Water level management is an effective tool for the ecological restoration of shallow lakes. In this study, we developed an ecologically-based approach to estimate the monthly suitable ecological water levels (EWLs). This approach took both the lake topographic features and aquatic plants’ growth characteristics into account. The aquatic vegetation coverage was used to characterize the degree of the lake ecological restoration. The relationship between water level and vegetation coverage was established. We chose the Tangxun Lake as a testbed, and the recommended lowest EWL was 16.6 m, as the minimum threshold for water level regulations. The results revealed that the predicted vegetation coverage decreased with the rise of water level during the germination period (February and March). To achieve the vegetation coverage goal of 30% and 50%, the lake’s water levels must be lowered to 17.1 m and 16.8 m respectively during germination. The EWLs were recommended to be low in spring and high in summer, which was matched with the natural water level regimes. The proposed approach can provide a reliable reference for water level regulation of shallow lakes especially the lakes with insufficient data.