Contaminants such as petroleum hydrocarbons, heavy metals and pesticides can cause direct toxic effects when released into aquatic environments. Sensitive species may be impaired by sublethal effects or decimated by lethality, and this ecological alteration may initiate a trophic cascade or a release from competition that secondarily leads to responses in tolerant species. Contaminants may exert direct effects on keystone facilitator and foundation species, and contaminant-induced changes in nutrient and oxygen dynamics may alter ecosystem function. Thus, populations and communities in nature may be directly and/or indirectly affected by exposure to pollutants. While the direct effects of toxicants usually reduce organism abundance, indirect effects may lead to increased or decreased abundance. Here we review 150 papers that reference indirect toxicant effects in aquatic environments. Studies of accidental contaminant release, chronic contamination and experimental manipulations have identified indirect contaminant effects in pelagic and benthic communities caused by many types of pollutants. Contaminant-induced changes in behavior, competition and predation/grazing rate can alter species abundances or community composition, and enhance, mask or spuriously indicate direct contaminant effects. Trophic cascades were found in 60% of the manipulative studies and, most commonly, primary producers increased in abundance when grazers were selectively eliminated by contaminants. Competitive release may also be common, but is difficult to distinguish from trophic cascades because few experiments are designed to isolate the mechanism(s) causing indirect effects. Indirect contaminant effects may have profound implications in environments with strong trophic cascades such as the freshwater pelagic. In spite of their undesirable environmental influence, contaminants can be useful manipulative tools for the study of trophic and competitive interactions in natural communities.