The spatially explicit and mechanistic model TREEGRASS was used to test the effects of tree density, tree spatial distribution, and tree size distribution on radiation absorption, net primary production (NPP), and water fluxes for a West African savanna. The model has previously been shown to adequately predict radiation absorption, production, and soil water balance in humid savannas. Using field measurements quantifying the spatial variations in grass NPP the model was found to predict correctly the effect of tree abundance on grass NPR Model simulations showed that annual photosynthetically active radiation (PAR), absorption efficiency, NPP, and transpiration of the tree layer increased with increasing tree density and decreased with increasing tree aggregation; the grass layer showed the opposite trends. Total NPP (tree plus grass) remained stable for all tree densities and decreased slightly for aggregated tree distributions. Total transpiration, increased with tree density and was not affected by tree aggregation. Changing the tree size distribution had no effect on radiation absorption or on carbon and water fluxes. This study showed that fine-scale vegetation structure can influence NPP and water fluxes. As such, it should be taken into account when assessing the functioning of treegrass systems. However, the detailed fine-scale structure of the tree layer is rarely available for savanna ecosystems. Thus we assessed the reliability of two common descriptors of savanna vegetation, leaf area index (LAI) and tree canopy cover, to predict PAR absorption, NPP, and evapotranspiration. Neither of these descriptors could adequately predict all the simulated effects. However, tree canopy cover can be used to reasonably estimate radiation absorption and carbon fluxes, whereas LAI is a good predictor of water fluxes. Therefore, mapping and monitoring approaches incorporating both LAI and tree canopy cover appear to be suitable alternatives to quantifying the fine-scale vegetation spatial structure when assessing ecosystem function in savanna-like ecosystems.