In order to understand the macroecological architecture of an amphibian metacommunity of a large southern European region located between the Eurosiberian and Mediterranean domains (Galicia), we analyzed nestedness from matrices of presence–absence of 14 species in 3,627 water points, including both ponds and streams, along an altitudinal gradient (0–2,036 m), during a 11-yr period (2003–2013). To quantify nestedness, we used the metric NODF (nested overlap decreasing fill). We also explored interannual variability in nestedness and in temporal patterns of alpha, beta, and gamma diversity. The maximally packed matrix for ponds showed a nested pattern at middle and high elevation, whereas for streams, the nested pattern occurred at low elevation. In both types of wetlands, the magnitude of nestedness was moderate, around 15–30%. On the other hand, nestedness was not found to increase or decrease over the study period, for both ponds and streams, or at the three levels of elevation. This temporary stability was also found for alpha, beta, and gamma diversities. The moderate nestedness pattern detected was most likely explained by selective removal of species, a poor connection among water points, historical destruction of wetlands, or major land-use changes associated with the abandonment of traditional farming activities. Our results denote a certain resilience to human disturbance by the studied amphibian species. However, these results stress the need of protecting the metacommunity as a whole (because of the relative importance of species turnover among sites), and emphasize the suitability of preserving the old mosaic landscape at least within protected areas. Our results are intermediate between those expected for the temperate zone and those expected for lower latitudes, likely because the study region is a biogeographical transition area.