Animals inhabiting environments with low productivity and food availability commonly have reduced energy demands and increased digestive efficiencies. The dry matter intake (DMI), apparent digestible dry matter (ADDM), digestible efficiency (DE) and digestible energy intake (DEI) of two populations of common spiny mouse Acomys cahirinus were compared during both winter and summer under conditions of simulated water stress. Mice were captured from the north- and south-facing slopes (NFS and SFS) of the same canyon that represent mesic and xeric habitats, respectively. Measured variables were also compared between F1 mice that had been born to either NFS or SFS mice, and raised in the laboratory. SFS mice were able to assimilate energy more efficiently than NFS mice during the summer. By comparison, NFS mice were able to assimilate more energy during the winter. During winter, NFS mice assimilated more energy at low levels of water stress, whereas SFS mice assimilated more energy at higher levels. Differences were also apparent in F1 mice. It is therefore suggested that local climatic conditions can impose physiological adaptations that are retained in succeeding generations, creating unique meta-populations.