The original Clean Water Act (CWA) applied to cleaning up surface water and had only some applications to agriculture. The act dealt with agriculture mostly from the perspective of large "Ag" operations, such as animal and stock feedlots. Feedlots were listed by the CWA as "point sources," which were very important in determining whether any water quality regulation would be permitted. If a point source was designated, more federal and state regulations would be allowed.
Federal Enforcement
Enforcing the federal rules in agriculture is left to the Environment Protection Agency (EPA) generally, and the National Pollutant Discharge Elimination System (NPDES) specifically. The NPDES can strictly monitor farm animal operations that have any effect on water supplies. Courts also are busy interpreting the CWA as it applies to farmers. For example, one federal court in 2009 ruled that “pesticide” applications are point source pollutants. This ruling affected over 350,000 wheat producers.
Changes to the original CWA have a lot to do with agriculture. Some of the changes to the CWA have added more than just surface water cleaning for agricultural point sources. Now, there a great number of specific CWA rules affecting agricultural practices as “secondary” sources, which often have some affect in agricultural practices:
Animal Feeding Operations
Aquaculture Projects
Concentrated Aquatic Animal Production Facilities
Bio-solids and Agriculture
Non-point Source Pollution and Agriculture
Estuaries and Agriculture
National Coastal Water Program and Agriculture
Oil Spill Prevention, Control and Countermeasures (SPCC) Plan and Agriculture
TMDLs and Agriculture
Wetlands and Agriculture
State Enforcement
In 2006, the Supreme Court limited the types of surface water under the CWA, but recent changes to the Act by Congress include more types of estuaries defined as “surface” water. The CWA also gives states some powers when it comes to deciding how to deal with agriculture and clean water. Many changes to water safety rules now force states to monitor farm water quality. This is especially important since there are no federal rules for “non-point” water pollution. The SWA requires every state to develop plans for monitoring water quality in the state, and your state rules may require non-point monitoring on farms.
Other Laws and Regulations
Generally, states will have their own sets of “best management practices” (or BMPs) for Ag water quality. Besides the SWA, there are also many other federal rules to expand water quality testing and enforcement. The federal Safe Drinking Water Act, for example, has a lot to say about groundwater pollution---while the SWA usually deals only with surface waters.