Springs serve as a primary water source in most households in the Jammu Himalaya due to the inaccessibility to water from major rivers flowing into deep valleys. However, over the past several decades, many of these springs have started drying up, while many have already suffered degradation. A total of 24 freshwater springs were mapped in the Jammu Himalayan region, out of which seven had dried up permanently. Water quality parameters (pH, temperature, DO, BOD) of the springwater were within the permissible limits for human consumption, but the presence of pathogenic bacteria could pose a health problem to the local population. Construction of concrete walls, dumping of domestic waste and bathing inside the enclosed ponds of springs have blocked the outflow in some springs, which has also resulted in the stagnation and contamination of spring water leading to the growth of pathogenic Gram-negative bacteria like Escherichia coli (E. coli) and some species of Shigella and Salmonella. The 16S rRNA gene was used for the molecular identification of the isolated bacterial species in addition to macro-morphological and biochemical analysis. The results showed the prevalence of indicator bacteria like E. coli, Shigella and Salmonella in the Jammu Himalayan springs at various places, rendering the water unsafe for drinking.