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California Conservation Groups Challenge Agricultural Runoff Exemption from Clean Water Act Permitting

July 28, 2011

A coalition of fishing associations and conservation groups (collectively “Conservation Coalition”)[1] has issued a notice of intent to sue letter to the U.S. Bureau of Reclamation (“Bureau”) and California’s San Luis & Delta-Mendota Water Authority (“Authority”) over alleged discharges of pollutants in water running off of California crop-land through canals known as the Grasslands Bypass Project and ultimately into the San Francisco Bay Delta. The Conservation Coalition’s letter is the first step toward a probable suit under the Clean Water Act (“CWA”)[2] testing whether the Bureau and the Authority are discharging water within the scope of the CWA’s exemptions for return flows from irrigated agriculture. If those exemptions are unavailable or narrower than previously understood then far more of the United States’ 330 million acres of agricultural land[3] will be subject to CWA jurisdiction and many farmers formerly exempt from permitting will be required to obtain and comply with water quality permits.  

The Grasslands Bypass Project

The Grasslands Drainage Area is an agricultural region on the west side of California's San Joaquin Valley.[4] The agricultural land there is productive, but the soil contains a high level of selenium, a naturally occurring trace element.[5] When farmers in the San Joaquin Valley irrigate their crops, selenium washes from the soil and accumulates in the agricultural drainage water that collects in the tiles installed to drain excess water from the fields.[6]

The Bureau and the Authority operate the Grasslands Bypass Project (“Project”).[7]  Before the Project began in 1996, drainage water from farms in the 97,000 acre Grassland Drainage Area was discharged into Salt Slough and other channels used to deliver water to wetland areas.[8] The drainage water contains high concentrations of selenium, salts, and other constituents that are harmful to wildlife.[9]

The Project prevents discharge of subsurface agricultural drainage water into wildlife refuges and wetlands in central California.[10] The drainage water is conveyed instead through a segment of the San Luis Drain to Mud Slough, a tributary of the San Joaquin River. According to the Bureau, “the Project improves water quality in the wildlife refuges and wetlands, sustains the productivity of 97,000 acres of farmland, and fosters cooperation between area farmers and regulatory agencies in drainage management reduction of selenium and salt loading.”[11] The Conservation Coalition alleges, however, that the Project is now conveying selenium and other pollutants into Mud Slough, the San Joaquin River, and the San Francisco Bay Delta and, therefore, violating the CWA.

Clean Water Act Permitting

CWA Section 301(a)[12] generally prohibits the discharge of a “pollutant” from any “point source” into waterways without a National Pollution Discharge Elimination System (“NPDES”) permit. The CWA defines a “point source” as “any discernible, confined and discrete conveyance, including but not limited to any pipe, ditch, channel, tunnel, [or] conduit . . . from which pollutants are or may be discharged.”[13] NPDES permits are governed under CWA Section 402.[14] NPDES permits require regulated facilities to manage and monitor water quality to ensure that contaminated water is not discharged to wetlands, creeks, rivers, and marine waters.

The CWA does not, however, require permits for certain agricultural water discharges. In 1977, Congress amended the CWA to expressly reverse a court decision in NRDC v. Train,[15] which would have required an NPDES permit for return flows from irrigated agriculture.[16] At the time, Congress made two relevant amendments to the CWA. First, Congress exempted irrigation return flows from NPDES permitting: “The Administrator shall not require a permit under this section for discharges composed entirely of return flows from irrigated agriculture.”[17]Second, Congress excluded return flows from the definition of point source: “This term does not include return flows from irrigated agriculture.”[18] As a result, the EPA does not consider return flows from agricultural lands to be point source pollution.[19]

The Conservation Coalition Challenges to the Return Flow Exemption

The Conservation Coalition argues that the Project’s “pumping and discharge of polluted water into Mud Slough, the San Joaquin River, and eventually the San Francisco Bay Delta constitutes the discharge of a pollutant from a point source into a water of the United States for which no permit has been issued.”[20] They further argue that the Project’s discharges threaten ecological resources – including delta smelt, salmon, steelhead, and sturgeon – and also the Bay-Delta drinking water supply. The Conservation Coalition demands that the Bureau and the Authority apply to the California Regional Water Quality Control Board for an NPDES permit or cease all unpermitted discharges.[21] The Conservation Coalition’s demands effectively seek to have the Bureau and the Authority manage and possibly treat contaminants in irrigation return flows.

The Conservation Coalition will likely look to several court decisions to support their arguments. They will look to the U.S. Supreme Court’s decision in South Florida Water Management Dist. v. Miccosukee Tribe of Indians (“Miccosukee”),[22] to argue that the return flows exemption does not apply to the Project’s discharges. In Miccosukee, the Court held that “point source” includes not only point sources that generate pollutants, but also conveyances that transfer pollutants originating elsewhere to navigable water.[23] The Court, however, ultimately remanded the case to the lower court to determine whether the canal, from which the polluted water was pumped, and the wetlands, to which the water was discharged, are distinct water bodies; if not, no permit is required since there can be no “addition” of pollutants. Although the Conservation Coalition cites Miccosukee for the proposition that under the CWA “any discharge that is not made up ‘entirely’ of agricultural return flows is not exempt”, the Bureau and the Authority will likely respond that the decision does not support such a broad holding. This will ultimately be one of the key issues in the pending litigation.

The Conservation Coalition may also look to the Ninth Circuit Court of Appeals’ recent decision in Northwest Environmental Defense Center (NEDC) v. Brown (“Brown”) for support.[24] In Brown, the Ninth Circuit severely limited the application of the EPA’s Silviculture Rule, which defines a limited class of activities as “silvicultural point sources,” and interprets “nonpoint source silvicultural activities” as outside the NPDES program.[25] The case involved two Oregon logging roads where stormwater runoff is collected in systems of ditches, channels, and culverts, and then discharged into adjacent rivers. The Ninth Circuit held that the stormwater collection systems at issue unambiguously constitute “point sources” under the CWA, and that such discharges therefore require NPDES permits.  In so holding, the court significantly limited a decades-old regulation that had historically been viewed as excluding logging road runoff from the NPDES program and charged EPA with developing a general permit to handle the discharges. For more on Brown, see Ninth Circuit Reissues Opinion Requiring NPDES Permits for Stormwater Discharges from Logging Roads, Marten Law Environmental News (May 20, 2011). 

The Bureau and the Authority may be able to distinguish the Brown case on grounds that it involved EPA regulations where, in the San Joaquin case, the relevant law is the CWA’s statutory definitions of point source and return flows. This argument may provide the Bureau and the Authority with a more defensible position than the one the State of Oregon faced in Brown because it may allow them to argue that Congress intended irrigation return flows to be broadly exempted from CWA permitting without relying on the EPA’s interpretation of the Act. Despite this possible distinction, the Conservation Coalition and the Bureau and the Authority appear on a course to litigate in the irrigated agriculture context CWA permitting issues parallel to those litigated in the timber context in Brown. The outcome of this dispute could have far reaching impacts on the Bureau and irrigators throughout the country, including possibly triggering CWA permitting requirements for a business sector believed to be exempt.

For more information about Marten Law’s Water Quality and Wetlands practice please contact Jeff Kray.

[1] The conservation groups involved are: the Pacific Coast Federation of Fisherman’s Associations, California Sportfishing Protection Alliance, Friends of the River, San Francisco Crab Boat Owners Association, Inc., The Institute for Fisheries Resources, and Felix Smith.

[2] 33 U.S.C. § 1342.

[3] http://www.epa.gov/owow_keep/NPS/agriculture.html.

[4] http://water.epa.gov/polwaste/nps/success319/Section319III_CA.cfm

[5] Id.

[6] Id.

[7] http://www.usbr.gov/mp/grassland/.

[8] Id.

[9] Id.

[10] Id.

[11] Id.

[12] 22 U.S.C. §1311(a).

[13] Id. § 1362(14).

[14] See 33 U.S.C. §§ 1311(a), 1342(p).

[15] 396 F.Supp. 1393 (D.D.C. 1975), affirmed, NRDC v. Costle, 568 F.2d 1369, 1382 (1977).

[16] The Train decision vacated NPDES regulations EPA had enacted in 1973. Those regulations had exempted discharges from several classes of point sources from the NPDES permit requirement. The exempted sources included all irrigation return flows (such as tailwater, tile drainage, surfaced ground water flow or bypass water) from areas less than 3,000 contiguous acres or 3,000 noncontiguous acres that use the same drainage system. 40 CFR § 125.4(i) (1973).

[17] 33 U.S.C. § 1342(l)(2).

[18] 33 U.S.C. § 1362(14).

[19] E&E News, Water Pollution: Calif. Groups plan suit over agricultural runoff water (June 8, 2011)quoting Karen Schwinn, associate director of EPA’s water division in the Pacific Southwest (subscription required).

[20] Notice of Intent to Sue Letter at p. 2.

[21] Id. at p. 7.

[22] 541 U.S. 95 (2004).

[23] Id. at 104-05.

[24] 640 F.3d 1063 (2011).

[25] 40 C.F.R. § 122.27. The Silviculture Rule limits “silvicultural point sources” to “rock crushing, gravel washing, log sorting, or log storage facilities which are operated in connection with silvicultural activities and from which pollutants are discharged into waters of the United States.” Falling outside the definition are “non-point source silvicultural activities such as nursery operations, site preparation, reforestation and subsequent cultural treatment, thinning, prescribed burning, pest and fire control, harvesting operations, surface drainage, or road construction and maintenance from which there is natural runoff.”

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