First comprehensive geothermal exploration in Sri Lanka was conducted in 2010 encompassing seven thermal springs, of which Kapurella records the highest temperature. The study consisted of passive magnetotelluric (MT) soundings, in which static shifts were corrected using time domain electromagnetic method (TDEM). A frequency range of 12,500–0.001Hz was used for MT acquisition and polar diagrams were employed for dimensionality determination. MT and TDEM data were jointly inverted and 2D models were created using both transverse electric and transverse magnetic modes. A conductive southeast dipping structure is revealed from both phase pseudosections and the preferred 2D inversion model. A conductive formation starting at a depth of 7.5km shows a direct link with the dipping structure. We suggest that these conductive structures are accounted for deep circulation and accumulation of groundwater. Our results show the geothermal reservoir of Kapurella system with a lateral extension of around 2.5km and a depth range of 3km. It is further found that the associated dolerite dike is not the source of heat although it could be acting as an impermeable barrier to form the reservoir. The results have indicated the location of the deep reservoir and the possible fluid path of the Kapurella system, which could be utilized to direct future geothermal studies. This pioneering study makes suggestions to improve future MT data acquisition and to use boreholes and other geophysical methods to improve the investigation of structures at depth.