Because of increased use of fertilizers to feed the increasing global population, the nutrient loads in surface and subsurface water have increased substantially in the last few decades. Many studies have been conducted to investigate the factors affecting nitrate load in surface and subsurface flow. The objective of this study is to investigate the relationship between the various factors affecting nitrate transport using principal component analysis (PCA) and nearest neighborhood analysis methods. Hydrological and biogeochemical data from a small (<500 km2) agricultural watershed in east central Illinois, USA for the duration of 10 years have been used in this study. The PCA approach divided various factors that influence nitrate transport into three principal components. The first component contained air temperature, cover phenotype, evapotranspiration, cover factor and dry mass factors. The second component contained precipitation and flow, which was defined as the hydrologic component. The third component included tillage practices and nitrogen application and was termed the anthropogenic component. The results from the PCA approach suggested all three components had significant influence on nitrate transportation and transformation. Among these three components, the hydrological components had the highest contribution on both surface and subsurface nitrate load. The nearest neighborhood analysis yielded a similar conclusion.