In the face of future climate change, Europe has encouraged the adoption of biofuel crops by its farmers. Such land-use changes can have significant impacts on the water balance and hydrological behavior of a system. While the heavy pesticide use associated with biofuel crops has been extensively studied, the water balance impacts of these crops have been far less studied. We conducted scenario analyses using the Soil and Water Assessment Tool (SWAT) to determine the effects of farm-scale biofuel crop adoption (rapeseed) on a basin’s water balance. We found that rapeseed adoption does not support the goal of developing a sustainable agricultural landscape in the Czech Republic. The adoption of rapeseed also had disproportionate effects on a basin’s water balance depending on its location in the basin. Additionally, discharge (especially surface runoff ratios), evapotranspiration, and available soil water content display significant shifts in the rapeseed adoption scenarios.