A recently completed study by Global Insight showed that higher levels of ethanol production lead to a greater degree of continuous corn planting, resulting in a greater need for weed control, more insect problems, and additional nitrogen fertilizer and insecticide use. 

Significantly higher fertilizer and pesticide use associated with higher corn crop-induced ethanol production levels will increase the likelihood of additional nutrient run-off and increased adverse environmental impacts on water resources.
U.S. corn production causes more total soil erosion, uses more herbicides, insecticides and nitrogen fertilizer than any other U.S. crop.

Atrazine, an herbicide used almost exclusively on corn, is EPA-classified as a possible carcinogen and is frequently found in drinking water supplies in the upper Midwest.  The USGS reports that nationally, atrazine is found about 5 times more frequently than MTBE in drinking water.

In some Western irrigated corn acreage, ground water is being mined 25% faster than the natural recharge of its aquifer.