To study the effects of ecological floating beds on the quality of aquatic products, three species of fish (Sparu latus, Oreochromis niloticus and Mugil cephalus) and two species of mollusk (Crassostrea rivularis and Tegillarca granosa) were collected from the polyculture pond with floating bed and traditional monoculture ponds. Concentrations of heavy metals including Ni, Cu, Zn, Cd and Pb were measured in muscles, gills and viscera of fish and in the edible part of mollusk for health risk assessment. Nutritional quality of S. latus and O. niloticus was analyzed in terms of their muscle nutrition, amino acids and fatty acids composition. The results showed that the concentrations of five heavy metals of all products from the experimental pond conformed to the criteria values for aquatic food in China. However, the concentrations of Cu (57.113 mg/kg wet wt) and Cd (1.163 mg/kg wet wt) in C. rivularis and the concentration of Cd in T. granosa from the control ponds were all beyond the criteria values. According to the Hazard Quotient, there will be no potential risks resulting from ingestion of fish from two kinds of ponds. Content of umami amino acid of S. latus from the experimental pond was significantly higher than that of the control pond. O. niloticus from the experimental pond had notably higher contents of TAA, EAA and DAA than those from control pond. Contents of polyunsaturated fatty acids of S. latus and O. niloticus from the testing pond were all higher than those in the control ponds, while opposite results were observed for the contents of saturated fatty acids. Generally, polyculture mode with in-situ ecological floating beds system demonstrated superiorities to the traditional monoculture mode according to the health risk assessment and nutritional quality of aquatic products.