Elucidating the spatiotemporal pattern of water quality and algal biomass is crucial for accurately tracing pollution sources and reducing the risk of algal blooms in lake systems. This study analyzed the spatiotemporal variability of water quality and algal biomass in Erhai Lake from 1994 to 2021 using water quality index (WQI), Mann-Kendall test and Sen’s slope combined methods. The potential causes of water quality deterioration and algal biomass dynamics were also elucidated. The results showed that the historical changes in the water environment of Erhai Lake mainly had three stages: satisfactory (1994‒2001), deteriorating (2002‒2010) and improving (2011‒2021). The changes in water quality and algal biomass were primarily affected by total nitrogen, total phosphorus and chemical oxygen demand in different stages. The water environment of Erhai Lake is currently improving significantly, starting in the southern area that is furthest from the sources of agricultural pollution, especially in summer and autumn. This is attributed to the implementation of control measures resulting in lower pollutant loads at particular times and places. Therefore, it is necessary to continue to promote standardized livestock farming, to strengthen rural wastewater collection and to investigate measures such as the interruption of the endogenous cycle.