Targeted physiological groups of bacteria were cultivated and identified in the brackish groundwaters of Obrenovačka Banja (OB), Lomnički Kiseljak (LK) and Velika Vrbnica (VV) using biological activity reaction tests (BARTs) to assess the biocorrosion, biofouling and health risks. The highest density of iron-related, sulfate-reducing, slime-forming, facultatively anaerobic heterotrophic, denitrifying bacteria and representatives of Pseudomonas spp. was recorded in the OB sample, while the lowest density of the same physiological groups of bacteria was recorded in the LK sample. Facultatively anaerobic heterotrophic bacteria were the most abundant in the OB and LK samples, while, in contrast, heterotrophic aerobic bacteria were the most abundant in the VV sample. All tested samples were characterized by a high degree of biochemical activity associated with iron-related, sulfate-reducing, slime-forming, heterotrophic aerobic and facultatively anaerobic bacteria. Also, high biochemical activity of denitrifying bacteria was recorded in the OB sample, and the same activity of Pseudomonas species was recorded in the OB and VV samples. For OB and LK groundwaters, the highest degree of risk was estimated for biocorrosion process, while for the OB and VV occurrences, the highest degree of risk was estimated for biofouling process. The health risk was present for all examined groundwaters. Caution is warranted in further use of all investigated occurrences due to the established public health risk and an immediate revitalization of the OB, LK and VV wells is necessary.