Animal waste contaminants can enter groundwater through poorly constructed wells, or by percolating through soil layers. Spills or leaks of fuels, solvents and pesticides are often the most reasonable explanations of well water contamination. The most common source of well contamination is inadequate well construction and maintenance. They combine to literally pour contaminants down the well into the groundwater. Plant nutrients from fertilizers and animal wastes are identical.
Fertilizer spills near a well pose a contamination threat.
To a much lesser degree, percolation of nitrates through soil layers to the groundwater can stem from land application of animal wastes or fertilizers. Note that nitrogen does occur naturally. Commonly grown legume plants, such as soybeans and alfalfa, produce nitrogen. This nitrogen also changes into nitrate. One cannot distinguish between these naturally occurring sources of nitrates and those added by fertilizers or animal wastes.