Factory farms contribute significantly to water contamination through several mechanisms. The large volumes of animal waste produced in confined animal feeding operations (CAFOs) often exceed the capacity of the surrounding land to absorb and break down these pollutants. This waste can contain harmful pathogens, excess nutrients such as nitrogen and phosphorus, and antibiotics, all of which can leach into nearby water sources.

Runoff from factory farms, particularly during heavy rainfalls, transports this waste into rivers, lakes, and groundwater. Nutrient overload from fertilizers and manure can lead to eutrophication, which causes harmful algal blooms that deplete oxygen in the water, affecting aquatic life. Contaminated water sources can pose serious health risks to humans, including gastrointestinal illnesses and long-term exposure effects.

Moreover, the use of pesticides and fertilizers on feed crops, often grown in proximity to factory farms, can further contaminate water with chemicals that may be hazardous to both wildlife and human health. The cumulative impact of these factors raises significant concerns about the sustainability of water resources in regions with high concentrations of factory farming operations..