We investigate the environmental effects due to pesticides for two different genetically modified (GM) seeds: insect resistant (IR) cotton and herbicide tolerant (HT) soybeans. Using an agricultural production model of a profit maximizing competitive farm, we derive predictions that IR trait decreases the amount of insecticides used and HT trait increases the amount of less toxic herbicides. While the environmental impact of pesticides for IR seeds is lower, for the HT seeds the testable predictions are ambiguous: scale as substitution effects can lead to higher environmental impacts. We use a dataset on commercial farms use of pesticides and biotechnology in Brazil to document environmental effects of GM traits. We explore within-farm variation for farmers planting conventional and GM seeds to identify the effect of adoption on the environmental impact of pesticides measured as quantity of active ingredients of chemicals and the Environmental Impact Quotient index. The findings show that the IR trait reduces the environmental impact of insecticides and the HT trait increases environmental impact due to weak substitution among herbicides of different toxicity levels.