The new, two-way coupled, distributed and transient MARMITES-MODFLOW (MM-MF) model, coupling land surface and soil zone domains with groundwater, is presented. It implements model-based partitioning and sourcing of subsurface evapotranspiration (ETss) as part of spatio-temporal water balance (WB). The partitioning of ETss involves its separation into evaporation (E) and transpiration (T), while the sourcing of E and T involves separation of each of the two into soil zone (Esoil and Tsoil) and groundwater (Eg and Tg) components. The objective of that development was to understand the system dynamics of a catchment with shallow water table, through spatio-temporal quantification of water fluxes and evaluation of their importance in water balances, focusing on the Eg and Tg components of ETss. While the Eg is computed using formulation from published study, the Tg is obtained through a novel phenomenological function, based on soil moisture availability and transpiration demand driven by climatic conditions. The MM-MF model was applied in the small La Mata catchment (~4.8 km2, Salamanca Province, Spain), characterized by semi-arid climate, granitic bedrock, shallow water table and sparse oak woodland. The main catchment characteristics were obtained using remote sensing, non-invasive hydrogeophysics and classical field data acquisition. The MM-MF model was calibrated in transient, using daily data of five hydrological years, between 1st October 2008 and 30th September 2013. The WB confirmed dependence of groundwater exfiltration on gross recharge. These two water fluxes, together with infiltration and Esoil, constituted the largest subsurface water fluxes. The Eg was higher than the Tg, which is explained by low tree coverage (~7%). Considering seasonal variability, Eg and Tg were larger in dry seasons than in wet season, when solar radiation was the largest and soil moisture the most depleted. A relevant observation with respect to tree transpiration was that during dry seasons, the decline of Tsoil, associated with the decline of soil moisture, was compensated by increase of Tg, despite continuously declining water table. However, in dry seasons, T was far below the atmospheric evaporative demand, indicating that the groundwater uptake by the tree species of this study constituted a survival strategy and not a mechanism for continued plant growth. The presented MM-MF model allowed to analyze catchment water dynamics and water balance in detail, accounting separately for impacts of evaporation and transpiration processes on groundwater resources. With its unique capability of partitioning and sourcing of ETss, the MM-MF model is particularly suitable for mapping groundwater dependent ecosystems, but also for analyzing impacts of climate and land cover changes on groundwater resources.