Critical zone is a heterogeneous, near surface environment, in which, complex interactions involving rock, soil, water, air, and living organisms, regulate the natural habitat and determine the availability of life sustaining resources and support all ecosystems on the earth. Rivers are the important components of the critical zone and are the major sites for the microbial carbon and nitrogen fixation. In current study, we have studied the spatio-temporal variation in the bacterial diversity from four sites, in a freshwater stream viz. Pranmati, of Himalayan Critical Zone using 16S rRNA illumina NovaSeq PE250 sequencing. Physico-chemical properties of water samples also recorded from the four sites of the Pranmati stream. Proteobacteria, Bacteroidetes and Cyanobacteria were the dominant phyla in the summer water samples. In winter samples, along with Proteobacteria, Cyanobacteria was dominant at sites two sites of the stream. The alpha and beta diversity indices were studied and correlated with the physico-chemical parameters of the water samples. The functional role of the microbial community was investigated. The metagenomics analysis of microbial communities of streams like Pranmati is important to estimate, evaluate and record the microbial taxa before they change or are lost due to climate change.