Aquatic environments are being contaminated with a myriad of anthropogenic chemicals, a problem likely to continue due to both unintentional and intentional releases. To protect valuable natural resources, novel chemicals should be shown to be environmentally safe prior to use and potential release into the environment. Such proactive assessment is currently being applied to room-temperature ionic liquids (ILs). Because most ILs are water-soluble, their effects are likely to manifest in aquatic ecosystems. Information on the impacts of ILs on numerous aquatic organisms, focused primarily on acute LC50 and EC50 endpoints, is now available, and trends in toxicity are emerging. Cation structure tends to influence IL toxicity more so than anion structure, and within a cation class, the length of alkyl chain substituents is positively correlated with toxicity. While the effects of ILs on several aquatic organisms have been studied, the challenge for aquatic toxicology is now to predict the effects of ILs in complex natural environments that often include diverse mixtures of organisms, abiotic conditions, and additional stressors. To make robust predictions about ILs will require coupling of ecologically realistic laboratory and field experiments with standard toxicity bioassays and models. Such assessments would likely discourage the development of especially toxic ILs while shifting focus to those that are more environmentally benign. Understanding the broader ecological effects of emerging chemicals, incorporating that information into predictive models, and conveying the conclusions to those who develop, regulate, and use those chemicals, should help avoid future environmental degradation.