Identifying and quantifying the main factors that are jeopardizing amphibian communities worldwide is essential for planning effective amphibian conservation. We collected data on the presence/absence of salamanders and newts (Caudata) and frogs and toads (Anura) in >3600 water points from a large region (30,000 km2) in NW Spain during a 10‐year period (2004–2013). We contrasted a large set of hypotheses explaining presence/absence as a function of anthropogenic factors across the regional elevation gradient (1–2036 m). Logistic regression modeling revealed that salamanders and newts were mainly influenced by pollution and by land use changes, and that the effect of these factors changed with elevation. However, frogs and toads were affected by a larger set of factors acting synergistically, although not including land use changes, and their effect operated at all elevation ranges, except in the case of biological factors (invasive species and wild boar abundance) with higher effects at low elevation. Changes in land use was the most common factor at any elevation and included the abandonment of rural areas, which favors shrub and tree encroachment on former open land, and loss of water points. The most resilient species at any elevation were two frogs, Pelophylax perezi and Rana parvipalmata. The least resilient species were two salamanders, Chioglossa lusitanica and Lissotriton helveticus, followed closely by two toads, Alytes obstetricans and Pelobates cultripes. Unoccupied sites had higher frequencies of biological effects and of changes in land use in the first 5 years of study and lower frequencies of direct human influence factors in the second period. Overall, our results showed that the studied amphibian metacommunity was negatively influenced both by direct and indirect anthropogenic factors, but also that many amphibian species were not only capable of occupying sites which had been altered by human action, but were even favored by land uses generating open habitat, a habitat type that is increasingly uncommon in the region, in the entire Iberian Peninsula and in Europe.
