Agricultural wastewater treatment is a farm management agenda for controlling pollution from confined animal operations and from surface runoff that may be contaminated by chemicals or organisms in fertilizer, pesticides, animal slurry, crop residues or irrigation water. Agricultural wastewater treatment is required for continuous confined animal operations like milk and egg production. It may be performed in plants using mechanized treatment units similar to those used for industrial wastewater. Where land is available for ponds, settling basins and facultative lagoons may have lower operational costs for seasonal use conditions from breeding or harvest cycles. Animal slurries are usually treated by containment in anaerobic lagoons before disposal by spray or trickle application to grassland. Constructed wetlands are sometimes used to facilitate treatment of animal wastes.

Nonpoint source pollution includes sediment runoff, nutrient runoff and pesticides. Point source pollution includes animal wastes, silage liquor, milking parlour (dairy farming) wastes, slaughtering waste, vegetable washing water and firewater. Many farms generate nonpoint source pollution from surface runoff which is not controlled through a treatment plant.

Farmers can install erosion controls to reduce runoff flows and retain soil on their fields. Common techniques include contour plowing, crop mulching, crop rotation, planting perennial crops and installing riparian buffers. Farmers can also develop and implement nutrient management plans to reduce excess application of nutrients and reduce the potential for nutrient pollution. To minimize pesticide impacts, farmers may use Integrated Pest Management (IPM) techniques (which can include biological pest control) to maintain control over pests, reduce reliance on chemical pesticides, and protect water quality.

Nonpoint source pollution from farms is caused by surface runoff from fields during rain storms. Agricultural runoff is a major source of pollution, in some cases the only source, in many watersheds.

Soil washed off fields is the largest source of agricultural pollution in the United States. Excess sediment causes high levels of turbidity in water bodies, which can inhibit growth of aquatic plants, clog fish gills and smother animal larvae.

Farmers may utilize erosion controls to reduce runoff flows and retain soil on their fields. Common techniques include:

Nitrogen and phosphorus are key pollutants found in runoff, and they are applied to farmland in several ways, such as in the form of commercial fertilizer, animal manure, or municipal or industrial wastewater (effluent) or sludge. These chemicals may also enter runoff from crop residues, irrigation water, wildlife, and atmospheric deposition.

Farmers can develop and implement nutrient management plans to mitigate impacts on water quality by: