This study presents an integrated approach to map groundwater-surface water (GW-SW) interactions in a scarcely anthropized Mediterranean mountain catchment (Ussita) characterized by fractured limestone rocks with complex spatial-temporal patterns of hydrological processes. Understanding GW contributions to streams like the Ussita is crucial for addressing environmental challenges, including water resources management and evaluating ecological flows to protect aquatic ecosystems. The use of traditional hydrological techniques, such as discharge measurements along various stream stretches, combined with hydrochemical-isotopic analyses and innovative thermal drone investigations, allowed us to quantify the specific contributions of different limestone aquifers in sustaining streamflow. Integrating satellite-based meteorological datasets with in-situ observations further helped to constrain the water budget and assess the extent of the recharge area. Hydrogeochemical data analyses also revealed that the contribution of snow melt to aquifer recharge is about 20%, which is an important issue to consider for GW availability in case of future spatial-temporal changes in snow patterns. These findings can support further studies in other catchments by guiding and optimizing field campaigns to identify site-specific conditions responsible for GW inflow, from the point source to the stream stretch. Moreover, the results can help optimize resource management, mitigate climate-related risks, and support the long-term sustainability of both upstream and downstream socio-ecological systems.