In the intensely farmed corn-growing regions of the mid-western USA, surface waters have often been contaminated by herbicides, principally as a result of rainfall runoff occurring shortly after application of these to corn and other crops. In some vulnerable watersheds, water quality criteria for chronic human exposure through drinking water are occasionally exceeded. We selected three settings representative of vulnerable corn-region watersheds, and used the PRZM-EXAMS model with the Index Reservoir scenario to predict corn herbicide concentrations in the reservoirs as a function of herbicide properties and use pattern, site characteristics and weather in the watersheds. We compared herbicide application scenarios, including broadcast surface pre-plant atrazine and alachlor applications with a glyphosate pre-plant application, scenarios in which losses of herbicides were mitigated by incorporation or banding, and scenarios in which only glyphosate or glufosinate post-emergent herbicides were used with corn genetically modified to be resistant to them. In the absence of drift, in almost all years a single runoff event dominates the input into the reservoir. As a result, annual average pesticide concentrations are highly correlated with annual maximum daily values. The modeled concentrations were generally higher than those derived from monitoring data, even for no-drift model scenarios. Because of their lower post-emergent application rates and greater soil sorptivity, glyphosate and glufosinate loads in runoff were generally one-fifth to one-tenth those of atrazine and alachlor. These model results indicate that the replacement of pre-emergent corn herbicides with the post-emergent herbicides allowed by genetic modification of crops would dramatically reduce herbicide concentrations in vulnerable watersheds. Given the significantly lower chronic mammalian toxicity of these compounds, and their vulnerability to breakdown in the drinking water treatment process, risks to human populations through drinking water would also be reduced.