Water quality issues in the Great Lakes Basin persist despite management and monitoring efforts. With changing land use and climatic conditions, the need for improved understanding of nutrient loss from agricultural field to surface water is imperative to reduce consequences on human and aquatic life, such as perpetual algal blooms and contaminated drinking water. There remains a gap in holistic rural water management studies that investigate the understanding of the water cycle in rural settings and the interconnections between different components of the water cycle, including artificial drainage. In the current study, a year-round paired investigation of subsurface and nutrient dynamics was conducted in a small, intensively managed agricultural watershed within southwestern Ontario, Canada. Nutrients (Nitrate and Phosphorus) and stable isotopes of water (δ2H and δ18O) were sampled at varying scales (i.e., field and watershed), from multiple hydrologic components (e.g., groundwater, surface water, tile flow, and soil water), from 2020 to 2022. Results indicate that nutrient concentrations in surface water were elevated during the growing season, while nutrient loading was greater during the non-growing season in surface water. Monthly nitrate loads were found to be significantly (p < 0.01) related to groundwater elevation, soil moisture and tile flow, whereas total phosphorus loading was found to be significantly (p < 0.01) related to soil moisture and tile flow. δ2H and δ18O signatures revealed that during the growing season nutrient movement was predominantly through interflow pathways (including tile drainage) comprised of event-water. In the non-growing season, there was an increased subsurface influence on nutrient transport. This study highlights the importance of including subsurface characterization in nutrient management studies. A comprehensive understanding of varying seasonal hydrologic mechanisms that control nutrient movement within an agricultural watershed is essential to sustain growing rural communities.