This study aimed to analyze stem anatomical characteristics of Trapa natans from five Skadar Lake locations (L1 - Milovića bay, L2 – inflow of the Morača river, L3 - Kamenik, L4 - Grmožur, L5 - Lipovik) with different concentrations of Cu, Mn, Zn, Co and Pb, during the summer period of the year 2012. Cross sections of stem were made using cryotechnic procedure. For all analyzed quantitative anatomical parameters, the minimum values at the location L2 were recorded, with the presence of maximum content for all investigated metals in stem of Trapa natans. On the other hand, except for cobalt, at the location L4 the minimum concentration for all investigated metals were recorded. Plants collected from this location have the largest average values of the most measured anatomical parameters. The results of Discriminant Analysis showed that plants from different location could be clearly classified into three groups according to their stem quantitative anatomical characteristics which corresponds with heavy metals content. Our research also showed that there is no statistically significant correlation between the content of most investigated metals (Co, Cu, Pb and Zn) and the values of anatomical parameters. Statistically significant negative correlation was found between Mn content in stem and values of two anatomical characters (stem cross-sectional area and Mn content, r = - 0.88; p < 0.05; number of hypodermal cell layers and Mn content, r = - 0.90; p < 0.05).