The Mareza karst aquifer is the most important drinking water resource for the water supply system of the City of Podgorica, the capital of Montenegro. This study presents the first assessment for the determination of the Mareza catchment area. Water chemistry and stable isotopic composition (δ¹⁸O and δ²H) of monthly precipitation samples (as inputs) are presented, in order to determine the Local Meteoric Water Line (LMWL) for the study area, and to analyze the behavior of the karst spring Mareza (as output) and the Zeta River water. The possible impact of the river on the Mareza springs was also investigated. Stable isotope compositions were used to analyze the origin of the four springs of the Mareza aquifer. Seasonal variations of δ¹⁸O and δ²H values and deuterium excess (d excess) changes in precipitation are explained by the mixing of air masses, such that a Mediterranean source prevails in the winter period, while in the summer period, the area is rather under the influence of air mass originating from the Atlantic Ocean. All spring water samples have lower δ values than the local precipitation and they plot above the LMWL, which may indicate recharge at a higher altitude in the distant mountainous area. The d excess values of all water samples (higher than 10‰) indicate the prevalence of the Mediterranean as a moisture source. Based on the analysis of the seasonal variations of δ¹⁸O and δ²H in precipitation and the Mareza spring, it has been estimated that the groundwater mean transit time (MTT) is 92–129 days, and that the young water fraction (F_yw) amounts to 40.9%–53.3%. These values are typical for the strong karstic springs of highly karstified terrains.