Baseflow defined as the contribution of groundwater and delayed subsurface flow, is generally described by indices such as the baseflow index (BFI), the long-term ratio of baseflow to streamflow. Characterizing baseflow is challenging because it is not directly accessible, particularly in sensitive areas to climate change like the mountainous Mediterranean regions with hard-rock aquifers. In these areas, little is known about the temporal and spatial contribution of baseflow to streamflow. This study aimed to address this scientific gap by using the first calibrated and validated recursive digital filter with natural tracers for such regions. Two watersheds of Corsica (France), the Tavignanu and the Fiumaltu, were chosen as application models for calibration and validation, respectively, due to their representative characteristics of these regions. Various methods exist for baseflow analysis, including empirical, analytical and physical methods. Empirical and analytical methods, such as digital filters, are easy to use but lack physical significance. Conversely, physical methods using natural tracers, such as isotopes and ions, are more physically representative but are difficult to implement. By calibrating and validating analytical methods with tracers in this specific context, we were able to leverage the strengths of both approaches for effective long-term baseflow analysis. This innovative approach confirmed that baseflow was the main contributor to river flow during dry months, with a contribution of 88–90 % for both watersheds. Notably, baseflow remained a significant contributor during periods of high flow, averaging 54 % for the Tavignanu and 60 % for the Fiumaltu. Over a 25-year period, the mean annual contribution was substantial, at 73 % for the Tavignanu and 77 % for the Fiumaltu. In a particularly dry year, which are expected to become more common with climate change, baseflow contribution was even higher, confirming its origin from deep groundwater and delayed subsurface components. Our results demonstrate that, in the context of climate change, groundwater and delayed subsurface flow will play an increasingly important role in sustaining rivers, connected ecosystems, as well as many human activities in the mountainous Mediterranean regions.