Ionic liquids (ILs) are nonvolatile organic salts that remain liquid over a wide range of temperatures. Ionic liquids are promoted as environmentally friendly alternatives to the volatile organic solvents that are currently in widespread industrial usage. Although ILs are unlikely to contribute to air pollution, their potential effects on aquatic ecosystems are largely unknown. Furthermore, information is lacking on how ILs will interact with common features of aquatic environments, such as dissolved organic matter (DOM). We assessed the effect of five IL-forming chemicals on the growth of duckweed, Lemna minor, a common aquatic vascular plant. In general, 1-alkyl-3-methylimidazolium chemicals with longer alkyl chains were more toxic to L. minor than those with short alkyl chain lengths. The concentration that produced a 50% reduction (the EC50) in root growth was 8.56 ppm when a butyl chain was present but was 0.25 ppm (i.e., much more toxic) when an octyl chain was substituted. Butyl-substituted 3-methylpyridinium (root growth EC50 of 7.49 ppm) and 3-methylimidazolium cations had similar toxicity, whereas a tetrabutyl ammonium cation was considerably less toxic (root growth EC50 of 32.71 ppm). When we tested whether DOM reduced the toxicity of these cations, we saw no effect of a low-molecular-weight organic acid or commercial humic matter. In contrast, natural DOM reduced the toxicity of imidazolium, but only at low concentrations. Design and use of ILs and other new chemicals should incorporate not only standard toxicity tests but also information on how such chemicals will interact with other components of aquatic ecosystems.