 This study examined the effects of seasonality and nutrient levels on the macrophite community structure in three shallow lakes located in the Chinling Mountains Plateau. The results suggest that the macrophite communities in the three lakes are co-regulated by seasonal changes and nutrient levels. In particular, the Shihu Lake has reached mild eutrophication with a trophic level index, TLI, a value of 56.33, while the Seabee Lake and Haksahai Lake are mesotrophic with TLI values of 36.03 and 33.48, respectively. Additionally, the macrophite communities in the three lakes are more similar in summer and autumn, but show a wider gap in spring and winter. Furthermore, the redundancy analysis indicates that nitrogen, phosphorus, water transparency, and water temperature contribute to 44.8% of the total variation in macrophite communities' structure. This article was authored by Yuching Tian, Yuching Tian, Chacho LV, and others.