Livestock Wastes and Water Quality Animal manure has organic matter, plant nutrients, salts, and pathogenic microorganisms that can reduce water quality. Organic matter in rainfall or snowmelt runoff breaks down in streams and ponds by biochemical reactions. Those reactions can use enough dissolved oxygen to cause a fish kill. Organic matter is filtered from water at the surface or in the soil. So, organic matter often reaches surface water, but groundwater is largely protected.
Microorganisms abound in animal intestinal tracts.
Although documented cases of human disease from livestock waste are rare, transmissible livestock diseases from pathogens do threaten humans. The soil-climate environment is hostile to such microorganisms. As is the case with organic matter, they are filtered by soil above groundwater. Microorganisms seldom seep to groundwater from land-applied manure, properly functioning lagoons, or earthen manure storages. However, they remain a threat where they can pass through a shallow layer of coarse sand to fractured rock.