Poplar plantations are used for biomass production in many countries. These plantations are often located in areas where the tree roots can reach the water table of shallow aquifers to reduce irrigation costs and increase evapotranspiration, mainly during the summer. This study aims to assess the effects of these plantations on an aquifer water budget and on the stream flow of a Mediterranean basin (Santa Coloma River, 321.3km2 NE Spain). A numerical flow model was constructed to simulate shallow aquifers and to simulate the stream–aquifer interaction for a period of 9years. Once the model was calibrated, different land use scenarios, such as deciduous forests, dry farming and irrigated farming, were simulated for comparison. The mass balance shows that poplar extracts an average of 2.40hm3 from the aquifer, i.e., approximately 18% of the average recharge of the modelled area. This effect reduces the groundwater flow to the main stream and increases the infiltration from the stream to the aquifer. As a result, there is an average reduction in the main stream flow by 46% during the summer, when the lowest flow occurs and when the river is most sensitive. The results indicate that these impacts should be considered in basin management plans and in evaluating the benefits of this type of biomass production.