Baseflow is a major transport pathway for non-point source (NPS) pollutants. Watershed water quality (WWQ) models calibrated by low-quality data may produce misleading predictions of baseflow NPS pollutant loads, resulting in poor management decisions. We evaluated how models of the baseflow nitrate loads in the Huron River basin, southwest of Lake Erie, were affected by uncertainty in the calibration data. Based on a five-year time series of daily streamflow, nitrate concentration, and specific conductance, two sets of “observed” baseflow nitrate load data that include uncertainty were estimated using various tracer-based and non-tracer-based hydrograph separation methods, in conjunction with assumptions regarding baseflow nitrate concentrations. We calibrated the Soil and Water Assessment Tool plus (SWAT+) model with the two “observed” data sets and used the Generalized Likelihood Uncertainty Estimation (GLUE) approach to quantify parameter and predictive uncertainties. The results showed that baseflow accounted for 26 %–34 % of the mean annual total streamflow (11.8 m3/s) and 8 %–37 % of the mean annual total nitrate load (14.3 kg·ha−1·year−1) in the Huron River basin. The baseflow and nitrate load estimates from the non-tracer-based methods resembled those from the tracer-based method but had greater uncertainty. The posterior parameter distributions, as well as the weighted means and 90 % prediction intervals of the simulated baseflow nitrate loads, exhibited minimal variation when different calibration data sets for SWAT+ and different threshold likelihood values for GLUE were used. Our analysis emphasizes the necessity of calibrating WWQ models with baseflow pollutant loads/concentrations when addressing water quality issues related to baseflow. It also demonstrates the feasibility of utilizing multiple non-tracer-based hydrograph separation methods to estimate baseflow NPS pollutant loads. These non-tracer-based methods offer a simplicity and broader applicability compared to tracer-based methods. This study has provided insights into how calibration data uncertainty impacts the modeling of NPS pollution in baseflow and highlights the practical value of non-tracer-based hydrograph separation methods.