With the public's enhanced awareness of eco-safety, environmentally benign measures based on microorganisms and microbial aggregates have become more accepted as methods of removing pollutants from aquatic systems. In this review, the application of microorganisms and microbial aggregates for removing pollutants from aqueous solutions is introduced and described based on mechanisms such as assimilation, adsorption, and biodegradation. The advantages of and future studies regarding the use of microorganisms and microbial aggregates to remove pollutants are discussed. Due to the limitation of a single microorganism species in adapting to heterogeneous conditions, this review demonstrates that the application of microbial aggregates consisting of multiple photoautotrophic and heterotrophic microorganisms, is a promising method of removing multiple pollutants from complex wastewaters and warrants further research. (C) 2011 Elsevier Ltd. All rights reserved.