In the current study, the relationships between lake morphological characteristics, water chemistry parameters and aquatic macrophyte data of nineteen lakes of Greece were investigated. Statistical and ordination analysis was performed in order to distinguish possible correlations between lake morphology features, key water quality parameters and hydrophyte distribution. Water quality and hydrophyte data for eleven out of nineteen lakes were obtained from field surveys carried out the last five years. Water quality parameters, lake morphology and hydrophyte data published in scientific papers and reports were used as well. Several lake morphology parameters such as average depth, maximum depth, relative depth, surface area, lake catchment area, volume, Schindler's ratio and morphoedaphic index (MEI) were included in the statistical analysis. The statistical assessment of our data included Pearson correlations between the lake morphology and water quality parameters, Principal component analysis (PCA), in order to distinguish the key morphological parameters and Redundancy Analysis (RDA) in order to estimate possible associations between the hydrophyte distribution and the morphology of the lakes. The results revealed several significant correlations between the physicochemical and geomorphological variables. Most notable correlations include those between Schindler's ratio, Morphoedaphic index, Secchi depth, conductivity and chlorophyll-a. The results of PCA indicated lake volume and altitude as key variables with the strongest influence on the lake discrimination, followed by Schindler's ratio and MEI. The RDA results revealed a possible association of several hydrophyte species in shallower lakes with greater values of MET. However, the RDA results between aquatic macrophyte and physicochemical data did not reveal any pattern of macrophyte species distribution among the studied lakes. According to our results, Schindler's ratio and relative depth are the most important morphological parameters indicating the combined influence of catchment and lake morphometry on the water quality. The MET was associated with key physicochemical parameters and therefore could provide an additional simple and efficient tool of classification of Greek lakes in the frame of establishing a new typology.