Bioremediation of polluted aquaculture sediment by immobilized and free microorganisms (FR-M) was studied in pond enclosures by measuring multiple water qualities of overlying water, total organic carbon (TOC) of sediment, value of bioremediation of sediment (G-value), heterotrophic bacteria and antisulfuration bacteria. Immobilized microorganisms included microorganisms immobilized by fibrous net active carbon (FC-M), biological active carbon (BC-M), zeolite (ZE-M) or diatomite (DI-M). The results were as follows: immobilized microorganisms indirectly impacted water qualities of overlying water in experimental enclosures. Concentrations of nitrate of overlying water in ZE-M, DI-M and FC-M were significantly higher than those in control enclosures during final experimental period(P＜0.05). Chemical oxygen demands (COD) of overlying water in BC-M and ZE-M were significantly lower than those in FR-M and Control(P＜0.05), indicating that immobilized microorganisms effectively remediated polluted materials in bottom water in experimental enclosures; FC-M, DI-M and ZE-M degraded sediment organic material more effectively compared to FR-M and Control. Effects of immobilized microorganisms on bioremediation value of sediment (G-value) were apparent. G-values in BE-M, DI-M and ZE-M were significantly higher than those in FR-M and Control(P＜0.05), which suggested that immobilized microorganisms accelerated bioremediation of polluted sediment in experimental enclosures. Immobilized microorganisms did not significantly affect the amount of heterotrophic bacteria(P＞0.05), which probably could be explained by the reasons that many other factors influenced the community of microorganisms. Immobilized microorganisms changed the amount of antisulfuration bacteria significantly(P＜0.05). Immobilized microorganisms (in particular in ZE-M and BC-M) more effectively reduced the amount of anti-sulfuration bacteria compared to Control and FR-M. All these results obtained in the present study showed that immobilized microorganisms could improve bioremediation of polluted aquaculture sediment significantly with best results in ZE-M and BC-M.