Farms with large livestock and poultry operations, such as factory farms, can be a major source of wastewater pollutions. These facilities are called concentrated animal feeding operations or confined animal feeding operations and are being subject to increasing government regulations.

Treatment
Whilst solid manure heaps outdoors can give rise to polluting wastewaters from runoff, this type of waste is usually relatively easy to treat by containment and/or covering of the heap.

Animal slurries require special handling and are usually treated by containment in lagoons before disposal by spray or trickle application to grassland. Constructed wetlands are sometimes used to facilitate treatment of animal wastes, as are anaerobic lagoons. Excessive application or application to sodden land or insufficient land area can result in direct runoff to watercourses, with the potential for causing severe pollution. Application of slurries to land overlying aquifers can result in direct contamination or, more commonly, elevation of nitrogen levels as nitrite or nitrate.

The disposal of any wastewater containing animal waste upstream of a drinking water intake can pose serious health problems to those drinking the water because of the highly resistant spores present in many animals that are capable of causing disabling disease in humans. This risk exists even for very low-level seepage via shallow surface drains or from rainfall run-off.

Some animal slurries are treated by mixing with straws and composted at high temperature to produce a bacteriologically sterile and friable manure for soil improvement.