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We conducted a study on water management at the Boise River Watershed in a changing global environment potentially induced by climate variability and urbanization. Environmental ‘hotspots’ associated with water quality and quantity were first identified to select suitable management options, such as Low Impact Development (LID is commonly used for urban storm water management to reduce impacts induced by flash flood in urban environment while improving water quality standard by filtering non-point source pollutants from predominant, impervious land segments in urban settings.) and Best Management Practices (BMPs) for urban and rural land segments, respectively. A decision-making process was employed to evaluate the cost-effectiveness for each management option based on multiple criteria, including water quality, financial challenges, and other environmental concerns. The results show that LID/BMPs were useful to control water quality in the watershed. The effectiveness of LID/BMPs implementation was subject to change with the placement location and consideration objectives associated with economic or environmental aspects. It appears that about 10% of the study area is required to implement water management options (LID/BMP) to improve water quality potentially driven by climate variability and urbanization. We anticipate that this study will make a case toward developing a sustainable water management plan in a changing global environment, especially for the urban–rural interface settings. Full article