Two subwatersheds located in Skaneateles Lake Watershed (SLW), New York, were monitored to evaluate the effectiveness of agricultural best management practices (BMPs) on surface water quality impacts associated with agricultural activities. Nonpoint source (NPS) transport of nutrients, sediment, and pathogens is a major concern in this area. This study seeks to quantify the effects of BMPs implementation on water quality by assessing the subsequent concentration of sediment and nutrients. In its initial stages, we synthesize watershed and the associated water quality data to determine relationships between hydrologic, weather and water quality parameters that have significant influence on stream water characteristics. Each sub-watershed was instrumented with an ISCO automated sampler near the outlet for downstream sampling and at the transition between forested land and agricultural land use. This instrumentation allowed collection of flow triggered samples that represented storm events and low flow from May 2007 through November 2007. Snow melt samples were collected as manual grab samples during March 2007 and April 2007 and sediment and nutrient concentrations were measured. Further, this study performs comprehensive modeling analyses, using the Annualized Agricultural Non-Point Source (AnnAGNPS) model to determine how impact of BMPs implementation on sediment and nutrient loadings from the various subwatersheds in the SLW. This paper presents our assessment and comparison of BMP impacts on paired watersheds for sediments and nutrient concentrations and loadings for 2007.