Abstract: To understand the effects of macrophyte growth on water environment and rotifer community structure, monthly survey lasted for one year from October 2015 to September 2016 was conducted in Lake Minghu and Lake Nanhu at Jinan University in Guangzhou. There was no macrophyte cultivation in Lake Minghu. A kind of macrophyte Hydrilla verticillata grows from March-October in Lake Nanhu and grows vigorously in June-September. In this study, 50 species belonging to 23 gene-ra of rotifer, were recorded in the two lakes. 32 species were found in Lake Minghu and 39 species in Lake Nanhu, respectively. The dominant species in Lake Minghu were Polyarthra vulgaris, Trichocerca pusilla and Liliferotrocha subtilis. The dominant species in Lake Nanhu were Keratella cochlearis, Colurella adriatica and Lecane (Monostyla) bulla. The highest abundance of rotifers in Lake Minghu was at 3790 ind·L^-1 in October 2015, and the lowest at 854 ind·L^-1 in March 2016. The highest abundance of rotifers in Lake Nanhu was at 3555 ind·L^-1 in November 2015, and the lowest at 977 ind·L^-1 in January 2016. Results from the ANOSIM (one-way) test revealed that the community structure of rotifers was significantly different between Lake Minghu and Lake Nanhu. The largest contribution rate of the difference between the two lakes was made by Keratella cochlearis and Polyarthra vulgaris. RDA analysis showed that total phosphorus, chlorophyll a, and water temperature had significant impacts on the community structure of rotifer in Lake Minghu. During the period with luxuriant macrophyte in Lake Nanhu, the rotifer community structure was most influenced by total phosphorus, water temperature, chlorophyll a and water depth, dominated by benthic species Squatinella mutica, Colurella adriatica and Lecane bulla. During the period with sparse macrophyte, the community was mainly influenced by total nitrogen and transparency, dominanted by planktonic species Polyarthra vulgaris and Trichocerca similis. During the period with no macrophyte, communities were mainly influenced by pH and dissolved oxygen, and also dominated by planktonic ones Polyarthra vulgaris and Anuraeopsis fissa. Macrophyte could effectively absorb nutrients in water, inhibit growth of phytoplankton, improve water quality, increase spatial heterogeneity, support more species of rotifer, and maintain a stable aquatic ecosystem.