Headwater streams are important lotic systems that represent more than 80% of the total stream lengths in watersheds. The dynamic coupling of hydrological and biogeochemical processes in headwaters is responsible for regulating the chemical form, residence time and longitudinal transport of nutrients. Over time, stream modification (e.g. to enhance drainage in agricultural watershed) has altered natural stream flow-paths and thus, stream functionality. Such alteration has resulted in degradation of habitat and water quality, both in upland and downstream waters. Currently, nutrients exported from the Grand River (Ontario) watershed are contributing to eutrophication and Harmful Algal Blooms in Lake Erie. With respect to the Grand River watershed, this thesis examined (1) the impact of agriculture on the existing stream network, (2) the utility of the Soil and Water Assessment Tool to simulate hydrology, sediment and nutrient export that closely correlate with measured data, and (3) the application of Best Management Practices in the watershed with the intent of meeting provincial and transnational nutrient targets. The results showed that compared to the actual ground-truthed stream network, the predicted stream network based on topography underpredicted a total of 2,535 km of actual channel present in the watershed. Channels not anticipated by topography were mostly first-order, with low sinuosity, and were most common in areas with high agricultural land use, and are likely excavated extensions to headwater streams to facilitate drainage. Then, the sediment and nutrient loading at Dunnville, discharging to entering Lake Erie, was predicted to be 2.3[superscript⁻1] 105 t yr[superscript-1] of total suspended sediment, 7.9 [superscript⁻1] 103 t yr-1 of total nitrogen, and 2.5 ⁻1 102 t yr-1 of total phosphorus. Finally, implementing wide buffer strips, stabilizing channel banks and grassed waterways were found to be the most effective practices for reducing sediment and phosphorus loading into Lake Erie.