The microbial abundance and diversity at source, after bottling and through 6 months of storage of a commercial still natural mineral water were assessed by culture-dependent and culture-independent methods. The results revealed clear shifts of the dominant communities present in the three different stages. The borehole waters displayed low cell densities that increased 1.5-fold upon bottling and storage, reaching a maximum (6.2 × 108 cells l−1) within 15 days after bottling, but experienced a significant decrease in diversity. In all cases, communities were largely dominated by Bacteria. The culturable heterotrophic community was characterized by recovering 3626 isolates, which were primarily affiliated with the Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. This study indicates that bottling and storage induce quantitative and qualitative changes in the microbial assemblages that seem to be similar as revealed by the two sample batches collected on 2 consecutive years. To our knowledge, this is the first study combining culture-independent with culture-dependent methods, and repeated tests to reveal the microbial dynamics occurring from source to stored bottled water.