Multivariate statistical methods were employed to study the morphological variation of the freshwater shrimp (Atyaephyra desmarestii), sampled from four distinct freshwater habitats of northwestern Greece. Principal Component Analysis (PCA) and Discriminant Function Analysis (DFA) were used in order to determine morphometrical differences among the biological categories (males, females and ovigerous females) and sampling sites. Statistical analysis of A. desmarestii morphometrical and population data showed that body heights and growth of appendages are correlated to biological category. Females found to have higher values for the measured body heights than males. On the other hand, morphometrical variables related mainly to body lengths such as rostral, telson and pleon lengths, were observed to be correlated to the study sites. Characters related to the swimming capacity, such as telson length, telson width, and pleon lengths, were generally found to have higher values in ovigerous females. Furthermore, among the four ecosystems, certain variables demonstrated higher values in the fluvial ecosystems and lower values in the lacustrine.