Mediterranean headwater catchments have experienced major land-use changes in recent centuries, namely characterized by afforestation with fast-growing tree species (e.g., pine and eucalyptus). This paper investigates differences in the hydrological response of two forested catchments with distinct Pinus pinaster Aiton (PIN) and Eucalyptus globulus Labill. (EUC) covers over 6 hydrological years, from 2010 to 2016. The study was developed in paired catchments located in North-Central Portugal, under wet Mediterranean climate and schist bedrock. Based on rainfall and streamflow measurements, the hydrological responses were analyzed through the water-balance calculations, rainfall-runoff event analyses, and correlations between rainfall characteristics, evapotranspiration, soil moisture, overland flow, and land-cover parameters. The study period recorded a wide range of annual rainfall, between 984 and 2127 mm per years. The annual streamflow displayed greater inter-annual variation, from 208 to 1430 mm for PIN and from 217 to 1291 mm for EUC. The runoff coefficient was higher in the wettest years, with a maximum of 58% for PIN and 61% for EUC, and decreased substantially in the driest year, representing only 17% of the rainfall in PIN and 22% in EUC. Rainfall was predominant during the winter season (41%), followed by autumn (30%) and spring (24%). The streamflow displayed a seasonal behavior in both catchments, with higher runoff coefficient for EUC that for PIN. Half of the annual streamflow occurs during the winter, with the highest average runoff coefficient attained for EUC and PIN respectively being 68% and 64% of the rainfall amount. Annual evapotranspiration was relatively constant through the six years of study and showed higher average values in PIN (907 mm) than EUC (739 mm), highlighting the importance of forest type and showing that mature pine plantations lead to higher water consumption than eucalypt stands. Annual rainfall amount affects evapotranspiration rate (%), the percentage of ET increasing from 37% to 78% for PIN and from 34% to 73% for EUC between the wettest and the driest years, which raises concerns regarding the impact of climate changes on water availability in the mountain areas of the Mediterranean region.