Farming and raising animals is not the same everywhere.  Each tract of land has its own soil type, bedrock, plant cover type and percentage, water flow and slope.  All of these factors play a part in the vulnerability of surface and ground water to contamination by farm run-off.  This runoff could contain manure, fertilizer, herbicides, insecticides or other substances from machinery and operations.  The contaminants in the run-off could kill aquatic plants and insects at the base of the food web, or make them grow too numerous.  Each situation puts the aquatic ecosystem off balance and lowers species diversity by decreasing the survival rate of sensitive organisms.