To improve the capabilities of conventional methodologies in facilitating industrial water allocation under uncertain conditions, an integrated approach was developed through the combination of operational research, uncertainty analysis, and violation risk analysis methods. The developed approach can (a) address complexities of industrial water resources management (IWRM) systems, (b) facilitate reflections of multiple uncertainties and risks of the system and incorporate them into a general optimization framework, and (c) manage robust actions for industrial productions in consideration of water supply capacity and wastewater discharging control. The developed method was then demonstrated in a water-stressed city (i.e., the City of Dalian), northeastern China. Three scenarios were proposed according to the city’s industrial plans. The results indicated that in the planning year of 2020 (a) the production of civilian-used steel ships and machine-made paper & paperboard would reduce significantly, (b) violation risk of chemical oxygen demand (COD) discharge under scenario 1 would be the most prominent, compared with those under scenarios 2 and 3, (c) the maximal total economic benefit under scenario 2 would be higher than the benefit under scenario 3, and (d) the production of rolling contact bearing, rail vehicles, and commercial vehicles would be promoted.