designed to collect and detain rain and storm water runoff from the industrial outlot and was seeded and planted with specific native vegetation intended to filter sediment and nutrients from the runoff. The biofilter has only one outlet, located near the northeast corner of the biofilter. The outlet is lower than the surrounding berm and has an “apron” of crushed rock that extends down the side of the biofilter. Whenever the biofilter’s water storage capacity is exceeded, water flows through the biofilter’s outlet. The water flowing out of the biofilter contains copper and zinc. On several occasions, defendant and the Wisconsin Department of Natural Resources have recorded water flowing out of the biofilter’s outlet that contained levels of copper exceeding Wisconsin’s acute toxicity criterion for copper. PPFOF ¶¶ 101-130, dkt. # 52. (“Acutely toxic” concentrations of copper are copper concentrations that are believed to be likely to cause fairly rapid damage to biological organisms.) On another occasion, sampling showed that the water flowing into the biofilter had copper levels at less than half the level of water flowing out of the biofilter. Id. at ¶ 131. The parties dispute whether the water and pollutants flowing out of the biofilter reach Stream C. Plaintiffs state that overflow from the biofilter flows approximately 10 feet down a broad, rock-lined outlet that slopes directly into Stream C. Plaintiffs rely on the testimony of John Coleman, who stated that he observed the biofilter discharging into Stream C on several occasions. Dkt. #51. Additionally, plaintiffs rely on the expert opinion of David Chambers, dkt. # 50, who analyzed data collected from defendant and the Department regarding levels of copper and zinc in the biofilter, Stream C and the Flambeau River. Chambers concluded that water from the biofilter is discharged to Stream C and that copper and zinc from the biofilter ultimately reach the river. An employee from the Department of Natural Resources who conducted sampling of the biofilter, Stream C and the river also concluded that at least some water and pollutants from the biofilter reach the river. Finally, plaintiff cites documents prepared by defendant over the years stating that water from the biofilter flows into or discharges into Stream C and ultimately reaches the Flambeau River. Defendant says that although it stated in various documents and reports that the biofilter discharges into Stream C, defendant was using the label “Stream C” as a convenient means for referring to the wetland area around the biofilter. Defendant states that overflow from the biofilter does not flow into Stream C; rather, it enters a grassy wetland that is approximately 30 feet from anything that could be considered a channel of Stream C. After examining the area, defendant’s expert, Elizabeth Day, concluded that there is no surface connection between biofilter discharges and Stream C and that discharges from the biofilter spread out into the ground of the wetland, do not enter a channel of Stream C and do not reach the river. Dkt. # 84, at ¶ 11. G. Monitoring Reports and Mediation Projects In approximately 2003, defendant determined that the soils in the industrial outlot contributed to elevated copper and zinc concentrations in storm water runoff delivered to the biofilter. Beginning in 2003, defendant undertook remediation projects on the site to address the elevated levels of copper found in the soils of the industrial outlot, including the removal of contaminated materials from the area. In 2004, defendant proposed a monitoring plan for Stream C to address concerns about copper discharged from the biofilter to Stream C. As part of the plan, defendant established several monitoring points in Stream C’s watershed. In 2004 and 2005, defendant discovered that certain areas of the industrial outlot may be contributing “elevated levels” of copper to runoff discharged from the biofilter. (“Elevated levels” means concentrations above background levels determined from samples taken in areas not affected by mining.) In 2005, defendant discovered “[rjelatively high copper concentrations” in the industrial outlot soils where track washing of the haul trucks during mine operations was performed. Also in 2005, defendant noted elevated concentrations of copper and zinc in storm water runoff from the industrial outlot and raised concerns about whether mitigation measures could achieve water quality criteria for copper and zinc. In 2006, defendant undertook additional activities in the industrial outlot to reduce particulate and dissolved solids entering the biofilter, including excavation and off-site landfilling of soils and ditch material and placement of limestone and paving over the parking areas. In 2007, defendant requested and was issued a certificate of completion for reclamation under Wis. Admin. Code. § NR 132 for the mine site, with the exception of the industrial outlot. Defendant agreed to withdraw its request for a certificate of completion for the industrial outlot and to commit to further environmental monitoring of the area, including monitoring of the sediments in the biofilter and Stream C. Since 2007, the Department has continued to collect surface water samples from the biofilter outlet, several locations along Stream C, several locations along the Flambeau River and from three nearby streams (Stream A, Stream B and an unnamed stream). On October 26, 2010, April 27, 2011 and June 19, 2011, the water samples taken at the biofilter’s outlet, Stream C below Copper Park Lane and the mouth of Stream C contained copper at levels that exceeded Wisconsin’s acute toxicity criteria. The three nearby streams contained copper concentrations lower than in Stream C and below Wisconsin’s acute toxicity criteria for copper. H. 2009 Notice of Intent to Sue In 2009, plaintiffs filed a notice of intent to sue with defendant and the Wisconsin Department of Natural Resources under the state’s mining laws. Assistant Attorney General Thomas Dawson, Director of the Environmental Protection Unit of the Wisconsin Department of Justice, sent a letter dated November 10, 2009 to Glenn M. Stoddard, one of plaintiffs’ counsel, regarding the notice of intent to file citizen suit. Dawson stated, in part, that although “[sjtormwater discharge from the Flambeau mine site would ordinarily be subject to one of the [Department’s] Wis. Admin. Code ch. NR 216 storm water permits and requirements and issued pursuant to Wis. Stat. § 283.33,” the Department had decided in 1998 to regulate defendant’s storm water discharges “under the runoff management provisions of [defendant’s] revised mining permit.” Dawson also stated that “[t]o date the storm water discharges from the Flambeau Mine have met the relevant requirements in the mining permit, so under Wis. Admin. Code § NR 216.21(4)(a), separate storm water permit coverage is not required.” Dkt. # 63-1. This letter was the first time the Department explained to plaintiffs that it was relying solely on Wis. Admin. Code § NR 216.21(4) and defendant’s mining permit as the basis for its regulatory determinations regarding defendant’s biofilter discharges. I. 2010 Notice of Intent to Sue On November 16, 2010, plaintiffs gave notice to the administrator and regional administrator of the Environmental Protection Agency, the Secretary of the Wisconsin Department of Natural Resources and defendant of its intent to sue defendant for violations of the Clean Water Act. Plaintiffs filed this case on January 18, 2011, at which time neither the state of Wisconsin nor the United States had commenced or was diligently prosecuting any civil or criminal action against defendant for any Clean Water Act violations. DISPUTED FACTS The parties disagree about the length and nature of Stream C. Plaintiffs have produced maps and eyewitness testimony indicating that Stream C flows on the mine site from the east of Highway 27 near Ladysmith, across the southeast corner of defendant’s industrial outlot and adjacent to the biofilter, under a road called Copper Park Lane and through a wooded area south of the outlot to the Flambeau River, with a total length of approximately 0.6 miles. Plaintiffs point to evidence that there are water lines in the four culverts between Highway 27 and Copper Park Lane and that below Copper Park Lane, there is obvious water flow. In addition, plaintiffs rely on the eyewitness testimony of John Coleman, an Environmental Section Leader for the Great Lakes Indian Fish and Wildlife Commission, who states that he has observed Stream C on several occasions and that there is an obvious channel along the entire length of Stream C. Defendant agrees that Stream C between Copper Park Lake and the Flam-beau River is a navigable waterway and tributary that contributes its flow to the Flambeau River. In this region, Stream C has several pools with flowing water that is 16-18 inches deep. Also, the Department of Natural Resources has counted 146 fish of six different species in Stream C south of the lane. However, it is defendant’s position that there is no channel that would qualify as a waterway north of Copper Park Lane. Defendant’s expert, Elizabeth Day, states that the section of Stream C north of the Lane is merely a grassy wetland, with some “channel-like segments” at each culvert. OPINION The Clean Water Act prohibits the “discharge of any pollutant by any person” without proper authorization, such as a permit. 33 U.S.C. § 1311(a); Sackett v. EPA, — U.S. —, 132 S.Ct. 1367, 1369, 182 L.Ed.2d 367 (2012). In the absence of federal or state enforcement, private citizens may enforce this provision by filing a citizen suit in federal court under 33 U.S.C. § 1365(a)(1). Sixty days before initiating a citizen suit, the would-be plaintiff must give notice of the alleged violation to the Environmental Protection Agency, the state in which the alleged violation occurred and the alleged violator. Id. § 1365(b)(1)(A). If the plaintiff prevails in a citizen suit, the court may order injunctive relief, civil penalties payable to the United States Treasury and legal costs and fees. Plaintiffs are bringing this suit under § 1365(a), alleging that defendant discharged pollutants into Stream C and the Flambeau River without a permit issued under the Clean Water Act. In their motion for partial summary judgment, plaintiffs seek to establish standing and defendant’s liability for discharges on 23 days. Defendant does not deny that plaintiffs have complied with the requirements of § 1365(b)(1)(A) by giving adequate notice more than 60 days before filing this suit. However, it contests plaintiffs’ standing to sue and raises several other defenses to plaintiffs’ claims. A. Article III Standing In any case brought in federal court, the plaintiffs’ first hurdle is showing that the court has jurisdiction to decide the merits of the case. DaimlerChrysler Corp. v. Cuno, 547 U.S. 332, 341-42, 126 S.Ct. 1854, 164 L.Ed.2d 589 (2006). Jurisdiction requires plaintiffs who have standing to argue the claims they are advancing. Sprint Communications Co. v. APCC Services, Inc., 554 U.S. 269, 273-74, 128 S.Ct. 2531, 171 L.Ed.2d 424 (2008). Under the Supreme Court’s interpretation of the “cases” and “controversies” limitation on federal court jurisdiction in Article III of the Constitution, plaintiffs have standing if they have suffered an “injury in fact” that is “concrete and particularized,” “actual or imminent,” “fairly traceable to the challenged action of the defendant” and “likely” to be remedied by a decision favoring plaintiffs. Id.; Summers v. Earth Island Institute, 555 U.S. 488, 493, 129 S.Ct. 1142, 173 L.Ed.2d 1 (2009); Friends of the Earth, Inc. v. Laidlaw Environmental Services, 528 U.S. 167, 180-81, 120 S.Ct. 693, 145 L.Ed.2d 610 (2000). Organizations like plaintiffs Wisconsin Resources Protection Council and Center for Biological Diversity have standing to bring suit on behalf of their members if (1) their members would have standing to sue in their own right; (2) the interests they seeks to protect are germane to their purpose as associations; and (3) neither the claim they assert, nor the relief they request, requires the participation of individual members. Laidlaw, 528 U.S. at 181, 120 S.Ct. 693. (The parties agree that the organizational plaintiffs can satisfy the second and third requirements for organizational standing. Thus, the only issue is whether plaintiffs’ members would have standing to sue in their own right.) Both plaintiffs and defendant have moved for summary judgment on the issue of standing. Plaintiffs request that the court find as a matter of law that they have standing under Article III of the Constitution, while defendant contends that this case must be dismissed because plaintiffs lack standing. To prove standing at the summary judgment stage, plaintiffs may not rest on mere allegations to support standing, but must set forth specific facts, that, if true, establish an injury in fact. Lujan v. Defenders of Wildlife, 504 U.S. 555, 560-61, 112 S.Ct. 2130, 119 L.Ed.2d 351 (1992). 1. Injury in fact Plaintiffs Wisconsin Resources Protection Council and Center for Biological Diversity rely on two of their members, plaintiff Gauger and Lori Andresen, to establish standing. The Council relies on injuries to Harold Flater. Plaintiffs in environmental suits may satisfy the injury in fact requirement of standing by proving that they use the affected area and are persons “for whom the aesthetic and recreational values of the area will be lessened” by the challenged activity. Sierra Club v. Morton, 405 U.S. 727, 735, 92 S.Ct. 1361, 31 L.Ed.2d 636 (1972). See also Lujan, 504 U.S. at 562-63, 112 S.Ct. 2130(holding that “the desire to use or observe an animal species, even for purely esthetic purposes, is undeniably a cognizable interest for purposes of standing”). Additionally, injury in fact can be established by “likely exposure” to pollutants. Sierra Club v. Franklin County Power of Illinois, LLC, 546 F.3d 918, 927 (7th Cir.2008). See also Sierra Club v. Johnson, 436 F.3d 1269, 1279 (11th Cir.2006) (“injury in fact exists as a result of concerns about pollution”); New York Public Interest Research Group v. Whitman, 321 F.3d 316, 325 (2d Cir.2003) (“allegations about the health effects of air pollution and of uncertainty as to whether the EPA’s actions expose them to excess air pollution are sufficient to establish injury-in-fact”); Texans United for a Safe Economy Education Fund v. Crown Central Petroleum Corp., 207 F.3d 789, 792 (5th Cir.2000) (“breathing and smelling polluted air is sufficient to demonstrate injury-in-fact and thus confer standing under the [Clean Air Act]”). Plaintiff Gauger enjoys recreational activities near the Flambeau River and Stream C adjacent to defendant’s mine. The copper and zinc discharged from defendant’s biofilter have diminished her enjoyment of the area and make her concerned for her health and the health of the fish and wildlife in the waterways. She has intentionally avoided venturing near the waters at the mouth of Stream C because of concern about the harmful effects of discharged pollutants. Similarly, Lori Andresen and Harold Flater have enjoyed recreational activities in the area near defendant’s mine, have plans to visit the area in the future and are concerned that discharges from defendant’s biofilter will have a negative impact on the fish and wildlife in the river and their own enjoyment of the area. Flater is also concerned that pollutants from the biofilter will cause economic harm to his fishing guide business. Defendant contends that the injuries alleged by plaintiff Gauger, Andresen and Flater are insubstantial and insufficient to confer standing. It contends that if these individuals were genuinely worried about pollutants or had been injured by defendant’s discharges, they would no longer visit the Flambeau River. However, the “injury-in-fact necessary for standing ‘need not be large, an identifiable trifle will suffice.’ ” Franklin County Power, 546 F.3d at 925 (citations omitted). If defendant is discharging pollutants into Stream C and the Flambeau River, Gauger, Andresen and Flater will be exposed to those pollutants. Additionally, plaintiffs need not abandon the river completely in order to establish injury for standing purposes. “[I]t is enough the confer standing that their pleasure is diminished even if not to the point that they abandon the site.” American Bottom Conservancy v. United States Army Corps of Engineers, 650 F.3d 652, 658 (7th Cir.2011). If these individuals avoid Stream C or certain areas of the river, or if their pleasure from their visits to those areas is diminished by the presence of pollutants, that constitutes an injury in fact. Laidlaw, 528 U.S. at 183-84, 120 S.Ct. 693(individual’s affidavit stating that he avoids canoeing near discharge point because of pollution concerns was sufficient to show injury in fact). Defendant also argues that because Andresen and plaintiff Gauger do not live near the mine site and visit the area infrequently, their injuries are speculative and not personal or imminent. However, even a threatened injury can satisfy the Article III standing requirements. MainStreet Organization of Realtors v. Calumet City, 505 F.3d 742, 744 (7th Cir.2007) (“[Standing in the Article III sense does not require a certainty or even a very high probability that the plaintiff is complaining about a real injury, suffered or threatened.”); Village of Elk Grove Village v. Evans, 997 F.2d 328, 329 (7th Cir.1993) (“even a small probability of injury is sufficient to create a case or controversy — to take a suit out of the category of the hypothetical”). Andresen has visited the area three times, Gauger has visited at least a dozen times; they both live within a few hours drive; and they have plans to visit in the spring or summer of 2012. These allegations are sufficient to show that Andresen and Gauger have a personal stake in this lawsuit and are threatened by pollutants in Stream C and the Flambeau River. Franklin County Power, 546 F.3d at 925-26 (finding standing for individual who visited affected area “every other year”); Bensman v. United States Forest Service, 408 F.3d 945, 963 (7th Cir.2005) (finding standing for plaintiff who had visited affected area “about a half-dozen times”); Ecological Rights Foundation v. Pacific Lumber Co., 230 F.3d 1141, 1149-50 (9th Cir.2000) (“Repeated recreational use itself, accompanied by a credible allegation of desired future use, can be sufficient, even if relatively infrequent, to demonstrate that environmental degradation of the area is injurious to that person ... An individual who visits Yosemite National Park once a year to hike or rock climb and regards that visit as the highlight of his year is not precluded from litigating to protect the environmental quality of Yosemite Valley simply because he cannot visit more often.”) (internal quotation and citations omitted). See also Buono v. Norton, 371 F.3d 543, 547 (9th Cir.2004) (“We have repeatedly held that inability to unreservedly use public land suffices as injury-in-fact.”). Finally, defendant contends that plaintiffs cannot establish injury in fact because plaintiffs have not proven that defendant discharged copper, zinc or any other pollutant directly into Stream C or the Flambeau River. This argument conflates the question of standing with whether defendant has violated the Clean Water Act. The relevant inquiry for standing purposes is not whether defendant has violated the Clean Water Act by discharging pollutants without a permit, but “whether [defendant’s] actions have caused ‘reasonable concern’ of injury” to plaintiffs. Covington v. Jefferson County; 358 F.3d 626, 639 (9th Cir.2004). See also Booker-El v. Superintendent, Indiana State Prison, 668 F.3d 896, 899 (7th Cir.2012) (courts should not “conflate[ ] standing with the merits of the case”); Arreola v. Godinez, 546 F.3d 788, 794-95 (7th Cir.2008) (“Although the two concepts unfortunately are blurred at times, standing and entitlement to relief are not the same thing. Standing is a prerequisite to filing suit, while the underlying merits of a claim ... determine whether the plaintiff is entitled to relief.”) (emphasis in original). To meet the injury in fact requirement for standing, plaintiffs need not show that they will prevail on their Clean Water Act claims, or even that defendant’s actions have caused an adverse environmental impact. American Canoe Association v. Murphy Farms, Inc., 326 F.3d 505, 517-18 (4th Cir.2003) (plaintiffs need not show harm to river to establish standing to assert Clean Water Act claims); Ecological Rights Foundation, 230 F.3d at 1152(plaintiffs “need not prove to a scientific certainty that Pacific Lumber has, in fact, discharged pollutants in violation of its permits in order to obtain standing; this, as just explained, is one of the merits questions in the case.”) (emphasis in original). Plaintiffs need show only that the conduct they challenge causes sufficient injury to them. As explained, plaintiffs have introduced sufficient evidence to satisfy this requirement. 2. Traceability Defendant contends that plaintiffs have failed to demonstrate that their asserted injuries are fairly traceable to any conduct by defendant. I disagree. The question for the traceability inquiry is “whether the alleged injury can be traced to the defendant’s challenged conduct, rather than to that of some other actor not before the court.” Ecological Rights Foundation, 230 F.3d at 1152. In Clean Water Act cases, this means that the plaintiffs must show that the pollutants discharged cause or contribute to the kinds of injuries alleged. Texas Independent Producers & Royalty Owners Association v. EPA 410 F.3d 964, 973-74 (7th Cir.2005); American Canoe Association, Inc. v. Louisa Water & Sewer Commission, 389 F.3d 536, 543 (6th Cir.2004); Domino v. Didion Ethanol, LLC, 670 F.Supp.2d 901, 917 (W.D.Wis.2009). Plaintiffs do not need to prove causation with scientific certainty to establish traceability. Texas Independent Producers, 410 F.3d at 973-74; Public Interest Research Group of New Jersey, Inc. v. Powell Duffryn Terminals, Inc., 913 F.2d 64, 72 (3d Cir.1990). Rather, plaintiffs can establish traceability if the plaintiffs have a rational belief that the defendant’s discharge of pollutants will adversely affect their enjoyment of the surrounding area. Franklin County Power, 546 F.3d at 927. Plaintiffs have adduced sufficient evidence to link defendant’s alleged illegal conduct to their diminished enjoyment of the Flambeau River and Stream C and their concerns regarding pollution in those areas. The EPA has listed copper and zinc as toxic pollutants under § 307(a)(1) of the Clean Water Act and the EPA and Wisconsin Department of Natural Resources regulate these metals as pollutants. Defendant owns the Flambeau Mine site, operates the biofilter and is responsible for discharges from it. Thus, discharges of copper or zinc from the biofilter and any injuries caused by those discharges are traceable to defendant. Ecological Rights Foundation, 230 F.3d at 1152 (“It requires no attenuated chain of conjecture ... to link [defendant’s] alleged illegal conduct [of discharging pollutants in violation of its permit] to [plaintiffs’] diminished enjoyment of Yager Creek.”). 3. Redressability Finally, defendant challenges plaintiffs’ ability to establish the redressability prong of standing, which requires plaintiffs to show that a favorable decision would redress their injuries. In this case, plaintiffs are requesting injunctive relief as well as imposition of civil penalties. Specifically, plaintiffs request that this court order defendant to cease all discharges from the biofilter that are not authorized by a Clean Water Act permit and to remediate the harm caused by its violations. Plaintiffs contend that such injunctive relief would improve water quality, recreation and fish and wildlife health. Also, civil penalties would deter defendant from future violations. Defendant contends that plaintiffs’ injuries cannot be redressed through this lawsuit because defendant cannot stop any discharges from the biofilter, it cannot obtain a permit from the Wisconsin Department of Natural Resources that would limit or control the discharges and civil penalties are not appropriate because it has been complying with its mining permit. Defendant’s arguments are not persuasive. Plaintiffs’ request for relief is not that defendant obtain a particular permit from the Department; rather, plaintiffs ask that defendant be enjoined from discharging from the biofilter in violation of the Act. Defendant has adduced no evidence showing that it would be impossible to stop discharges from the biofilter. (Defendant also has adduced no evidence that the Department would deny a request from defendant for a permit if the court ordered defendant to apply for one.) Defendant’s arguments regarding civil penalties are arguments about the merits of plaintiffs’ claims and about the amount of civil penalties that may be appropriate. 33 U.S.C. § 1319(d) (“In determining the amount of a civil penalty the court shall consider ... any good-faith efforts to comply with the applicable requirements”). If plaintiffs establish that defendant violated the Clean Water Act by discharging pollutants without a permit, plaintiffs’ injuries can be redressed by requiring defendant’s compliance with the Act, requiring remediation efforts or by creating a credible deterrent against future violations through the imposition of fines. Therefore, plaintiffs have established redressability and have satisfied all of the elements necessary to show standing. Accordingly, I will grant plaintiffs’ motion for summary judgment and deny defendant’s motion on the issue of standing. B. Indispensability of the Wisconsin Department of Natural Resources The next threshold issue is whether this case may proceed without the Wisconsin Department of Natural Resources. Defendant has moved to dismiss plaintiffs’ complaint, contending that the Department is an indispensable party under Fed.R.Civ.P. 19. Although defendant filed its motion to dismiss several months after the dispositive motion deadline, the issue is sufficiently important that it can be raised at any stage of the proceedings, even sua sponte. Provident Tradesmens Bank & Trust Co. v. Patterson, 390 U.S. 102, 111, 88 S.Ct. 733, 19 L.Ed.2d 936 (1968) (instructing courts to take steps on their own initiative to protect an absentee party). See also MasterCard International Inc. v. Visa International Service Association, Inc., 471 F.3d 377, 382-83 (2d Cir.2006) (“Because Rule 19 protects the rights of an absentee party, both trial courts and appellate courts may consider this issue sua sponte even if it is not raised by the parties to the action.”); 7 Charles Alan Wright, Arthur R. Miller, Mary Kay Kane, Federal Practice and Procedure § 1609 (3d ed. 2011) (“[B]oth the trial court and the appellate court may take note of the nonjoinder of an indispensable party sua sponte”). In deciding a motion under Rule 19, a court must first determine whether the absent party is “necessary” under the terms of Rule 19(a). If the party is necessary, the court considers whether it is “feasible” to join the party. If the absent party is necessary to the action but cannot be joined, the court must determine whether the absent party is “indispensable” as defined by Rule 19(b), which requires the court to conduct a multifactor analysis to “determine whether, in equity and good conscience, the action should proceed among the existing parties or should be dismissed.” Defendant contends that the Department is a necessary party under Rule 19(a)(1)(B), which requires joinder of a party that “claims an interest relating to the subject of the action and is so situated that disposing of the action in the person’s absence may ... as a practical matter impair or impede the person’s ability to protect the interest.” Defendant contends that the Department is a necessary party because plaintiff has attacked the Department’s storm water permitting regulations and its decision to use only a mining permit to regulate defendant. According to defendant, plaintiffs’ real dispute is with the Department, not defendant, and the disposition of the action without the Department would impair or impede the Department’s ability to protect its interests in administering its storm water and mining permit programs. Additionally, defendant contends that because the Department is not a proper party in a citizen suit under 33 U.S.C. § 1365 and is entitled to sovereign immunity, it cannot be joined and this case must be dismissed. I am not persuaded that the Department has an interest in this lawsuit that can be protected only by it is joined as a party. Plaintiffs’ complaint does not allege wrongdoing by the Department; rather, it alleges that defendant discharged pollutants without a permit required by federal law. Such allegations are the proper subject of a citizen suit under the Clean Water Act, 33 U.S.C. § 1365. Congress’s purpose in allowing such suits was to insure enforcement of federal environmental requirements “irrespective of the failings of agency participation.” Friends of the Earth v. Carey, 535 F.2d 165, 173 (2d Cir.1976). See also Sierra Club v. Young Life Campaign, Inc., 176 F.Supp.2d 1070, 1078 (D.Colo.2001) (“[I]t has long been settled that federal and state agencies that administer federal environmental programs are not necessary, let alone indispensable, parties to citizen suits to enforce permitting and other federal environmental requirements against alleged violators.”). Defendant has cited no citizen environment suit in which a court has held that the government agency providing oversight was a necessary party because disposition of the action in the agency’s absence could impair or impede its ability to protect its interests in the federal environmental program or state permit program at issue. Instead, defendant cites Boles v. Greeneville Housing Authority, 468 F.2d 476 (6th Cir.1972), McCowen v. Jamieson, 724 F.2d 1421 (9th Cir.1984) and Aztec Minerals Corp. v. Romer, 940 P.2d 1025, 1033-34 (Colo.App.1997), but these cases are distinguishable. In Boles, the court held that the federal Department of Housing and Urban Development was an indispensable party in a case that indirectly attacked the Department’s administrative decision approving a plan for an urban renewal project. In McCowen, the court determined that the Department of Agriculture was an indispensable party because the district court’s judgment rested on a determination that the Department had erred in a decision concerning the issuance of replacement food stamp coupons by a state agency. In Aztec, the court held that the Environmental Protection Agency was a necessary party in an action in which the plaintiffs were challenging the agency’s response the under Comprehensive Environmental Response, Compensation, and Liability Act. Each of these cases involved an attack on an order or decision by a federal agency, or some degree of involvement on the part of the federal agency that made its appearance in the action necessary. In this case, plaintiffs are challenging the actions of a private company, not an action taken by the Wisconsin Department of Natural Resources. M.B. Guran Company, Inc. v. City of Akron, 546 F.2d 201, 204, n. 3 (6th Cir.1976) (no need to determine whether Department of Housing and Urban Development was indispensable party where plaintiff alleged that defendant was violating Department rule, not that Department was violating its own rule); Dorsey v. Tompkins, 917 F.Supp. 1195, 1200 (S.D.Ohio 1996) (distinguishing Boles and holding that agency is not necessary party where plaintiff is contending that defendant acted in violation of statute, not that agency acted in violation of statute). Further, although defendant has asserted a “permit shield” defense that relies on a state mining permit issued by the Department, resolution of this issue will not require the court to “invalidate” the Department’s state mining and storm water permit programs, as defendant suggests. Rather, the court will be required to determine whether defendant’s particular metallic mining permit protects it from suit under the Clean Water Act. That the Department has offered an opinion on this issue does not change the nature of plaintiffs’ claims or make the Department a necessary party. Young Life, 176 F.Supp.2d at 1078-79 (“That [the state agency] has taken actions or positions relating to the terms of [defendant’ wastewater discharge] permit does not change this rule or convert this citizen suit to enforce the Permit into a challenge to the validity of [the agency’s] post-Permit actions. The subject of this action is [defendant’s] compliance with the Permit ... not the validity of [the agency’s] post-Permit representations to [defendant] regarding” permit requirements). This case is about whether defendant’s alleged discharges violate federal law or whether they are authorized by defendant’s specific mining permit. It is not about the Department’s state storm water or mining regulations generally and the case does not require the court to consider whether any other entity’s particular storm water permit would act as a shield to Clean Water Act claims. As plaintiffs point out, courts frequently interpret state and federal regulations and agency actions in the context of environmental suits. In United States v. Cinergy Corp., 623 F.3d 455, 457-59 (7th Cir.2010), the court of appeals considered whether the United States could enforce particular state regulations against a power plant under the Clean Air Act. The court concluded that although th