Although ionic liquids (ILs) hold salient features and considered as a replacement of conventional organic solvents, but their possible toxicological and ecotoxicological impacts must be considered equally in the design and development stage. Predicted no-effect concentration (PNEC) plays a vital role in assessing the ecotoxicological hazards in the ILs. A systematic methodological framework is presented for assessing the predicted environmental concentration (PEC) of ionic liquids. Initially, an effect level is predicted with a general quantitative structure-activity relationship (QSAR). Secondly, predicted no-effect concentration (PNEC) is calculated by using assessment factor (AF). The PEC is compared to the PNEC to characterize the risk for the freshwater aquatic organisms. If the ratio continued to exceed one, ionic liquids under investigation will need further aquatic risk assessment procedures, which involve iterative steps to refine the PEC and PNEC. © 2016 The Authors.