Filter-feeding shellfish are common benthos and significantly affect the biogeochemical cycle in the shallow coastal ecosystems. Ark clam Scapharca subcrenata is one of the widely cultured bivalve species in many coastal areas owing to its tremendous economic value. However, there is little information regarding the effects of the bioturbation of S. subcrenata on the fluxes of nutrient exchange in the sediment-water interface (SWI). In this regard, S. subcrenata was sampled during October 2016 to determine the effects of its bioturbation activity on the nutrient exchange flux of the SWI. The results showed that the biological activity of S. subcrenata could increase the diffusion depth and the rate of the nutrients exchange in the sediments. The bioturbation of S. subcrenata could allow the nutrients to permeate into the surface sediments at 6–10 cm and increase the release rate of nutrients at the SWI. The releasing fluxes of DIN and PO 4 3−-P in the culture area were found to be around three times higher than that in the non-cultured region. The culture of S. subcrenata has been proved to be an important contributor to nutrient exchange across the SWI in the farming area of Haizhou Bay. Nutrients exchange in the SWI contributes a part of 86% DIN, 71% PO 4 3−-P and 18% SiO 3 2−-Si for the aquaculture farm.