The ecological environment of urban lakes affected by human activities is deteriorating rapidly. As a source and sink of pollutants in the lake environment, sediments have become the focus of environmental assessments. At present, most of the studies only conduct pollution assessments on surface sediments. In this study, taking the typical urban lakes GanTang Lake and NanMen Lake (G&N Lake) as the background, not only is the planar spatial distribution of their nutrient elements, seven kinds of heavy metals, and As analyzed in detail, but risk assessments are also carried out on the pollution conditions at different depths. The causes of pollution at different depths are analyzed. It is found that in this lake, with the increase in depth, the pollution situation decreases slightly, but the pollution of nutrient elements is severe. There is severe pollution of nutrient elements at a depth of up to 1 m in the whole lake sediment. In the sediments with a depth of up to 1 m, more than 90% of the areas in the whole lake are at or above the moderate pollution level of Hg, and more than 70% of the areas are under slight pollution of Cd, resulting in the ecological risk level of the whole lake being at or above the high-risk level. Urban lake sediment management is inherently complex, driven by multifaceted factors where intensive anthropogenic activities constitute the primary pollution source. This research provides insights to guide restoration strategies and sustainable development policies for lacustrine ecosystems.