Model-based predictions of the impact of land management practices on nutrient loading require measured nutrient flux data for model calibration and evaluation. Consequently, uncertainties in the monitoring data resulting from sample collection and load estimation methods influence the calibration, and thus, the parameter settings that affect the modeling results. To investigate this influence, we compared three different time-based sampling strategies and four different load estimation methods for model calibration and compared the results. For our study, we used the river basin model Soil and Water Assessment Tool on the intensively managed loess-dominated Parthe watershed (315 km(2)) in Central Germany. The results show that nitrate-N load estimations differ considerably depending on sampling strategy, load estimation method, and period of interest. Within our study period, the annual nitrate-N load estimation values for the daily composite data set have the lowest ranges (between 9.8% and 15.7% maximum deviations related to the mean value of all applied methods). By contrast, annual estimation results for the submonthly and the monthly data set vary in greater ranges (between 24.9% and 67.7%). To show differences between the sampling strategies, we calculated the percentage deviation of mean load estimations of submonthly and monthly data sets as related to the mean estimation value of the composite data set. For nitrate-N, the maximum deviation is 64.5% for the submonthly data set in the year 2000. We used average monthly nitrate-N loads of the daily composite data set to calibrate the model to achieve satisfactory simulation results [Nash-Sutcliffe efficiency (NSE) 0.52]. Using the same parameter settings with submonthly and monthly data set, the NSE dropped to 0.42 and 0.31, respectively. Considering the different results from the monitoring strategy and the load estimation method, we recommend both the implementation of optimized monitoring programs and the use of multiple load estimation methods to improve water quality characterization and provide appropriate model calibration and evaluation data.