Different types of locomotion in phylogenetically close rodent species can lead to significantly different growth patterns of certain skeletal structures. In the present study, we compared the allometric and phenotypic trajectories of the humerus in semiaquatic (Arvicola sapidus) and fossorial (Arvicola scherman) water vole taxa, using three-dimensional geometric morphometrics, to investigate the relationships between functional and ontogenetic differences. Results revealed shared humerus traits between A. sapidus and A. scherman, specifically an expansion of the epicondylar and deltopectoral crests along postnatal ontogeny. In both species, the humerus of young specimens is more robust than in adults, possibly as a compensatory response for lower bone stiffness. However, significant interspecific differences were detected in all components of allometric and phenotypic trajectories. Noticeably divergent allometric trajectories were observed, probably as a result of different functional pressures exerted on this bone. Important differences in the form of the adult humerus between taxa were also found, particularly in features located in muscle insertion zones. Furthermore, the allometric regression revealed certain shape variation not associated with size in A. scherman, suggesting mechanical stress produced by the persistent digging activity during adulthood. A. scherman is a chiseltooth digger that shares several traits in the humerus morphology with scratch-digger rodent species. Nevertheless, these shared characteristics are less pronounced in fossorial water voles, which is congruent with the different implications of the forelimb in the digging activity in these two types of diggers.