Nutrient imbalance in groundwater and surface water resources can have severe implications on human and aquatic life, including contamination of drinking water sources and the degradation of ecosystems. A field-based watershed-scale study was completed to investigate nutrient dynamics and hydrologic processes in an agriculturally-dominant clay plain system within the Great Lakes Basin. Spatial and temporal variations of nitrogen and phosphorus were examined by sampling groundwater and surface water regularly over a period of one year (June 2017 to July 2018) for nutrients including nitrate, soluble reactive phosphorus, total dissolved phosphorus and total reactive phosphorus. Nitrate transport from surrounding agricultural land to surface water was intensified with an increase in precipitation events in spring and early winter and phosphorus transport to surface water was increased during freeze-thaw cycles in the winter. The results are pertinent to the improvement of current nutrient and water management policies in clay plain systems where nutrient imbalances in surface water are a concern.