Rotifers are closely related to the process of lake eutrophication and can rapidly respond to changes of water environment. In this study, we selected five small shallow lakes with different nutrient levels in Hanyang water network to explore the spatiotemporal changes of rotifer community structure and species diversity and its driving factors, in order to provide scientific basis for lake ecological restoration and biodiversity protection. Twenty-six sites were investigated in June (summer), September (autumn), December (winter) of 2021, and March (spring) of 2022, respectively. Most of the environmental and biological factors in the water network had significant spatiotemporal difference. In total, 51 species of rotifers were collected and dominated by Anuraeopsis fissa, Filinia longiseta, Keratella cochlearis, Polyarthra trigla and Trichcoerca similis. The average annual density of the five lakes ranged from 109.65 to 995.92 ind./L, and the average annual Shannon-Wiener index and Margalef index ranged from 0.86 to 1.68 and 0.65 to 1.44, respectively. Non-metric multi-dimensional scale analysis revealed significant seasonal difference in rotifer community structures, with relatively small spatial difference except for Lake Houguan. Multiple stepwise regression analysis showed that rotifer species number and Margalef index were mainly affected by protozoa density; rotifer density was mainly affected by phytoplankton density; Shannon-Wiener index was mainly affected by water temperature. Canonical correspondence analysis (CCA) showed that the spatiotemporal changes of rotifer community structure were related to water temperature, ammonia nitrogen (NH₃-N), transparency (SD), total nitrogen (TN), phytoplankton density and cladocera density. Within a specific region, the segmented linear regression model demonstrated a positive correlation between the complete nutrient status index (TLI(Σ)) and the species, density, and diversity index of rotifers. When the TLI(Σ) reached about 70, the species, density, and diversity index of rotifers showed a downward trend.