Applications of the SWAT model typically involve delineation of a watershed into subwatersheds/subbasins that are then further subdivided into hydrologic response units (HRUs) which are homogeneous areas of aggregated soil, landuse, and slope and are the smallest modeling units used within the tool. In a standard SWAT application, multiple potential HRUs (farm fields) in a subbasin are usually aggregated into a single HRU feature. In other words, the standard version of the model combines multiple potential HRUs (farm fields) with the same landuse/landcover (LULC), soil, and slope, but located in different places within a subbasin (spatially non-unique), and considers them as one HRU. In this study, ArcGIS pre-processing procedures were developed to spatially define a one-to-one match between farm fields and HRUs (spatially unique HRUs) within a subbasin prior to SWAT simulations to facilitate input processing, input/output mapping, and further analysis at the individual farm field level. Model input data such as LULC, soil, crop rotation and other management data were processed through these HRUs. The SWAT model was then calibrated/validated for the Raccoon River watershed in Iowa for 2002 to 2010 and the Big Creek River watershed in Illinois for 2000 to 2003. SWAT was able to replicate annual, monthly and daily streamflow, as well as sediment, nitrate and mineral phosphorous within recommended accuracy in most cases. The one-to-one match between farm fields and HRUs created and used in this study is a first step in performing LULC change, climate change impact, and other analyses in a more spatially explicit manner. The calibrated and validated SWAT model was then used to assess agricultural scenario and climate change impacts on watershed water quantity, quality, and crop yields. Modeling impacts of agricultural scenarios and climate change on surface water quantity and quality provides useful information for planning effective water, environmental, and land use policies. Despite the significant impacts of agriculture on water quantity and quality, limited literature exists modeling the combined impacts of agricultural scenarios and climate change on crop yields and watershed hydrology. Here, SWAT, was used to model the combined impacts of five agricultural scenarios and three climate scenarios downscaled using eight climate models. These scenarios were implemented in a well calibrated SWAT model for the Raccoon River watershed (RRW), IA. We run the scenarios for the historical baseline, early-century, mid-century, and late-century periods. Results indicate that historical and more corn intensive agricultural scenarios with higher CO2 emissions consistently result in more water in the streams and greater water quality problems, especially late in the 21st century. Planting more switchgrass, on the other hand, results in less water in the streams and water quality improvements relative to the baseline. For all given agricultural landscapes simulated, all flow, sediment and nutrient outputs increase from early-to-late century periods for the RCP4.5 and RCP8.5 climate scenarios. We also find that corn and switchgrass yields are negatively impacted under RCP4.5 and RCP8.5 scenarios in the mid and late 21st century. Finally, various agricultural best management practice (BMP) scenarios were evaluated for their efficiency in alleviating watershed water quality problems. The vast majority of the literature on efficiency assessment of BMPs in alleviating water quality problems base their scenarios analysis on identifying subbasin level simulation results. In the this study, we used spatially explicit HRUs, defined using ArcGIS-based pre-processing methodology, to identify Nitrate (NO3) and Total Suspended Solids (TSS) hotspots at the HRU/field level, and evaluate the efficiency of selected BMPs in a large watershed, RRW, using the SWAT model. Accordingly, analysis of fourteen management scenarios were performed based on systematic combinations of five agricultural BMPs (fertilizer/manure management, changing cropland to perennial grass, vegetative filter strips, cover crops and shallower tile drainage systems) aimed to reduce NO3 and TSS yields from targeted hotspot areas in the watershed at field level. Moreover, implications of climate change on management practices, and impacts of management practices on water availability and crop yield and total production were assessed. Results indicated that either implementation of multiple BMPs or conversion of an extensive area into perennial grass may be required to sufficiently reduce nitrate loads to meet the drinking water standard. Moreover, climate change may undermine the effectiveness of management practices, especially late in the 21 st century. The targeted approach used in this study resulted in slight decreases in watershed average crop yields, hence the reduction in total crop production is mainly due to conversion of croplands to perennial grass.