Hydrological processes of lakes in the Tibetan Plateau are an important indicator of climate change. Due to the high elevation, inaccessibility and limited availability of historical observations, water budget evaluation of typical lake basins has been inadequate. In this study, stable isotopes are used to trace the multiple water sources contributing to two adjacent lakes on the north slope of the Himalayas, Gongmo-tso and Drem-tso. The two lakes have nearly the same elevation, lake area and climatic condition. However, the isotopic composition of the two lakes presents significant differences. Qualitative observations attribute the differences to hydrological discrepancies: Gongmo-tso is a through-flow lake, whereas Drem-tso is a terminal lake. Quantitative analyses, including water and isotope mass balance modelling, clarify the fluxes and isotopic compositions among the various hydrological elements. The isotopic composition of input water, calculated as the summation of rainfall and upstream runoff, is estimated using the local meteoric water line (LMWL) combined with the time series of lake water isotope values. The isotopic composition of evaporation is calculated with a linear resistance model using local meteorological data. The results show that Drem-tso is a closed lake in a hydrological steady state with relatively more enriched lake water isotope values resulting mainly from evaporation. In contrast, through-flow accounts for more than 88% of the water input into Gongmo-tso. The large amount of upstream runoff with lower isotopic composition and enrichment due to evaporation are the major contributions to the observed lake water isotope values. Isotopic modelling of the two neighbouring lakes is effective for isotopic and hydrological research in this region with limited in situ observations. Copyright © 2013 John Wiley & Sons, Ltd.