Potamogeton crispus absorbs a large amount of nutrients from the water during its growing period thus can effectively inhibit water eutrophication. However, the decay of Potamogeton crispus when it is dead, its residues will release nutrients to the overlying water, causing instantaneous impact on the lake ecosystem. Through laboratory simulation, Potamogeton crispus was immersed in different concentrations of overlying water for natural decomposition, in order to study the change of overlying water quality during the decomposition of Potamogeton crispus residues and the driving effects of environmental factors on bacterioplankton. Results showed that: (1) In the diluted groups (group B and C), there was a short-term shock (1st day) of nitrogen in the decomposition of Potamogeton crispus and the degree of shock was positively correlated with the dilution ratio. (2) The better quality of the overlying water, the higher the percentage of the common OTUs (operational taxonomic units) of bacterioplankton, and the more drastic change of the structure of the bacterioplankton population by the nitrogen shock. On the 30th day of the experiment, the proportion of mutual OTUs in the 4-fold diluted group (group C) was 61%, which was higher than that in the raw water group (group A, OTUs accounted for 40%) and the 2-fold diluted lake water group (group B, OTUs accounted for 45%). The dramatic changes in community structure were mainly achieved by affecting the relative abundance size of Firmicutes, Verrucomicrobiota, Actinobacteriota and Cyanobacteria. (3) Proteobacteria was the first dominant group in the whole decomposition process and in all three groups. Water quality enhancement helped the growth and reproduction of Firmicutes. The second dominant group in groups B and C was Firmicutes, the higher the dilution ratio, the greater the total relative abundance of the two phylums of bacteria. (4) Total suspended solids, oxidation-reduction potential, turbidity and total nitrogen had major effects on the structure of bacterium communities. The decomposition process could be divided into 2 stages, and the changes of environmental factors on bacterial community structure were related to the decomposition process. Hence, by strategically harvesting the residues of submerged plants and adjusting the overlying water's physicochemical parameters such as nitrogen and turbidity, relevant authorities can mitigate the negative repercussions caused by seasonal aquatic plant decomposition, thereby accomplishing the ultimate objective of scientifically managing submerged plants.