Hulun Lake and Taihu Lake are both large shallow lakes in China. In summer and winter of 2009, water, sediments and fish samples were collected from the two lakes and the concentrations of metal(loids) were analyzed. The results demonstrated that aqueous concentrations of arsenic (As), chromium (Cr), cadmium (Cd), nickel (Ni) and copper (Cu) in Hulun Lake were significantly higher than those in Taihu Lake. Especially, the As concentrations (about 130 μg/L) in Hulun Lake dramatically exceeded the permissible level of drinking water. Compared with Taihu Lake, metal(loid) concentrations in the sediments of Hulun Lake were significantly lower, which might have less impacts on the metal exchanges between water and sediments. In contrast, concentrations of the measured metal(loids) (including As) in fish from Hulun Lake and Taihu Lake were comparable, suggesting that the dramatic difference in aqueous and sediment metal(loid) concentrations had less influence on the metal(loid) bioavailability. The higher concentrations of dissolved organic carbon (DOC) and cations (e.g., Na+, K+ and Mg2+) in lake water might contribute to the reduced metal(loid) bioavailability to fish in Hulun Lake.