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Phytoplankton in shallow urban lakes are influenced by various environmental factors. However, the long-term coupling effects and impact pathways of these environmental variables on phytoplankton remain unclear. This is an emerging issue due to high urbanization and the resultant complex climate, lake hydrology and morphology, human interference, and water quality parameter changes. This study used Tangxun Lake, the largest urban lake in the Yangtze River Economic Belt, as an example to assess for the first time the individual contributions and coupled effects of four environmental variables and fourteen indicators on chlorophyll-a (Chla) concentrations under two scenarios from 2000 to 2019. Additionally, the influence pathways between the environmental variables and Chla concentration were quantified. The results indicated that the Chla concentration was most affected by lake hydrology and morphology, as were the total nitrogen, total phosphorus, and transparency. Especially after urbanization (2015–2019), the coupling effect of human interference, lake hydrology and morphology, and water quality parameters was strongest (18%). This is mainly due to fluctuations in the lake water level and an increase in the shape index of lake morphology, large amounts of nutrients were input, which reduced lake transparency and indirectly changed the Chla content. In addition, due to the rapid development of Wuhan city, the expansion of construction land has led to an increase in impervious surface area and a decrease in lake area. During periods of intense summer rainfall, a substantial amount of pollutants entered the lakes through surface runoff, resulting in decreased lake transparency, and elevated concentrations of nitrogen and phosphorus, indirectly increasing the Chla content. This study provides a scientific basis for aquatic ecological assessment and pollution control in urban shallow lakes. • Environmental influence of 14 environmental variables on the lake trophic state is revealed. • A new phytoplankton assessment framework is designed for urban lakes. • The most influential variables are related to high urbanization. • Lake inundation area and water level changes affected phytoplankton biomass. [ABSTRACT FROM AUTHOR]