As the second largest freshwater lake in China, Taihu Lake provides water supply to approximately 32 million inhabitants around the lake. However, dramatically increased pollution has threatened the safety of drinking water supply in recent years. In the present study, we investigated the contaminations of nutrients and heavy metals in the sediments of an intake and inflow canals in Gonghu Bay, Taihu Lake. Moreover, we also examined the impact of human activities on spatial distribution characteristics of contaminations. Our results showed that the intake presented relatively lower concentrations of phosphorus and nitrogen compared with inflow canals. However, the concentrations of Cr, Ni, Cu, Zn and Pb in the sediments of the intake exceeded the lowest effect level (LEL) values, indicating a potential risk to drinking water resource. In addition, the concentrations of Ni in the sediments of Tianji Canal and Jinshu Canal exceeded the severe effect level (SEL) value. More importantly, the concentrations of Cu in the sediments of Tianji Canal exceeded three times of the SEL value. Multivariate statistical analysis confirmed that the domestic sewage primarily contributed to the nutrient accumulation, and the leakage of electronic trash dominated the enrichment of metals in the sediments. Taken together, more effort should be made to ensure the security of water resources in Taihu Lake, especially for the treatment of domestic sewage and industrial wastewater.