Aquaculture is one of the most important agriculture practices worldwide; however it can generate environmental impacts by introducing nutrients, which possibly are diverse and complex based on different farming practices. In this study, an in situ filed experiment was conducted to investigate effects of two representative fish dominated by grass carp (GC, Ctenopharyngodon idella) and Chinese mitten crab (CMC, Eriocheir sinensis) farming practices on sediment nutrient storage, microbial community and enzyme activities in the ponds at four farm sites around Hong Lake, middle Yangtze River, China. The results showed that sediment TOC, TN and TP were significantly lower in GC ponds than CMC ponds, and where the same trends for sediment pH and moisture content. Moreover, the bacterial communities among the pond sediments were closely defined by sediment TOC, pH, and TN. Significant different sediment bacterial communities were observed between GC and CMC ponds, with higher bacterial richness and diversity in GC ponds. In addition, we found lower activities of β‑1,4‑glucosidase, leucine-aminopeptidase, and alkaline phosphatase in the sediments of GC ponds compared to CMC ponds, and positive correlations between the three enzyme activities and sediment nutrients and parameters; whereas the higher lipase activities in the sediments of GC ponds than CMC ponds, and the lack of correlation with sediment properties among the ponds. Our results here indicates that fish and crab farming practices diversely affect nutrient storage, bacterial assemblies and enzyme activities in the sediments, suggesting different nutrients-driven sediment biological processes by farming practices in aquaculture.