To assess the sediment environmental quality synthetically from Shanghai aquaculture ponds, 360 sediment samples collected from 36 farms from 2016 to 2019 were investigated and the distribution characteristics of total nitrogen (TN), total phosphorus (TP), total organic carbon (TOC), and heavy metals (Cu, Zn, Pb, Cd, Cr, Hg, As) were analyzed. The results showed there was no significant difference between the average concentrations of TN, TP, TOC, and those heavy metals in the 0-10 cm and 10-20 cm layers. The mean values of TN, TP, and TOC (dry weight) in the surface 20 cm pond sediment were (873.37±352.45) mg/kg, (685.66±199.66) mg/kg, and (6.62±3.05) mg/g respectively, and in pond sediments there was a significant positive correlation among them. Methods of comprehensive index and the organic index were used to evaluate the accumulation of nitrogen, phosphorus and organic matter, and the results indicated that the nitrogen and organic matter accumulation in pond sediments was relatively low and phosphorus accumulation was high, but was still lower than the high-yielding ponds in other areas. The over-limit ratio of Cr, Cd, Cu, and Hg was 6.42%, 3.21%, 4.13%, and 1.38%, respectively and concentrations of Zn, Pb, and As in all samples met the certain criteria. The sediment assessment was conducted using a geo-accumulation index (I_geo), potential ecological risk index (RI), and consensus-based sediment quality guidelines (CBSQGs). Results of the risk assessment indicated that, generally, Shanghai pond sediments were unpolluted, had a low ecological risk, and were nontoxic.