The autochthonous microbiota from a granitic aquifer in Spain were studied. Several bacterial strains were isolated and identified. The major components of the microbiota were Pseudomonas-like strains, Flavobacterium, Acinetobacter, and Alcaligenes. The variation in the number of microorganisms after the bottling process was studied. The initial bacterial population increased over the first 5 days after bottling. This increase was higher in samples from polyvinyl chloride bottles. Sonication usually increased the total cell counts. As expected, most of the autochthonous microbiota were not detected in the viable cell counts.