Monoculture of sea cucumber(pond S) and polyculture of shrimp with sea cucumber(pond SS) were established to evaluate the effect of shrimp on the environmental conditions of sea cucumber farming pond. Contributions of sediment organic matter(SOM2) resuspended from benthic sediment and the suspended particulate organic matter(SPOM) deposited from the water column to the precipitated organic matter(SOM1) collected with sediment traps were estimated with carbon stable isotope analysis. The results showed that the levels of SPOM and SOM2 in pond SS significantly decreased in comparison with those in pond S at the end of experiment(P < 0.05), indicating that co-culturing shrimp in sea cucumber farming pond could purify the farming water. Carbon stable isotope analysis showed that the proportion of SOM2 in SOM1 in pond SS(84.97% ± 0.38%) was significantly lower than that in pond S(95.20% ± 0.30%)(P < 0.05), suggesting that the resuspension of organic matter from benthic sediment into overlying water was reduced in polyculture pond. In contrast, the proportion of SPOM in SOM1 in pond SS(15.03% ± 0.38%) was significantly higher than that in pond S(4.80% ± 0.30%)(P < 0.05), indicating that the sedimentation of SPOM from water column was enhanced in pond SS owing to the biodeposition effect of shrimp. Monoculture of sea cucumber (pond S) and polyculture of shrimp with sea cucumber (pond SS) were established to evaluate the effect of shrimp on the environmental conditions of sea cucumber farming pond. Contributions of sediment organic matter (SOM2) resuspended from benthic sediment and the suspended particulate organic matter (SPOM) deposited from the water column to the precipitated organic matter (SOM1) collected with sediment traps were estimated with carbon stable isotope analysis. The results showed that the levels of SPOM and SOM2 in pond SS significantly decreased in comparison with those in pond S at the end of experiment (P <0.05), indicating that co-culturing shrimp in sea cucumber farming pond could purify the farming water. Carbon stable isotope analysis showed that the proportion of SOM2 in SOM1 in pond SS (84.97 % ± 0.38%) was significantly lower than that in pond S (95.20% ± 0.30%) (P <0.05), suggesting that the resuspension of organic matter from benthic sediment into overl The contrast of the proportion of SPOM in SOM1 in pond SS (15.03% ± 0.38%) was significantly higher than that in pond S (4.80% ± 0.30%) (P <0.05), indicating that the sedimentation of SPOM from water column was enhanced in pond SS due to the biodeposition effect of shrimp.