Exploring the distribution and their historical changes of taxonomic and functional diversity in urban lakes improved our understanding on the effects of human disturbances on ecosystems. The Lake Donghu is a medium-sized shallow lake in the middle reaches of the Yangtze River, located in the eastern part of Wuchang District, Wuhan City. It was a river-connected lake formed by natural siltation of the Yangtze River on the basis of the tectonic movement. To understand the historical changes of its zoobenthic taxonomic and functional diversity, this study conducted three seasonal surveys of zoobenthos in Lakes Guozheng, Tangling, Hou, Tuan, Lingjiao, Yujia and Miao during 2020-2021, and collected historical data from previous literatures and books during 1970-2020. We compared the distribution and historical changes of taxonomic, functional and phylogenetic diversity. By obtaining the proportions of different land use types in 1 km buffer zone in 2000, 2010 and 2020, we analyzed the correlations between zoobenthic diversity and environmental factors. The results showed that 97 taxa of zoobenthos were identified with the highest number of taxa in Lake Tuan. The functional diversity of zoobenthos was the highest in Lake Hou, and the functional evenness was the highest and the lowest in Lake Miao and Lake Lingjiao, respectively. For phylogenetic diversity, the taxonomic diversity index was the highest in Lake Tuan, and the taxonomic distinctness index was the highest in Lake Miao. The total number of taxa was negatively correlated with total nitrogen and total phosphorus. The number of pollution-tolerant species was negatively correlated with total phosphorus. The functional evenness was positively correlated with the proportion of cultivated land. The functional richness was negatively correlated with total nitrogen and total phosphorus. The taxonomic diversity index was negatively correlated with total nitrogen and total phosphorus. Combined with historical data from 1970s to 2020s, aquatic insects showed a trend of decreasing first and then increasing. The groups of zoobenthos showed a trend of individual miniaturization in the 2010s, and then recovered.