The hummocky Balaton Highland is located in western Hungary and is part of the Transdanubian Mountains, the most extensive carbonate aquifer system in Hungary. The study region also encompasses Lake Balaton, the biggest lake in central Europe, which is to the south of Balaton Highland. The surface water–groundwater interaction in the Balaton Highland–Lake Balaton region and the groundwater contribution to Lake Balaton are revisited in this paper. Hydrostratigraphic classification was performed first; then, groundwater flow directions by hydraulic head distribution were analysed, and baseflow indices of surface watercourses were calculated. Regarding hydrochemical characterisation, general hydrochemical facies were identified, natural tracers of temperature, chloride and uranium were applied, and the stable isotopic composition of oxygen and hydrogen was determined. Finally, groundwater flow and heat transport were simulated in a 2D numerical model. A high level of hydraulic interaction was evidenced between surface water and groundwater and the sub-regions of Bakony Mountains, Balaton Highland and Lake Balaton by physical and chemical parameters, numerical simulation and groundwater-flow-related natural manifestations, revealing hydraulic continuity in the study region. Based on the results, the division of legislative water bodies can be reconsidered, especially that surface water and groundwater should be regarded as interconnected, and Lake Balaton can be considered a groundwater-dependent ecosystem in any water-use planning in the region.