The landuse landcover (LULC) patterns have potential control on recharge and discharge processes, dictating the hydrological behaviour, which is essential for informed decision-making in sustainable groundwater management at micro-watershed levels. The stable isotopes (oxygen and hydrogen) can characterise various components of the hydrological cycle, including gaining insights into the recharge and discharge dynamics of the mountainous springs. We collected high-frequency meteorological and hydrological (stream and springs) data and analysed their stable isotopic imprints in a 32 km2 micro watershed of a Himalayan region. Further, we examined the effect of LULC, geology and topography on recharge and discharge dynamics of the springs. The altitude effect in rainfall isotopic signatures was estimated to demarcate the potential spring recharge zones at the springshed level. The current observations were consistent with the global altitude effect, showing a decrease of -0.26 ‰ per 100 meters of elevation gain. Moreover, the precipitation isotopes and spring water flux changes were determined by the Craig-Gordon model. The study found that springs in barren land areas experience higher evaporation, while those in agricultural lands show lower evaporation. Differences in stable isotope values in spring water highlight their usefulness in tracking how land use and environmental changes affect water movement in small watersheds. By combining information on topography, geology, weather, water flow, and isotopes, the study helps to better understand how sensitive spring recharge and discharge are to land use. This research improves our knowledge of spring water sustainability in mountain regions with bimodal precipitation sources. This data set contains all the raw data collected for this paper and presented in tabular format.