In this study, we employ the Soil and Water Assessment Tool (SWAT), to simulate the hydrological cycle in the Napanee River and Wilton Creek watersheds located in the Bay of Quinte Area of Concern. The geomorphological attributes of the two sites presented challenges in successfully reproducing the observed streamflow with a conceptual model, like SWAT. After adjusting the model inputs and revising the boundary conditions, SWAT performance for the Napanee River model was found to be “very good” within both calibration (Nash-Sutcliffe efficiency, NSE, =0.83 and NSE = 0.87 for the daily and monthly streamflow rates, respectively) and validation (NSE = 0.87 and NSE = 0.91) domains. In contrast, despite the small size of Wilton Creek (∼233 km2) and the lack of permanent or human-regulated dams, the observed streamflow patterns displayed considerably delayed response to extreme precipitation events which posed challenges in achieving satisfactory model performance. Field evidence suggests that model residual variability is driven by excessive surface storage of water, the presence of beaver dams and narrowing of the stream channels under the bridges, which could potentially delay the flow of water for many days. After delineating the areas of flooding and treating them as reservoirs in Wilton Creek, we were able to overcome the modelling challenges with minor modifications in the original SWAT configuration and achieve satisfactory fit for both the calibration (NSE = 0.55 and NSE = 0.73) and validation (NSE = 0.59 and NSE = 0.76) periods. Our study suggests that the reservoirs play a significant role in buffering the impact of extreme flow conditions, especially during the spring freshet