This research explored the microbial diversity in two underexplored natural springs, Arincho Chumik and Chutron, located in the Shigar Valley, Gilgit Baltistan, utilizing a culture-centered method combined with Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS). The outcomes revealed a diverse microbial landscape, with a total of 18 unique bacterial strains isolated, comprising nine from each spring. From the total 18 isolated strains, 7 (39%) were noticed to be gram-positive while 11 (61%) were gram-negative. Interestingly, species like Brevundimonas and Acinetobacter were present in Arincho and Chutron springs, respectively, highlighting the unique physiochemical environments and their impact on microbial populations. The examination also uncovers the existence of pigment-producing bacteria, suggesting potential biotechnological applications. The chilly freshwater spring of Arincho possessed certain opportunistic bacteria, including Bacillus cereus, Dietzia cinnamea, and Microbacterium species. Likewise, Human-related microorganisms like Micrococcus leuteus were also identified in samples from the Chutron thermal spring. Additionally, the recognition of opportunistic pathogens among the strains underlines the health effects for the local communities, especially for old aged and immune-deficient individuals. The quality of these water resources ought to be supervised by regulatory authorities to decrease public health risks and pathogen transmission.