Geomicrobiology of sulfur–boron-dominated, neutral-pH hydrothermal systems was revealed in a Trans-Himalayan spring named Lotus Pond, located at 4436 m, in Puga Valley, Ladakh (India), where water boils at 85$^{\circ}$C. Water sampled along Lotus Pond’s outflow (vent to an adjacent river called Rulang), representing an 85–14$^{\circ}$C gradient, had high microbial diversity and boron/chloride/sodium/sulfate/thiosulfate concentration; potassium/silicon/sulfide/sulfite was moderately abundant, whereas cesium/lithium small but definite. Majority of the bacterial genera identified in the 85–72$^{\circ}$C samples have no laboratory-growth reported at >45$^{\circ}$C, and some of those mesophiles were culturable. Sulfur-species concentration and isotope-ratio along the hydrothermal gradient, together with the distribution of genera having sulfur-oxidizing members, indicated chemolithotrophic activities in the 85–72$^{\circ}$C sites. While biodiversity increased in the vent-to-river trajectory all-day, maximum rise was invariably between the vent (85–81$^{\circ}$C) and the 78–72$^{\circ}$C site; below 72$^{\circ}$C, diversity increased gradually. Biodiversity of the vent-water exhibited diurnal fluxes relatable to the sub-surface-processes-driven temporal fluxes in physicochemical properties of the discharge. Snow-melts infiltrating (via tectonic faults) the $\sim$160$^{\circ}$C geothermal reservoir located within the breccia, at $\sim$450 m depth, apparently transport mesophilic microbes into the thermal waters. As these micro-organisms emanate with the vent-water, some remain alive, illustrating that natural bacterial populations are more heat-resilient than their laboratory counterparts.