The article focuses on modelling surface runoff in a small river basin taking into consideration climate change projections. The runoff was modelled using the Soil and Water Assessment Tool (SWAT), while three Representative Concentration Pathways (RCP2.6, RCP4.5, and RCP8.5) were considered for modelling the future climate. Despite the identified uncertainties, all the scenarios pointed towards decreasing runoff and losing available water resources. The expected runoff of the case study basin (Bălţata River in the Republic of Moldova) will decrease under all considered scenarios. The risk of diminishing runoff will be low in the middle-term perspective and moderate in the long-term one, if considered from the yearly changes. However, there are months with a high risk of diminishing runoff, especially important for proper crop production. While in the middle-term perspective, traditional adaptation measures can be used, in the long-term one, a totally new approach should be sought.