Sediment and overlying water samples were collected seasonally from five different geomorphic structures (i.e., pools, riffles, gravel bars, point bars, and runs) from two urban reaches of the Shiwulihe River in the Chaohu Lake Basin dominated by high ammonia concentration between July 2017 and March 2018. Both the sediment potential and areal nitrification rates were measured and their seasonal and geomorphological variability were evaluated. The specific differences between every two geomorphic structures were determined using the Mann-Whitney test and the relationship between the overlying water environment or benthic sediments and sediment nitrification was explored based on regression analysis. The results show that:① The studied reaches are seriously polluted by nitrogen and phosphorus and most of the oxidation-reduction potential (ORP) values in the overlying water were are below 0 mV, suggesting strong reducing conditions of the water column. ② The potential nitrification rates (PNRs) across the five geomorphic structures range from 0.002 to 0.079 μmol·(g·h), with a mean value of 0.023 μmol·(g·h). The ranking order of PNRs is pools > point bars > riffles > gravel bars > runs, with a seasonal change pattern of summer > spring > autumn > winter. ③ The areal nitrification rates (ANRs) across the five geomorphic structures range between 0.140 and 13.543 μmol·(m·h), with an average of 3.658 μmol·(m·h). In general, the highest mean value was observed in riffles, followed by runs, and gravel bars and point bars; the smallest value was observed in pools. In addition, ANRs appear to have seasonal change patterns similar to that of the PNRs. ④ According to the difference analysis, there are significant differences between pools or riffles and other features of the PNRs. Extremely significant ANR differences were observed between more than half of the geomorphic structures. ⑤ Regression analysis shows a stronger correlation between sediment nitrification and the overlying water environment, compared with the surface sediment properties.

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