Mineral water must be safe for consumption. The study aimed to assess the bacterial diversity of mineral water samples collected directly from extraction wells through both cultivation-dependent and cultivation-independent analysis and their correlation with physicochemical properties. The physicochemical characterization included the analysis of 40 different minerals and parameters such as pH, conductivity, oxidation-reduction potential (ORP), total dissolved solids (TDS), salinity (PSU), and temperature (T). For the cultivation-dependent analysis, the counts included heterotrophic bacteria at 22 and 36 °C, total coliforms (TC), Escherichia coli (EC), and Pseudomonas aeruginosa (PSA). The cultivation-independent analysis comprised 16 S rRNA metataxonomic data analysis. The pH of the mineral water samples at wells ranged from 5.02 to 6.73 (non-dimensional), conductivity ranged from 20 to 174 μS/cm, ORP varied between 3.1 and 289 mV, TDS ranged from 10 to 87 mg/L, PSU ranged from 0.01 to 0.08 (non-dimensional), and the temperature range was between 19 and 22 °C. The results revealed counts of PSA in the mineral water samples from wells P-01 and P-02, with an average of 0.18 log CFU/250 mL. The samples from well P-09 exhibited average counts of EC at 0.40 log CFU/250 mL (0.5 SD) and TC at 1.00 log CFU/250 mL (0.0 SD). At 36 °C, the heterotrophic bacterial counts in mineral water samples from all wells were <1.0 log CFU/mL. However, at 22 °C, the samples from wells P-01, P-03, and P-04 showed average heterotrophic bacterial counts of 1.11 log (0.03 SD), 1.61 log (0.09 SD), and 1.30 log (0.02 SD) CFU/mL, respectively. The microbiota varied among the analyzed wells, indicating different microbial community profiles likely influenced by the soil microbiota rather than the physicochemical parameters of the well water samples.