Data concerning the biodegradability and ecotoxicity of ionic liquids (ILs) obtained so far are insufficient in the context of IL removal from wastewater in activated sludge systems. Thus, in this work the selected imidazolium ionic liquids and two organic solvents (methanol and acetone) were tested with respect to their influence on activated sludge processes, particularly on the morphology of sludge flocs. The presence of ionic liquids with the chemical structure of 1-alkyl-3-methyl imidazolium bromide in wastewater did not deteriorate biological wastewater treatment processes if their concentration was not higher than 5 mg l−1. Regarding the structure of the ILs studied, the longer the alkyl substituent was, the stronger the effect on sludge flocs. The highest decrease in activated sludge floc area and biomass concentration was exerted by the ionic liquid with the longest alkyl chain, i.e. 1-decyl-3-methylimidazolium bromide. The action of both methanol and acetone on floc size, activated sludge concentration and efficiency of organic pollutants removal was weaker compared to all tested 1-alkyl-3-methyl imidazolium bromides.