Irrigation discharge is a relevant water resource for lake ecosystems in arid and semi-arid regions. However, high concentrations of nitrogen and phosphorus in the irrigation discharge raise concerns over potential lake eutrophication in these regions. A Delft3D hydrodynamic-water quality model was used to explore the effects of multiple water sources on water quality of a large shollow lake in the semi-arid west of Northeast China, which is surrounded by irrigated rice paddies. Eighteen scenarios in a combination of different precipitation rates, irrigation discharge operations, and flow conditions were simulated to analyze time and water allocation required in order to achieve nutrient standards of total nitrogen (TN) ≤ 1.5 mg/L and total phosphorus (TP) ≤ 0.1 mg/L. The results showed that time required for the optimal combination to achieve nutrient management objectives displayed an increasing trend from the east to west. In the best control scenario where the irrigation discharge was regulated into the lake, TN and TP concentrations could be reduced by 60% and 70%, respectively. Water diversion from a freshwater reservoir can effectively improve lake water quality even though sediment nutrient resuspension could occur in the eastern region of lake. The findings suggest that using multi-source water supplies can attain nutrient management objectives in order to reduce eutrophication risk for a lake that receives nutrient-rich irrigation discharge. The study also demonstrates the great usefulness of hydrodynamic-water quality modeling for assessing water resource allocation and science-based decision making in intensive agriculture practices.