Microbial diversity and functions within the Earth’s deep subsurface remain pivotal in the Earth’s major biogeochemical activities. Microbial communities of groundwater systems hosted by ~65-million-year-old Deccan basalts are investigated to delineate their characteristics, biogeochemical functions and environmental control. Quantitative PCR-based bacterial cell counts suggest 4.3 × 102–3.9 × 103 cells/mL. 16S rRNA gene sequence analysis shows considerable bacterial diversity and the existence of a core microbiome (16 amplicon sequence variants [ASVs] out of a total of 2020 ASVs) across the groundwater samples. Members of Burkholderiaceae and Moraxellaceae are predominant taxa within the groundwater. In comparison, the spring water and surface water microbiomes are significantly distinct. Non-metric multidimensional scaling highlights that the basaltic groundwater communities are influenced by local environmental parameters. Analysis of whole metagenomes indicates that the Calvin–Benson–Bassham cycle is a primary mode of carbon fixation in the subsurface water system of the Deccan traps. Metagenome-assembled genomes are affiliated to the genera Limnohabitans and Methylotenera, among others. Together with the presence of sulfate and nitrate in the groundwater environment, the presence of genes involved in dissimilatory nitrate and sulfate reduction indicates the prevalence of anaerobic/facultative anaerobic lifestyles among the microorganisms in this system. Amplicon and whole metagenome sequence-based analyses suggest the presence of microbial populations involved in local biogeochemical cycling. This study on the geomicrobiology of the water systems of Deccan traps elucidates microbial community composition and biogeochemical function in the igneous rock-hosted deep biosphere.