Summary Stable isotope measurements and isotope mass balance (IMB) calculations are presented in support of an unprecedented 20-year water balance assessment for a tailings pond and a chain of downstream lakes at the Salmita–Tundra mine site, situated near Courageous Lake, Northwest Territories, Canada (65°03′N; 111°11′W). The method is shown to provide a comprehensive annual and interannual perspective of water balance fluxes along a chain of lakes during the period 1991–2010, without the need for continuous streamflow gauging, and reveals important lake-order-dependent patterns of land-surface runoff, discharge accumulation, and several key diagnostic ratios, i.e., evaporation/inflow, evaporation/evapotranspiration, land-surface-runoff/precipitation and discharge/ precipitation. Lake evaporation is found to be a significant component of the water balance, accounting for between 26% and 32% of inflow to natural lakes and between 72% and 100% of inflow to mine-tailings ponds. Evaporation/evapotranspiration averages between 7% and 22% and is found to be higher in low-precipitation years, and in watersheds with a higher proportion of lakes. Runoff ratios for land-surface drainages and runoff ratios for watersheds (including lakes) ranged between 14–47% and 20–47%, respectively, and were higher in low precipitation years, in watersheds with a higher proportion of lakes, and in watersheds less affected by mining development. We propose that in general these two runoff ratios will likely converge as lake order increases and as land cover conditions become regionally representative. Notably, the study demonstrates application of IMB, validated with streamflow measurements, to constrain local water balance in a remote low-arctic region. For IMB chain-of-lakes applications, it underlines the importance of accounting for evaporatively-enriched upstream sources to avoid overestimation of evaporation losses.