The physical surface of the Earth is in constant change due to climate forcing and human activities. In the Midwestern United States, urban area, farmland, and dedicated energy crop (e.g., switchgrass) cultivation are predicted to expand in the coming decades, which will lead to changes in hydrological processes. This study is designed to (1) project the land use and land cover (LULC) by mid-century using the FORecasting SCEnarios of future land-use (FORE-SCE) model under the A1B greenhouse gas emission scenario (future condition) and (2) assess its potential impacts on the water cycle and water quality against the 2001 baseline condition in the Cedar River Basin using the physically based soil and water assessment tool (SWAT). We compared the baseline LULC (National Land Cover data 2001) and 2050 projection, indicating substantial expansions of urban area and pastureland (including the cultivation of bioenergy crops) and a decrease in rangeland. We then used the above two LULC maps as the input data to drive the SWAT model, keeping other input data (e.g., climate) unchanged to isolate the LULC change impacts. The modeling results indicate that quick-response surface runoff would increase significantly (about 10.5%) due to the projected urban expansion (i.e., increase in impervious areas), and the baseflow would decrease substantially (about 7.3%) because of the reduced infiltration. Although the net effect may cause an increase in water yield, the increased variability may impede its use for public supply. Additionally, the cultivation of bioenergy crops such as switchgrass in the newly added pasture lands may further reduce the soil water content and lead to an increase in nitrogen loading (about 2.5% increase) due to intensified fertilizer application. These study results will be informative to decision makers for sustainable water resource management when facing LULC change and an increasing demand for biofuel production in this area.