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Fish and shellfish aquaculture industries in Dapeng Cove, South China, have profound impacts on the coastal marine ecosystem in recent years. In this study, the local seaweed Sargassum hemiphyllum was introduced into oyster and fish farms as a biofilter during winter and early spring of 2013. Results showed that S. hemiphyllum grown in the fish farm suffered greater fouling and herbivory than these in the oyster farm. Thalli grown in both sites could achieve high growth rates during January and February; meanwhile, the specific growth rates for wet weight (SGR W ) of seaweeds in the oysters farm at January, February and April samplings (7.16, 6.16 and 2.25% d − 1 , respectively) were all higher than those in the fish farm at the same sampling period (2.89, 3.19 and 0.90% d − 1 , respectively). The mean fresh-weight biomass increments for thalli grown in the oyster and fish farms were ~ 40 and 7 times, respectively, during the 4-month culture period. The N and P contents of S. hemiphyllum grown in both sites all varied significantly over time, and P contents of thalli in the oyster farm always higher than those of the fish farm at the same sampling period. The C, N and P bioaccumulation capacities of S. hemiphyllum cultured in the oyster farm were 15016.90 ± 6241.78, 1112.45 ± 459.81 and 134.69 ± 55.46 mg thallus − 1 , respectively, over the study period, which were all significantly higher than those in the fish farm (2457.46 ± 1073.78, 180.27 ± 75.23 and 13.69 ± 5.88 mg thallus − 1 , respectively). The nutritional composition of S. hemiphyllum in both sites were always comparable or higher than those of the seaweeds used as holothurian feed, and the heavy metal contents (Pb, Cd and Cr) were all well below the maximum allowable concentration for aquatic feed; thalli grown in the oyster farm were always with higher crude protein and fat contents, but lower heavy metal levels than those in the fish farm. We consider large-scale cultivation of S. hemiphyllum in Dapeng Cove can efficiently relieve the total environmental impact of aquaculture on the ecosystem of the whole bay, while give high yield of seaweed product with better quality. Statement of relevance This article provides useful information on the seaweed-based integrated multi-trophic aquaculture in fish and shellfish farms, and it can also give suggestion for the practice of large-scale cultivation of Sargassum and sustainable aquaculture in coastal area. [ABSTRACT FROM AUTHOR]