Lake sediments play a crucial role in the elemental cycling of water bodies and represent one of the current challenges in managing eutrophication. To uncover the pollution characteristics and sources of total nitrogen (TN), total phosphorus (TP), and organic matter (OM) in the sediments of urban lakes and provide a new traceability perspective for assessing the environmental effects of comprehensive water environment management, this study collected and measured TN, TP, and OM contents in sediment points from 25 sites in Lake Yiai, Huanggang City. Water quality at nine lake sampling sites and at CSO (combined sewer overflow) outlet was monitored. Analyze the spatial distribution characteristics of TN, TP, and OM in lake water and sediment. The comprehensive pollution index method was employed to quantitatively assess the pollution risks of TN, TP, and OM in the sediments. Cluster analysis combined with stoichiometric characteristics was used to qualitatively identify and quantitatively analyze the sources of N, P, and OM in lake sediments. The results indicate that: There were spatial differences in the distribution of TN, TP and OM in sediments. The horizontal distribution of TN, TP and OM contents ranged from 940-3677 mg/kg, 323-1667 mg/kg and 1.03%-7.44%, the high-concentration sites of TN, TP, and OM were concentrated along the lake shores and near the discharge outlets. Vertically, the overall trend showed that the surface layer had higher concentrations than the middle and bottom layers. Specifically, the content ranges of TN, TP, and OM in the surface sediments were 920-4450 mg/kg, 208-1970 mg/kg and 2.05%-7.48%, respectively. The TP content of surface sediments was higher than the average value of shallow lakes in eastern China, and was similar to the level of lakes with serious sediment pollution in China. The comprehensive pollution index method revealed severe TP pollution in the surface sediments, with 76% of the lake area experiencing moderate to severe TP pollution, while TN pollution and overall pollution levels were relatively low. Cluster analysis combined with stoichiometric characteristics showed that the C/N ratio in sediments at locations with CSO pollution was 11, and the C/N ratio in the surface sediments of Lake Yiai was 10.67, with C/P values ranging from 20.16 to 190.97. Approximately 44% of OM originated from the decomposition of dead algae, while 20% was influenced by overflow discharges and 36% by diffuse pollution. TP primarily came from diffuse pollution, followed by overflow sewage, while the sources of TN were similar to those of OM.