The morphological plasticity of bivalve species may impair their correct identification. Pisidium species (Sphaeriidae) are difficult to distinguish, notably the common pea clam, Pisidium casertanum (Poli, 1791), which is a polymorphic species, often misidentified and confused with other Pisidium species. This is especially true since this species is the most euryecious of the genus, being able to colonize very different habitats. In this study, elliptic Fourier Analysis, a geometric morphometric method, was used to assess intraspecific variation in P. casertanum. Sampling of specimens was done in three habitat types – springs, lakes and streams – in the Mediterranean biodiversity hotspot region, using the Sebou basin in Morocco as a study area. In addition to the geometric morphometric method, linear measurements of the shell were used to assess growth patterns. Results revealed differences in the hinge plate, which is broader in shells collected from lakes, whereas it is higher in shells of springs. The geometric morphometric method clearly showed shape differences between individuals of the three habitats. Specimens of lakes were the most distinguishable, presenting more elongated shells than those from springs and streams, which are shorter but higher. Individuals from the three habitat types presented a negative allometric growth pattern whereby the shell of animals grows more slowly in height than in length. The use of linear and geometric morphometric methods led to conclude that the morphology of P. casertanum is, in fact, highly influenced by its environment, in particular, its habitat type.