Submarine groundwater discharge (SGD) plays a pivotal role in coastal biogeochemistry, yet it is still challenging to accurately quantify water and solute fluxes driven by this process due to its complex hydrogeological dynamic. This work aims to improve the methods to identify and independently quantify different pathways of SGD by combining direct measurements through seepage meters and Amphibious Electrical Resistivity Tomography (AERT) at a heterogeneous karstic system in the Mediterranean Sea. The integrated approach identified and quantified distinct SGD pathways, including beach-face recirculation, focused discharge zones, submarine springs, and diffusive discharge, each uniquely influencing SGD dynamics. Given that each pathway is characterized by specific geochemical signatures and discharge rates, nutrient fluxes supplied by different pathways varied significantly in magnitude. In the study site, while diffusive discharge was the primary process for transporting fresh groundwater and ammonium, nitrate and phosphate were mainly delivered to the coastal ocean through focused discharge, especially via submarine springs. The combined methodology proved more accurate for determining water and nutrient fluxes than straightforward extrapolations from seepage meters, which were consistently 20 to 120 % higher. This discrepancy highlights the need of combining qualitative and quantitative methods, particularly in regions where multiple SGD pathways coexist.