This study presents the findings derived from a three-year monitoring programme focusing on the hydrochemical composition and stable isotope signatures (δ18O, δ2H) within the vulnerable karst groundwater system in Croatia's northern Dinaric karst region. Covering an area of 1980 km2 across Kapela Mountain and its foothills, this groundwater system falls within the Kupa River basin and encompasses the catchment areas of the main springs across two spring levels of the Dobra, Mrežnica, and Slunjčica Rivers (namely the Vitunj, Zagorska Mrežnica, Dretulja, Veliko Vrelo, Gojak, Tounjčica, Mrežnica, and Slunjčica springs). Given the complex hydrogeological framework, prior studies have not extensively addressed the hydrochemical characteristics of this region, thereby necessitating a comprehensive investigation to elucidate system dynamics. This paper outlines the first investigation employing stable isotopic analyses within the karst groundwater system of Kapela Mt. The main results and conclusions of the research include: (i) the aquifers across Kapela Mt. drain mainly limestones, (ii) water–rock interaction and carbonate weathering are significant contributors to water geochemistry, (iii) there is a slight human impact on the Gojak and Tounjčica spring waters, (iv) the mean residence time of water in the observed aquifer is up to 1.5 years, (v) the new LMWL was calculated for Kapela Mt. based on a three-year dataset (June 2018 – May 2021), (vi) in the north Dinaric karst, the predominant origin of precipitation is from the Mediterranean air mass, (vii) Velebit Mt. has a strong influence on the precipitation isotopic composition of the study area.