Application of the gravity-driven regional groundwater flow (GDRGF) concept to the hydrogeologically complex thick carbonate system of the Transdanubian Range (TR), Hungary, is justified based on the principle of hydraulic continuity. The GDRGF concept informs about basin hydraulics and groundwater as a geologic agent. It became obvious that the effect of heterogeneity and anisotropy on the flow pattern could be derived from hydraulic reactions of the aquifer system. The topography and heat as driving forces were examined by numerical simulations of flow and heat transport. Evaluation of groups of springs, in terms of related discharge phenomena and regional chloride distribution, reveals the dominance of topography-driven flow when considering flow and related chemical and temperature patterns. Moreover, heat accumulation beneath the confined part of the system also influences these patterns. The presence of cold, lukewarm and thermal springs and related wetlands, creeks, mineral precipitates, and epigenic and hypogenic caves validates the existence of GDRGF in the system. Vice versa, groups of springs reflect rock–water interaction and advective heat transport and inform about basin hydraulics. Based on these findings, a generalized conceptual GDRGF model is proposed for an unconfined and confined carbonate region. An interface was revealed close to the margin of the unconfined and confined carbonates, determined by the GDRGF and freshwater and basinal fluids involved. The application of this model provides a background to interpret manifestations of flowing groundwater in thick carbonates generally, including porosity enlargement and hydrocarbon and heat accumulation.