The present study highlights the importance of geological, hydrogeological, and hydrogeochemical characterization of a karst aquifer in building a conceptual model of the system. The karst system of Krania-Elassona in central Greece was chosen for this application. Hydrogeological research included geological mapping and hydrogeological analysis. Additionally, hydrochemical analysis of water samples was performed in boreholes, rivers, and the system's main spring. The Krania-Elassona aquifer consists of three horizons of marbles and is characterized by mature karstification. The karst aquifer is characterized by allogenic recharge mainly from the River Deskatis that accounts for up to 92% of the total flow. Groundwater and spring water are generally characterized as good quality and are suitable for irrigation and domestic use. The water type of the spring water is classified as Mg-HCO3. The application of a SARIMA (Seasonal Autoregressive Integrated Moving Average Model) model verified the conceptual model and successfully simulated spring discharge for a two-year period. The results of this study highlight the importance of basic hydrogeological research and the initial conceptualization of karst systems in reliably assessing groundwater vulnerability and modeling.