To test if habitat could shape shell features of freshwater turtles starting from birth, we tested hatchlings of Emys orbicularis, randomly chosen from four clutches of the same locality, under two treatments, stagnant (pond habitat) vs lotic (river habitat) water regimes. Due to mortality at the beginning of the experiment, we finally considered only two clutches. Turtle shells were characterized initially at hatching and then after one year of treatment by means of traditional and geometric morphometrics, and phenotypic trajectories analyses were conducted on both types of data. Carapace growth was isometric both in proportion and shape, while plastron showed an allometric pattern: length increased more than width, while the contour showed an expansion at the rear and a compression of the front. The hydrodynamic conditions during growth did not seem to affect the phenotypic trajectories of the shell proportions or the plastron. On the contrary, a significant effect was found on the phenotypic trajectory of the carapace: the size component (but not the angle one) was positively influenced by the "lentic" treatment, suggesting a different growth rate between the two environmental conditions