Mediterranean-climate catchments are characterized by significant spatial and temporal hydrological variability caused by the interaction of natural as well human-induced abiotic and biotic factors. This study investigates the non-linearity of rainfall-runoff relationship at multiple temporal scales in representative small Mediterranean-climate catchments (i.e., <10 km2) to achieve a better understanding of their hydrological response. The rainfall-runoff relationship was evaluated in 43 catchments at annual and event—203 events in 12 of these 43 catchments—scales. A linear rainfall-runoff relationship was observed at an annual scale, with a higher scatter in pervious (R2: 0.47) than impervious catchments (R2: 0.82). Larger scattering was observed at the event scale, although pervious lithology and agricultural land use promoted significant rainfall-runoff linear relations in winter and spring. These relationships were particularly analysed during five hydrological years in the Es Fangar catchment (3.35 km2; Mallorca, Spain) as a temporal downscaling to assess the intra-annual variability, elucidating whether antecedent wetness conditions played a significant role in runoff generation. The assessment of rainfall-runoff relationships under contrasted lithology, land use and seasonality is a useful approach to improve the hydrological modelling of global change scenarios in small catchments where the linearity and non-linearity of the hydrological response—at multiple temporal scales—can inherently co-exist in Mediterranean-climate catchments.