Abstract The seasonal hydrological mechanisms of two thermokarst lakes on the northeastern Qinghai-Tibet Plateau (QTP) were characterized by three-year intensive field observations and a water balance model. In three ice-free seasons, the supra-permafrost discharge contributed a mean ratio of over 170% of the precipitation. In the ice-cover seasons, the supra-permafrost discharge contribution varied between -20% and 22% of the water storage change. Results show that a large portion of the lake water storage change is because of the supra-permafrost discharge resulting from precipitation. Furthermore, a precipitation-subsurface runoff function is preliminarily identified in which the supra-permafrost discharge nonlinearly increased with more precipitation. Our results show that the recent lake expansion is linked with increasing supra-permafrost discharge dominated by precipitation. This study also suggests that we need to pay attention to the nonlinear increase of precipitation-controlled supra-permafrost discharge on the large lake expansion at the catchment scale in the QTP region, instead of only looking at the inputs (e.g., precipitation and river discharge) as shown in the previous studies.