In this work, sediments were treated with calcium nitrate, aluminum sulfate, ferric sulfate, and Phoslock (R), respectively. The impact of treatments on internal phosphorus release, the abundance of nitrogen cycle-related functional genes, and the growth of submerged macrophytes were investigated. All treatments reduced total phosphorus (TP) and soluble reactive phosphorus (SRP) in interstitial water, and aluminum sulfate was most efficient. Aluminum sulfate also decreased TP and SRP in overlying water. Treatments significantly changed P speciations in the sediment. Phoslock (R) transformed other P species into calcium-bound P. Calcium nitrate, ferric sulfate, and Phoslock (R) had negative influence on ammonia oxidizers, while four chemicals had positive influence on denitrifies, indicating that chemical treatment could inhibit nitrification but enhance denitrification. Aluminum sulfate had decreased chlorophyll content of the leaves of submerged macrophytes, while ferric sulfate and Phoslock (R) treatment would inhibit the growth of the root. Based on the results that we obtained, we emphasized that before application of chemical treatment, the effects on submerged macrophyte revegetation should be taken into consideration.