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Abstract Background Intensive and large-scale aquaculture has a high biological density, and a large amount of artificial feed must be provided. As a result, residual feed would be discharged into natural water bodies with water exchange. Due to heavy metal pollution in surface water, residual feed may adsorb heavy metals in the water, affecting the subsequent microbial degradation of feed and the restoration of the water environment. The combined ecological impacts of these two types of pollution urgently need to be explored. Results This study explored the adsorption effect of residual feed on heavy metals and its impact on microbial degradation of residual feed. The results showed that both the insoluble component (mainly fiber, ash, and ether extract, abbreviated as FAE) and soluble component (soluble protein and starch) of the feed had adsorption effects on heavy metals. As the salinity increased, the adsorption capacity of Cu2+ and Cd2+ decreased, while the adsorption effect on Pb2+ was not changed significantly. The adsorption of heavy metals by residual feed could affect the biological degradation of residual feed. The residual feed could adsorb heavy metals and bacterial cells simultaneously, forming FAE-B(bacteria)-S(starch)-Pr(protein)-metal adsorption complex. This adsorption effect could reduce the negative impact of heavy metals on microbial degradation of residual feed. The simulated degradation experiments in actual water bodies also confirmed this. However, the accumulation of heavy metals in residual feed may bring negative effects, such as being consumed by aquatic organisms and entering the food chain. Conclusions The results of this study provide a basis for the collection and centralized treatment of residual feed in aquaculture, as well as the control and remediation of residual feed pollution in natural water bodies. Graphical Abstract