Ionic liquids (ILs) are low-melting organic salts that are being researched intensively as possible environmentally friendly replacements for volatile organic solvents. Despite their nonmeasurable vapor pressure, some quantities of ILs soon will be present in effluent discharges because solubility of ILs in water is small, but far from negligible. Therefore, it is important to understand how ILs will influence aquatic ecosystems. In the present study, the toxic effects of imidazolium-based ILs (1-butyl-3-methylimidazolium cation associated with bromide [BMIM] [Br] and tetrafluoroborate [BMIM] [BF4]) to the freshwater green alga Selenastrum capricornutum were investigated. Two approaches were followed to quantify toxicity of these compounds: Analyses of photosynthetic activity and cell proliferation. The obtained data showed that the relative declines of growth rates generally were more pronounced than those of photosynthetic activity. The ecotoxicity of a range of common organic solvents also was examined. It was revealed that both imidazolium-based ILs studied were some orders of magnitude more toxic than methanol, isopropanol, and dimethylformamide. In addition, with respect to IL incorporating perfluorinated anion, EC50 values (concentrations which lead to a 50% reduction of the exposed organisms relative to control) of the previously prepared stock solution were significantly lower compared to those of the freshly made one. This might be due to hydrolytic effects of [BMIM][BF4] leading to fluoride formation, which was confirmed by ion chromatography analysis. This indicates that, after ILs are discharged into the aqueous system, they can become more toxic than expected by laboratory data with fresh ILs.