Future climate change is projected to have significant impact on water resources availability and quality in many parts of the world. The objective of this paper is to assess the effect of projected climate change on water quantity and quality in two lowland catchments (the Upper Narew and the Barycz) in Poland in two future periods (near future: 2021–2050, and far future: 2071– 2100). The hydrological model SWAT was driven by climate forcing data from an ensemble of nine bias-corrected General Circulation Models—Regional Climate Models (GCM-RCM) runs based on the Coordinated Downscaling Experiment—European Domain (EURO-CORDEX). Hydrological response to climate warming and wetter conditions (particularly in winter and spring) in both catchments includes: lower snowmelt, increased percolation and baseflow and higher runoff. Seasonal differences in the response between catchments can be explained by their properties (e.g., different thermal conditions and soil permeability). Projections suggest only moderate increases in sediment loss, occurring mainly in summer and winter. A sharper increase is projected in both catchments for TN losses, especially in the Barycz catchment characterized by a more intensive agriculture. The signal of change in annual TP losses is blurred by climate model uncertainty in the Barycz catchment, whereas a weak and uncertain increase is projected in the Upper Narew catchment.