Nine metals, Cd, Cu, Ni, Pb, As, Cr, Zn, Fe, and Mn in sediment and pore water from 57 sampling sites in Chaohu Lake (Anhui Province, China) were analyzed for spatial distribution, temporal trends and diffuse flux in 2010. Metals in the surface sediment were generally the highest in the western lake center and Nanfei-Dianbu River estuary, with another higher area of As, Fe, and Mn occurring in the Qiyang River estuary. Metal contamination assessment using the New York sediment screening criteria showed that the sediment was severely contaminated in 44% of the area with Mn, 20% with Zn, 16% with Fe, 14% with As, and 6% with Cr and Ni. An increasing trend of toxic metals (Cd, Cu, Ni, Pb, As, Cr, Zn) and Mn with depth was shown in the western lake. Compared with metal content data from the sediment survey conducted in 1980s, the metal content of surface sediment in 2010 was 2.0 times that in the 1980s for Cr, Cu, Zn, and As in the western lake, and less than 1.5 times higher for most of the metals in the eastern lake. Among the metals, only Mn and As had a widespread positive diffuse flux from the pore water to overlying water across the whole lake. The estimated flux in the whole lake was on average 3.36 mg/(m2. day) for Mn and 0.08 mg/(m2. day) for As, which indicated a daily increase of 0.93 μg/L for Mn and 0.02 μg/L for As in surface water. The increasing concentration of metals in the sediment and the flux of metals from pore water to overlying water by diffusion and other physical processes should not be ignored for drinking-water sources.