Removal of organic compounds and inorganic nutrients from aquaculture wastewaters prior to discharge can not only minimize deterioration of receiving water quality, but it could also be further reused to culture prawn, fish and shellfish. Chitosan can be used as a coagulant, adsorbent, or bactericide; therefore it has been used to improve aquaculture wastewater quality as it could remove suspended solids (SS), organic compounds, NH3, PO43-, and pathogens. The best performance of chitosan in removing turbidity, SS, chemical oxygen demand (COD), NH3, and PO43- was 90%, 61%, 69.7%, 89.2%, and 95.6%, respectively. In addition, the chitosan could selectively remove the pathogen Edwardsiella ictaluri while leaving beneficial nitrifying bacteria in the aquaculture wastewater unaffected. The treatment efficiency of chitosan was highly dependent on its deacetylation degree and the pH of the wastewater. A high deacetylation degree and low pH value improved the performance of chitosan. In summary, the multi-functional chitosan deserves a wider role in treating aquaculture wastewater.