Lake disappearance is one of the results of water eutrophication which leads to lake shallowing and overgrowth, and small and shallow lakes are the most threatened with degradation. We studied the effect of lake shallowing on its overgrowth, taking into account the morphometric parameters of water bodies. The study was performed in 20 lakes located in the central west part of Poland. The degree of lake shallowing was evaluated on the basis of bathymetric maps made in the 1960s and studies carried out presently. Additionally, an analysis of littoral coverage and macrophyte growth forms was investigated. Moreover, the composition, intensity of phytoplankton blooming, and physico-chemical parameters of the lake water were analyzed. Redundancy analysis shows that the lake volume, average depth, shallowing rate, and change in volume were the parameters that most strongly correlated with the share of macrophytes in the lakes. According to the regression analysis, the share of emergent macrophytes was significantly correlated with lake shallowing. No relation was found between phytoplankton abundance and lake shallowing. Conversely, the lakes with the highest rate of shallowing were characterized by the greatest share of vegetation, which suggested that vegetation growth had a significant impact on lake shallowing.