The water quality of Lake Erhai has deteriorated in recent decades due to socioeconomic development in the lake basin. After the massive implementation of water environmental protection measures in Lake Erhai in 2016, the trend of water quality deterioration has been curbed and the intensity and frequency of algal blooms has decreased. However, water quality monitoring data show that pollutant concentrations in Lake Erhai still exceed acceptable values, and there is a risk of water quality standard limits being further exceeded in the future. Therefore, it is urgent to systematically study the variability characteristics of water quality in Lake Erhai to provide practical methods to predict the future evolution of water quality. Based on water quality monitoring data from 2009 to 2019, the current water quality characteristics of Lake Erhai were analyzed, and a two-dimensional hydrodynamic and water quality mathematical model was built to predict the water quality in 2025. The results showed that the total phosphorus (TP) concentration declined after 2016, mainly due to the significant reduction of TP entering the lake due to pollution interception. However, the concentrations of the potassium permanganate index (CODMn) and total nitrogen (TN) increased after 2016, demonstrating that the pollution control measures have had little effect on the improvement of CODMn and TN. The spatial and temporal distribution of pollutants showed that the water quality in winter and spring was better than in summer and autumn, and the water quality in the southern lake was better than in the northern lake. This analysis indicates that non-point source pollution remains the main source of pollution in Lake Erhai, and that rainfall is the main driving force of pollutants exceeding the water quality standard. According to the water quality predictions, without additional pollution control measures, pollutant concentrations in Lake Erhai will exceed the Class II water quality standard by 2025. This study analyzes the water quality characteristics, predicts the direction of future water quality changes, and provides a theoretical basis for the future water quality protection of Lake Erhai.