Many water quality models have been successfully used worldwide to predict nutrient losses from anthropogenically impacted catchments, but hydrological and nutrient simulations with limited data are difficult considering the transfer of model parameters and complication of model calibration and validation. This study aims: (i) to assess the performance capabilities of a new and relatively more advantageous model, namely, Hydrological Predictions for the Environment (HYPE), that simulates stream flow and nutrient load in agricultural areas by using a multi-site and multi-objective parameter calibration method and (ii) to investigate the temporal and spatial variations of total nitrogen (TN) and total phosphorous (TP) concentrations and loads with crop rotation by using the model for the first time. A parameter estimation tool (PEST) was used to calibrate parameters. Results show that the parameters related to the effective soil porosity were highly sensitive to hydrological modeling. N balance was largely controlled by soil denitrification processes. P balance was influenced by the sedimentation rate and production/decay of P in rivers and lakes. The model reproduced the temporal and spatial variations of discharge and TN/TP relatively well in both calibration (2006–2008) and validation (2009–2010) periods. Among the obtained data, the lowest Nash-Suttclife efficiency of discharge, daily TN load, and daily TP load were 0.74, 0.51, and 0.54, respectively. The seasonal variations of daily TN concentrations in the entire simulation period were insufficient, indicated that crop rotation changed the timing and amount of N output. Monthly TN and TP simulation yields revealed that nutrient outputs were abundant in summer in terms of the corresponding discharge. The area-weighted TN and TP load annual yields in five years showed that nutrient loads were extremely high along Hong and Ru rivers, especially in agricultural lands.
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