Monitoring physicochemical properties in stream ecosystems is essential for sustaining their ecological health and services. The primary factor contributing to the decline in water quality is human pressure, encompassing land use, pesticide and fertiliser use, urbanisation, forest loss, and climate change. The present study assessed 11 physicochemical parameters at four distinct sites in the snow-fed stream of Ladakh, Trans-Himalaya, from March 2022 to February 2024. Multivariate statistical approaches were employed to generate precise information on the parameters of the streams. Significant (p < 0.05) spatiotemporal variations in the above parameters were identified. Linear regression revealed significant (p < 0.05) correlations among multiple physicochemical parameters, with substantial magnitudes and extents. PCA shows that seasonal variation was more substantial than site-specific variation in determining water quality patterns. The physicochemical parameters including air temperature (AT), water temperature (WT), electrical conductivity (EC), total dissolved solids (TDS), free carbon dioxide (CO₂), total alkalinity (TA), pH, nitrate-nitrogen (NO2–N), chloride (Cl−), and calcium (Ca2+) played a significant role in determining the qualitative characteristics of the snow-fed streams of trans-Himalayan region. Overall, the measured water quality parameters remained within the permissible limits prescribed by various national and international standard-setting agencies. While CA indicated that the high-altitude sites Hanle and Yaya Tso show less-impacted sites, and the low-altitude site Shey is relatively more susceptible to pollution. The present study could serve as a baseline for managing and conserving the most important resource of the aquatic ecosphere, thereby improving water quality for humans and their resident faunal communities. The findings also provide valuable insights for ecologists, limnologists, and policymakers, supporting the formulation of long-term management frameworks and conservation strategies aimed at preserving the freshwater ecosystems of the Trans-Himalayan region.