Pesticide impacts are usually discussed in the context of applied amounts while disregarding the large but environmentally relevant variations in substance-specific toxicity. Here, we systemically interpret changes in the use of 381 pesticides over 25 years by considering 1591 substance-specific acute toxicity threshold values for eight nontarget species groups. We find that the toxicity of applied insecticides to aquatic invertebrates and pollinators has increased considerably—in sharp contrast to the applied amount—and that this increase has been driven by highly toxic pyrethroids and neonicotinoids, respectively. We also report increasing applied toxicity to aquatic invertebrates and pollinators in genetically modified (GM) corn and to terrestrial plants in herbicide-tolerant soybeans since approximately 2010. Our results challenge the claims of a decrease in the environmental impacts of pesticide use.