The Shihmen Reservoir, located in northern Taiwan, features the second storage volume of impoundments on the island. The watershed of the Shihmen Reservoir has been subjected to serious pollutants due to anthropogenic interference. This study applies a watershed model, BASINS, to simulate the flow and nutrients loads from the watershed. BASINS then drives the CE-QUAL-W2 model for water quality predictions in the reservoir. The watershed modelling results are compared with field data. They reveal that significant nutrient loads were generated from the watershed during storms. The model calibration and verification were achieved with water surface elevation, temperature, and water quality constituents including nutrients, dissolved oxygen, and chlorophyll a in the reservoir using the eutrophication model.