Significant landscape level changes have occurred in Indiana since European settlement, there are no scientific accounts of the ecological conditions that may have occurred across Indiana landscapes prior to this period. Clearing forests, draining wetlands, and altering headwater streams have facilitated the grown of agricultural productivity; it has also compromised stream ecosystems. Excessive loss of nutrients and soil from upland areas decreases agricultural sustainability as it relates to soil heath and water quality. Water quality issues associated with agricultural land use are scientifically quantifiable however it is difficult to prescribe solutions for nonpoint source pollutants that are realistic at a spatial scale necessary to detect an improvement in stream ecosystem integrity. This research examines the efficacy of best management practices, through a paired-watershed approach, by evaluating two adjacent subwatersheds and the response of chemical, physical, and biological parameters as they relate to the reduction in movement of nonpoint source pollution. Each experimental watershed is a subwatershed (HUC 12) of the Middle Eel River Watershed 9HUC 10), waterways flow into the Eel River of northern Indiana and each watershed is less than 3,000 acres. Automatic water samples, pressure transducers, and data loggers were placed at the headwaters and confluence of Beargrass Creek and at the headwaters of Paw Paw Creck for purposes of this study. An ecological and water quality baseline assessment was developed in 2012, prior to the implementation of best management practices (BMPs). This project will be evaluating the chemical and biological changes that occurred throughout 2013 and 2014 in two adjacent subwatersheds in rural Indiana. Overall the goal of the project is to determine the long-term effects of agricultural best management practices on the chemical, physical and biological parameters of warmwater streams.