Abstract: The water environment is critical to ecosystem health and the sustainable development of human society. Water environment governance in the lower reaches of the Yangtze River is characterized by long-term complexity. Therefore, promoting the construction of a modern water environment governance system and improving governance efficiency are key to realizing high-quality development of the water environment in the lower reaches of the Yangtze River. In this paper, the Super-SBM model, based on non-expected output, was used to measure the spatio-temporal differences and the dynamic evolution characteristics of water environment governance efficiency in the lower reaches of the Yangtze River from 2013 to 2022. The influencing factors of water environment governance efficiency was explored using the Tobit model. The results showed that: 1) The average value of the comprehensive efficiency of water environment governance in the study area was 0.7931. The overall efficiency was at a medium-high level, but there existed significant regional differences. Pure technical efficiency and comprehensive efficiency changed in a coordinated manner. The changes in pure technical efficiency was the main cause of the fluctuations in overall efficiency. 2) The overall development trend of the comprehensive efficiency of water environment governance remained positive. Technical efficiency, pure technical efficiency, and scale efficiency all showed a steady upward trend. However, changes in the level of technology were the main reason for changes in the ML index of water environment governance efficiency, which were the key factor restricting the lower total factor productivity growth rate of environmental governance in the region and its internal areas. 3) The spatial differences in water environment governance efficiency were substantial, with inter-group differences being the main source of overall differences. In comparison, the efficiency of water environment governance exhibited a contraction trend in the “northeast to southwest”direction, indicating an enhanced stability and a correlation, with the center of gravity always concentrated around Nanjing, Zhenjiang, and Changzhou. 4) The level of technological innovation and economic development had a positive impact on environmental governance efficiency. In contrast, the increase in the level of industrialization, the development of industrial structure, and the advancement of urbanization all had an inhibitory effect on the environmental governance efficiency. Meanwhile, foreign direct investment and the degree of opening up also played a positive role in the environmental governance efficiency of the region.