Heavy metals (HMs) in aquatic environments are characterized by high toxicity, a propensity for bioaccumulation, and non-degradability, and pose significant risks to biological communities. Previous studies of HMs in lakes have shown that the physical and chemical characteristics of the lake water may control both the migration of HMs in the sediments and the concentration of heavy metals in the lake water. In fact, the change in aquatic environments changes the heavy metal fraction in the sediment, which controls the release of HMs. In this paper, we investigated the effects of the pH, temperature, and salinity levels of overlying water on the chemical fraction of Cu and Zn in Wuliangsuhai Lake surface sediments. The results show that lower water pH and higher water salinity and temperature could increase Cu and Zn release from the sediment. An increase in pH led to changes in the speciation of solid fractions of Zn, namely increases in the residual fraction and decreases in the organic matter and sulfide, whereas acid-extractable and Fe-Mn oxide fractions remained largely the same. Increases in temperature and salinity led to opposite changes in the speciation of solid fractions, namely decreases in the residual fraction and increases in the organic matter and sulfide and Fe-Mn oxide fractions, whereas acid-extractable fractions remained largely the same. The effect of pH, temperature, and salinity on Cu fractions in the solids was much smaller. According to the ratio of the secondary phase to the primary phase (RSP), acidic, high-temperature, and high-salt conditions increase the release risks of Zn. Changes in water temperature have the greatest influence on the risk of Zn and Cu release from sediments, followed by the influence of salinity changes.