Chemical contaminants are ubiquitous in nature and a major goal of ecologists has been to understand and predict their impacts on natural communities. While direct toxic effects can be garnered from single-species laboratory studies, the full suite of possible effects can only be observed when organisms are embedded within a community. In this study, we manipulated the concentration of malathion (a broad-spectrum insecticide) to determine the impacts on aquatic communities containing phytoplankton, periphyton, and 27 species of animals (16 zooplankton, 5 snails, 3 tadpoles and 3 predatory insects). Using relatively low concentrations (0.13 to 0.46 mg l−1), we found important direct (and interactive) effects of predators and malathion on the food web as well as a number of apparent density- and trait-mediated indirect effects. Malathion initiated an indirect effect by decreasing zooplankton diversity and abundance, which propagated an increase in phytoplankton, a decrease in periphyton, and a subsequent decrease in the growth of leopard frog tadpoles. There also was an apparent trait-mediated indirect effect whereby increased amounts of the pesticide reduced predation rates on amphibians without affecting the survival of the primary amphibian predator (larval Anax dragonflies). In contrast, snail survival and growth was unaffected by the pesticide but there were strong, species-specific effects from their primary predator (adult Belostoma water bugs). This is one of few studies to examine the impacts of malathion on aquatic communities across a range of concentrations, despite the fact that it is currently the most commonly applied insecticide in the United States, it is applied around the world, and it can be legally directly sprayed over aquatic habitats to control the mosquitoes that carry malaria and West Nile virus. Our results suggest several mechanisms by which a wide variety of pesticides with similar modes of action might impact aquatic communities.