Here, the Corn Belt states are the largest corn-production areas in the United States because of their fertile land and ideal climate. This attribute is particularly important as the region also plays a key role in the production of bioenergy feedstock. In much of the nation, agricultural nutrients are a primary cause of water quality degradation. This study focuses on potential change in streamflow, sediment, nitrogen, and phosphorus due to climate change and land management practices in the South Fork Iowa River (SFIR) watershed, Iowa. Thirty-six projections from select Regional Climate Models (RCM) for Representative Concentration Pathways (RCP) 2.5, 4.5, and 8.5 were used to develop climate change scenarios for the SFIR watershed and incorporated into the Soil and Water Assessment Tool (SWAT). The watershed is covered primarily with annual crops (corn and soybeans). Three scenarios of land use change and conservation practices were further developed to examine their impacts on water quality under historical and modeled future climate. With cropland conversion to switchgrass, stover harvest, and best management practices (BMPs) (such as establishing riparian buffers and applying cover crops) significant reductions in nutrients were observed in the SFIR watershed under historical climate and future climate scenarios. Under historical climate, suspended sediment (SS), total nitrogen (N), and phosphorus (P) at the outlet point of the SFIR watershed could decrease by up to 56.7%, 32.0%, and 16.5%, respectively, compare with current land use when a portion of the cropland is converted to switchgrass and cover crop is in place. Climate change could cause an increase in 12.0% (SS), 4.7% (N), and 7.7% (P) from current land use. This increase could be mitigated through land management and practices by 53.6% (SS), 27.8 (N), and 7.0% (P). Climate change reduced crop yield. Nutrient and sediments loadings distributed heterogeneously across the watershed. Water footprint analysis further revealed changes in green water that are highly dependent on land management scenarios. The study highlights the versatile approaches in landscape management that are available to address climate change adaptation and acknowledged the complex nature of different perspectives in water sustainability. Further study involving implementing landscape design and management using long-term field to watershed water monitoring data is necessary to verify the findings and moving towards watershed specific regional programs for climate adaptation.