Source: https://www.aglaw.us/schroeder-ag-law-blog/2015/9/26/clean-water-act-basics-for-farmers
Timestamp: 2019-04-21 22:58:42+00:00

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One central law in approaching wetlands in agricultural areas is the Clean Water Act ("CWA"). 33 USC § 1251 et seq. The CWA allows the EPA to enforce its provisions and provides for citizen suits. Non-compliance with the CWA can lead to fines and lawsuits. Farmers should make sure they are not violating the CWA anytime they move dirt on their farm.
The definition of wetlands under the CWA is essentially the same as under Swampbuster. Again, "wetlands" are those areas that are inundated or saturated by surface or groundwater at a frequency and duration sufficient to support, and that under normal circumstances do support, a prevalence of vegetation typically adapted for life in saturated soil conditions. 40 CFR § 230.3(t).
The national pollutant discharge elimination system ("NPDES") permit program controls water pollution by regulating point sources that discharge pollutants into waters of the United States. Section 404 of the CWA establishes a program to regulate the discharge of dredged or fill material into waters of the United States, including wetlands. It is also unlawful to discharge dredged or fill material into the waters of the U.S. without first receiving authorization from the U.S. Corps of Engineers. Waters of the U.S. generally includes wetlands. (There are scores of cases discussing exactly what "waters of the U.S." means, but suffice to say that it likely includes most wetlands.) “Discharge of dredged material” means any addition of dredged material into, including redeposit of dredged material other than incidental fallback within, the waters of the United States. This is the area most likely to affect farmers and agricultural areas. While most ongoing farming activities do not require Section 404 permits, a farmer likely does need a permit to discharge soil or any other deposit into a wetland because of the broad language in the statute. See 33 USC § 1311(a); 33 CFR § 323; 40 CFR 232.2. Point sources are discrete conveyances such as pipes or man-made ditches. Surface waters can include wetlands. Point sources may not discharge pollutants to surface waters without an NPDES permit from the Environmental Protection Agency ("EPA") in partnership with state agencies. In Indiana, the state agency responsible for NPDES permits is the Indiana Department of Environmental Management ("IDEM"). IDEM issues its NPDES permits, called "Rule 5" permits, for discharges pursuant to 327 IAC 15-5. Certain non-point sources (including agricultural stormwater discharges and irrigation return flows) are not subject to the federal permit program.
There is no CWA jurisdiction over isolated waters or wetlands, but many wetlands that might appear "isolated" to a layman could be considered to have a "significant nexus" to traditional navigable waters. That is enough for the federal government to exercise jurisdiction under the CWA. The recent Supreme Court decision on this issue is called Rapanos v. United States, 547 U.S. 715 (2006). It includes five separate opinions and no majority, and is the perfect piece of reading material if you're having trouble sleeping.
There are exemptions to the Clean Water Act that might apply to a farmer's discharges into the water or wetland area. The "agricultural exemption" applies to "normal farming" activities. Those activities must be part of an established, ongoing program. Changing crops as part of a crop rotation is exempt. Resumption of farming fallow areas as part of a rotation is also exempt. "Normal farming" activities include cultivating, harvesting, plowing, seeding, and "minor damage." These words are all specifically defined in regulations. 40 CFR § 232.3(d). The agricultural exemption also applies to stormwater discharges, return flow from irrigated agriculture, normal activities associated with farm roads, and normal activities associated with construction and maintenance of irrigation ditches or maintenance of drainage ditches. The agricultural exemption, like other CWA exemptions, is construed narrowly. Farmers must be careful, because "maintenance" of a ditch does not include changing the location or footprint of the ditch or levee. The agricultural exemption is subject to a "recapture provision." Any discharge of dredged or fill material into the waters of the U.S. incidental to any activity intended to bring an area of the water or wetland into a new use, whether the flow, circulation, or reach of navigable waters might be impaired is required to have a Section 404 permit. This "recapture provision" can bring a large swath of activities back under the CWA, even if at first glance it appeared the agricultural exemption applied. For instance, courts have held that converting from silviculture (growing trees) to soybean production and even from wetlands farming to dryland farming can subject the activities in question to recapture, particularly if it involves hydrologic alterations, such as loss of wetlands.
Non-exempt discharges are not necessarily prohibited, but they do require either a general or individual Section 404 permit. Like the Swampbuster, the CWA contains mitigation provisions. When considering mitigation options, a farmer should seek to "avoid, minimize, and compensate" for the loss of wetlands. The farmer should work with the local Corps, NRCS, and state agencies to determine the appropriate use of mitigation in each situation.
Like the Swampbuster, the CWA is not something to be ignored. Farmers and consultants should be aware of these federal statutes and the way in which those statutes can affect agricultural land use. Contact an attorney if you have questions. As always, this blog post should not be considered legal advice.
By Brianna J. Schroeder. Used by permission.

References: § 1251
 § 230
 § 1311
 § 323
 v. 
 § 232