Stream flow, as a part of a basin hydrological cycle, will be sensible to water scarcity as a result of climate change. Stream vulnerability should then be evaluated as a key component of the basin water budget. Numerical flow modeling has been applied to an alluvial formation in a small mountain basin to evaluate the stream-aquifer relationship under these future scenarios. The Arbucies River basin (116 km(2)) is located in the Catalan Inner Basins (NE Spain) and its lower reach, which is related to an alluvial aquifer, usually becomes dry during the summer period. This study seeks to determine the origin of such discharge losses whether from natural stream leakage and/or induced capture due to groundwater withdrawal. Our goal is also investigating how discharge variations from the basin headwaters, representing potential effects of climate change, may affect stream flow, aquifer recharge, and finally environmental preservation and human supply. A numerical flow model of the alluvial aquifer, based on MODFLOW and especially in the STREAM routine, reproduced the flow system after the usual calibration. Results indicate that, in the average, stream flow provides more than 50% of the water inputs to the alluvial aquifer, being responsible for the amount of stored water resources and for satisfying groundwater exploitation for human needs. Detailed simulations using daily time-steps permit setting threshold values for the stream flow entering at the beginning of the studied area so surface discharge is maintained along the whole watercourse and ecological flow requirements are satisfied as well. The effects of predicted rainfall and temperature variations on the Arbucies River alluvial aquifer water balance are also discussed from the outcomes of the simulations. Finally, model results indicate the relevance of headwater discharge management under future climate scenarios to preserve downstream hydrological processes. They also point out that small mountain basins could be self-sufficient units so long as the response of the main hydrological components to external forces that produce water scarcity, as climate change or human pressures, is appropriately considered in water resource planning. (C) 2012 Elsevier B.V. All rights reserved.