Increased urbanization and industrialization globally have led to the widespread pollution of water bodies (e.g., lakes) by heavy metals (HMs) and nutrients. These pollutants accumulate in water and surface sediments, posing risks to both aquatic organisms and human health. In November 2022, surface sediment samples from three lakes—Lianhua Lake, Mati Lake, and North Lake—were collected to assess nutrient (nitrogen and phosphorous) and HM content. Total N (TN), total P (TP), and HM concentrations were analyzed. The pollution status was evaluated using comprehensive pollution index (FF) methods and the potential ecological risk index (RI) (Eri). The results were as follows: (1) Variations in nutrient and HM contents were observed among the three lakes. Lianhua Lake exhibited the highest average TN content (1600 mg/kg), while North Lake had the highest average TP content (2230 mg/kg). The average concentrations of Cd, Hg, and As in the surface sediment surpassed the soil background values of Hubei Province, reaching 1.41, 2.74, and 1.76 times the background values, respectively. Notably, Hg exceeded the standard in Lianhua Lake by 3.39 times, followed by North Lake (2.52 times) and Mati Lake (2.24 times). (2) The FF and potential Eri revealed that the average RI values for Mati Lake, North Lake, and Lianhua Lake were 106.88, 126.63, and 162.18, respectively. These indices categorized the ecological risk levels as moderate, while nutrient salts in the surface water reached a severe pollution level. (3) Correlation and PCA indicated that Cu, Pb, Cd, and Ni were linked to mineral smelting, aquaculture feed, and agricultural fertilizers. Hg and nutrient salts originated from atmospheric deposition of surrounding domestic waste water and traffic exhaust gases. Agricultural activities seemed to contribute to As concentration in the lakes, while Cr has its main origin in the weathering of the rock matrix.