Microbial communities in natural ecosystems are subjectto strong ecological rules.The study of local communi-ties along a regional metacommunity can reveal patternsof community assembly, and disentangle the underlyingecological processes. In particular, we seek drivers ofcommunity assembly at the regional scale using a largelacustrine dataset (>300 lakes)along the geographical,limnological and physico-chemical gradients in the Pyre-nees. By using high throughput amplicon sequencing ofthe 16S rRNA gene, and inferring environmental sourcesof bacterial immigrants, we showed that surface aquaticbacterial assemblages were strongly influenced by ter-restrial populations from soil, biofilms or sediments, andprimarily selected by a pH-alkalinity gradient. Indeed,source proportions explained 27% of the community vari-ation, and chemistry 15% of the total variation, half of itshared with the sources. Major taxonomic groups suchas Verrucomicrobia, Actinobacteria and Bacteroidetesshowed higher aquatic affinities than Parcubacteria,Gammaproteobacteria, Alphaproteobacteria or Betapro-teobacteria, which may be recruited and selected throughdifferent hydrographic habitats. A regionalfingerprintwas observed with lower alphadiversity and higher betadiversity in the central Pyrenees than in both ends. Wesuggest an ecological succession process, likelyinfluenced by complex interactions of environmentalsource dispersal and environmentalfiltering along themountain range geography.