Mustang valley in the central Himalaya of Nepal is a unique landscape formed by massive soil mass during a glacial period, which is attributed to a mix of vegetations and long agricultural history. Soil nutrients and their sourcing is highly important to understand the vegetation assemblage and land productivity in this arid zone. Twenty soil samples (from 0 to 20 cm depth) were collected from three landscape positions in Mustang district: valley, ridge, and midslope. We explored nutrient sourcing using natural abundance carbon (δ13C) and nitrogen isotope (δ15N) employing isotope ratio mass spectrophotometry. The results showed that the total soil carbon (TC) and total nitrogen (TN) ranged from 0.3 to 10.5% and 0.3 to 0.7%, respectively. Similarly, the CN ratio ranged from 0.75 to 15.6, whereas soil pH ranged from 6.5 to 7.5. Valley soil showed higher values of TN, CN, and soil pH than the ridge and midslope soils. The valleys had more positive δ15N signatures than ridge and midslope, which indicates higher inorganic and organic N fertilizer inputs in the valley bottom than in the midslope and ridge. This suggests that a higher nutrient content in the valley bottom likely results from agro-inputs management and the transport of nutrients from the ridge and midslope. Soil pH and CN ratio were a non-limiting factor of nutrient availability in the study regions. These findings are crucial in understanding the nutrient dynamics and management in relation to vegetation and agricultural farming in this unique topography of the Trans-Himalayan zone of Mustang in central Nepal.