The impact of sulfate (SO42−) and chloride (Cl−) on phosphorus (P) release from sediment in the drinking water reservoir of Yangtze River Estuary was studied systematically. A significant correlation between sodium (Na+), Cl−, SO42− and total P was found, suggesting that P was directly or indirectly associated with these ions. SO42− and Cl− were important factors that had an impact on P release from the sediment. The results showed that both sulfate and chloride enhanced phosphorus release from sediment. In the sulfate treatment, the decrease of organic phosphorus (OP) suggested that the mineralization of OP enhanced P release from sediment. Phosphonate was the main factor affecting the P release under sulfate condition. In chloride treatment, the sediment composition of iron (Fe), aluminum (Al), calcium (Ca) and magnesium (Mg) increased. The P fractions of Fe/Al-P, Ca-P and OP in sediment also increased. However, the increase of P was unstable after chloride treatment and was easy to release under disturbance. In this study, it was observed that sulfate and chloride could increase the risk of eutrophication in the Yangtze River Estuary drinking water reservoir.