This review meticulously examines the dynamics of river microbiomes, with an emphasis on the Ganges and Yamuna rivers of South Asia. These rivers are vital for both ecological and cultural landscapes and offer to understand the interaction between ecological and anthropogenic factors and their impact on microbial communities and activities. Ecological and hydrological factors such as seasonal changes, water flow and physico-chemical properties of rivers influence microbial diversity and abundance. The effect of heavy metals from industrial and agricultural sources on the river microbiome and how these pollutants modify microbial community structures and ecosystem health are not understood well yet. This underscores the need for sustainable water treatment and remediations for practical engineering solutions. The study reveals how these interactions, whether symbiotic or competitive, affect the composition and functionality of riverine microbial communities. An innovative aspect of our research is the potential of river microbiomes as indicators of urban sewage contamination. We demonstrate how microbial patterns can signal pollution levels, proving valuable for environmental monitoring, management and mitigation. A special attention to the role of microbes in river ecosystems' biogeochemical cycles has been paid to how these microbes contribute to nutrient recycling, organic matter decomposition and overall ecosystem productivity, underlining their crucial role in maintaining the aesthetic value of the river. Additionally, study evaluates the latest methodologies for analysing microbiome metagenomic data, including functional annotation and microbial community analysis techniques. Findings highlight the key importance of understanding river microbiomes for hydrology, ecology and microbiology researchers.