Benthic fluxes of carbon dioxide (CO 2 ) and methane (CH 4 ) were evaluated in grass carp Ctenopharyngodon idella (G), silver carp Hypophthalmichthys molitrix (S), and bighead carp Aristichthys nobilis (B) polyculture systems, to which topmouth culter Erythroculter ilishaeformis (T), Pacific white shrimp Litopenaeus vannamei (P), or common carp Cyprinus carpio (C) were added. These systems, GSBT, GSBP, and GSBC, respectively, were monitored over 5 mo (May to September 2014). The presence of L. vannamei and C. carpio increased CO 2 and CH 4 emissions in GSBP and GSBC, respectively. From June to August, CO 2 and CH 4 fluxes increased in the 3 systems, and in July and August these fluxes were significantly higher in GSBC than in GSBP and GSBT, and significantly higher in GSBP than in GSBT. The metabolisms of L. vannamei and C. carpio contributed to decrease dissolved oxygen, pH, and oxidation−reduction levels, and the bioturbation of the upper sediment layers caused by these species increased organic matter degradation rate, resulting in a significant increase in particulate and dissolved organic carbon in the overlying water. Our results indicate that improving feeding efficiency and reducing organic carbon accumulation on the bottom of aquaculture ponds, as well as increasing dissolved oxygen and decreasing bioturbation across the sediment−water interface during farming seasons, is likely to reduce CO 2 and CH 4 release from aquaculture pond sediment, especially in July and August.