Site conditions include the depth to groundwater, the geologic conditions, and the climate. The shallower the depth to groundwater, the less soil there is to act as a filter. There are also fewer opportunities for degradation or adsorption of pesticides. Therefore, extra precautions should be taken to protect groundwater in areas where it is close to the ground surface. In humid regions and low valleys associated with lakes and river bottoms, groundwater may be only a few feet below the soil surface. If rainfall is high and soils are permeable, water carrying dissolved pesticides may take only a few days to percolate downward to groundwater. In arid and/or high mesa regions, groundwater may lie several hundred feet below the soil surface, and leaching of pesticides to groundwater may be a much slower process.

In addition to depth to groundwater, it is important to look at the permeability of the geologic layers between the surface soil and groundwater. Highly permeable materials, such as gravel deposits, allow water and dissolved pesticides to freely percolate downward to groundwater. On the other hand, layers of clay are much less permeable and, thus, inhibit the movement of water. Groundwater quality is most vulnerable in areas where permeability of geologic layers is rapid. Carbonate bedrock, such as limestone, can make groundwater particularly susceptible to contamination because it is easily dissolved by water to form solution channels and depressions in the land surface. The depressions, called sinkholes, can provide a direct connection between the soil surface and the groundwater. Contaminated water that drains into a sinkhole can readily enter groundwater because the soil that lines the bottom of a sinkhole is often thin and provides little filtering of pollutants. Areas with high rates of rainfall or irrigation may have large amounts of water percolating through the soil and therefore are highly susceptible to leaching of pesticides, especially if the soils are highly permeable.