Understanding the dynamic interactions between forest ecosystems and water in the Mediterranean region is essential for increasing ecosystem services. Even if many studies were implemented to analyse the variations of water and net primary productivity ( NPP) in the last decade, this is still an important research question especially for the Eastern Mediterranean, where the research attempts are limited. The main objective of this study was to carry out a comparative analysis of catchment runoff generation and forest NPP and to reveal their temporal dynamics at basin scale in a semi-arid Mediterranean environment. The methodology consisted three steps: ( i) estimating catchment runoff generation by implementing process-based J2000 modelling suite, ( ii) modelling NPP of the land cover/use types by adapting an ecosystem-process model ( BIOME-Biogeochemical cycles) and ( iii) assessing the spatio-temporal variability of NPP and runoff dynamics by incorporating the modelling results with multiple regression analysis. Model simulations showed that temperature highly contributed to NPP variations of needle-leaf forests and grasslands. The multiple regression analysis also indicated that runoff was influenced by elevation, precipitation and forest cover. This relationship showed that the inter-annual variability in forest NPP would relate to the variations in runoff distribution across a small Mediterranean subcatchment.