Travertines are terrestrial carbonates that are commonly associated with fault activity in extensional and transtensional basins. The faults serve as conduits for the rise and mixing of carbonate enriched fluids with thermal and meteoric CO2 inputs promoting travertine precipitation at the surface. Therefore, travertine successions provide key constrain on the faulting, depositional environments, fluid flow and climate. This work focuses on the travertine succession in the Miocene Levač Basin, the marginal basin of the Morava Corridor situated at the junction of the Dinarides and the southernmost Carpathians. Detailed sedimentological, geochronological (U‐Pb age, laser ablation – inductively coupled plasma – mass spectrometry) and structural analyses of the travertines are used to reconstruct the evolution of the feeding hydrothermal system. Furthermore, these data were used to understand the controlling factors governing alternation of fluid flows enriched in thermally generated and meteoric CO2, and precipitation of travertines in Levač Basin, and finally to elucidate the late stage of basin evolution. Four facies associations are distinguished within the succession, i.e. travertine slope, ridge, flat, and travertine flat under the fluvial influence. The results demonstrated that travertine deposition was controlled by north‐west/south‐west and north‐east/south‐east normal fault arrays. Stable isotope data show positive δ13C values (with δ18O being negative) shifting to negative in the distal and stratigraphically younger deposits implying dilution of deep hydrothermal fluids by mixing with meteoric waters. Finally, travertine deposits yielded a new U‐Pb age of ca 14 Ma indicating that the Middle Miocene extensional phase known from other intermountain basins in the Dinarides reached as far east as the Levač Basin and Morava Corridor.