Understanding toxicant effects at higher levels of biological organization continues to be a challenge in ecotoxicology and ecological risk assessment. This is due in part to a tradition in ecotoxicology of considering the direct effects of toxicants on a limited number of model test species. However, the indirect effects of toxicity may be a significant factor influencing the manner in which ecosystem structure and function respond to anthropogenic stressors. Subsequently, failure to incorporate indirect effects into risk assessment paradigms may be a significant source of uncertainty in risk estimates. The current paper addresses the importance of indirect effects in an ecotoxicological context. Laboratory, mesocosm, and whole ecosystem research into indirect effects is reviewed. The implications of indirect effects for ecological risk assessment and potential areas of profitable future research are also discussed.