As with life cycle assessment (LCA) studies in general, agricultural LCAs often rely on static and outdated inventory data, but literature suggests that agricultural systems may be highly dynamic. Here, we applied life cycle impact assessment methods to investigate the trends and underlying drivers of changes in non-global environmental impacts of major crops in the US. The results show that the impact per hectare corn and cotton generated on the ecological health of freshwater systems decreased by about 50% in the last decade. This change is mainly due to the use of genetically modified (GM) crops, which has reduced the application of insecticides and relatively toxic herbicides such as atrazine. However, the freshwater ecotoxicity impact per hectare soybean production increased by 3-fold, mainly because the spread of an invasive species, soybean aphid, has resulted in an increasing use of insecticides. In comparison, other impact categories remained relatively stable. By evaluating the relative ecotoxicity potential of a large number of pesticides, our analysis offers new insight into the benefits associated with GM crops. Our study also implies that because different impact categories show different degrees of changes, it is worthwhile focusing on the rapidly changing categories when updating agricultural LCA databases under time and resource constraints.