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Riverine systems play an important role in the global carbon cycle, and they are considered hotspots for bacterial activities such as organic matter decomposition. However, our knowledge about these processes in tropical or subtropical regions is limited. The aim of this study was to investigate anthropogenically induced changes of water quality, the distribution of selected pharmaceuticals, and the effects of pollution on greenhouse gas concentrations and bacterial community composition along the 800 km long Cauvery river, the main river serving as a potable and irrigation water supply in Southern India. We found that in situ measured pCO₂ and pCH₄ concentrations were supersaturated relative to the atmosphere and ranged from 7.9 to 168.7 μmol L⁻¹, and from 0.01 to 2.76 μmol L⁻¹, respectively. Pharmaceuticals like triclosan, carbamazepine, ibuprofen, naproxen, propylparaben, and diclofenac exceeded warning limits along the Cauvery. <i>Proteobacteria</i> was the major phylum in all samples, ranging between 26.1% and 82.2% relative abundance, and it coincided with the accumulation of nutrients in the flowing water. Results emphasized the impact of industrialization and increased population density on changes in water quality, riverine carbon fluxes, and bacterial community structure.