Hydrogeologic processes and shallow subsurface flows control runoff generation, groundwater dynamics, and permafrost distribution at high latitudes and elevations. Electrical resistivity tomography (ERT) can effectively delineate the frozen and thawed zones in the cold environment and can be applied in permafrost hydrogeology by measuring the differences in subsurface electrical potential. A combined approach of ERT and borehole measurements is implemented to map the flow paths of the supra-permafrost and sub-permafrost waters around the Wanlong Worma Lake (WWL) basin in the headwaters of the Yellow River (northeastern Qinghai-Tibet Plateau, China). The ERT sounding results are further validated using drilling records and measured data on ground temperatures and groundwater level. Then, basic features for permafrost hydrogeology are outlined according to the ERT sounding, vegetation distribution, and geological data in the WWL basin. The results show the presence of permafrost at depths up to 15 m, in which electrical resistivity is >250 Ωm. Below the permafrost (at depth 15–80 m), electrical resistivity is generally <100 Ωm. At the depth where an aquifer occurs (20–60 m), electrical resistivity is in the range 1–25 Ωm. The sub-permafrost water moves towards the zone of taliks (unfrozen ground) under the hydraulic gradient controlled by local permafrost distribution and is affected by terrain relief. This work demonstrates the capability of ERT for delineating the distribution of the aquifers of the supra- and sub-permafrost waters and for understanding changes in hydraulic connections in a rapidly degrading alpine permafrost basin.