For decades, water shortages, unreliable water supplies, poor water quality, and flooding disaster have been considered as major obstacles to sustainable water resources development at the watershed scale. These have led to a variety of adverse impacts on the social-economic development and human life. One of the major reasons for the raised issues is the lack of efficient, equitable and sustainable water resources management as well as effective policy instructions from decision-makers. Issues of water resources management are highly complicated, involving a large number of social, economic, environmental, technical, and political factors, coupled with complex spatial variability and cascading effect. At the same time, a water resources system comprises plenty of interactive parts, such as rivers, streams, lakes, groundwater regimes, reservoirs, dams and bifurcations, as well as cities, towns, and water users. Climate change and human activity could affect the systems at a regional scale and lead to more significant spatial and temporal variations of water resources in the basin and thus the associated environmental and ecological conditions. There are many potential risks existing in water-related activities within a multi-user, multi-region and multireservoir context, such as water resources allocation, flooding prevention and control, environmental and ecological protection, and sustainable development. Such complexities have forced planners to contemplate and propose ever more comprehensive, complex and ambitious plans for water resources systems. Decisions pertaining to water resources management must be based on an in-depth understanding of vulnerabilities and risks. Therefore, it is desired that vulnerability and risk of the related water users to such variations be well assessed, in order to provide bases for effective water resources management and planning. This special issue is devoted to the latest research results of emerging technologies for initiate extensive discussions in terms of methodologies and case studies of risk analysis and management for water resources systems. A broad range of topics associated with modeling and experimental studies were selected to present, including pollution investigation and prediction, modelling formulation, flood risk assessment, water resources allocation, and wastewater recycle and reuse. This issue includes three papers on pollution investigation and prediction. Generally, water pollution is a widespread and challenging issue for water supply to both developed countries and developing countries. Topics about risk analysis of arsenic groundwater in Bangladesh, non-point source (NPS) pollution load estimation in Three Gorges Reservoir of China and improved dissolved-oxygen (DO) prediction of Bow River in Calgary (of Canada) are discussed, respectively. To begin with, Khan et al. propose a non-linear fuzzyset based methodology to characterize and propagate uncertainty through a multiple linear regression (MLR) model to predict DO using flow and water temperature as the regressors in Bow River in the City of Calgary, Canada. To reflect uncertainty and variability existing in the input data, in their study, the output is depicted as probabilistic Y. P. Li MOE Key Laboratory of Regional Energy Systems Optimization, S-C Resources and Environmental Research Academy, North China Electric Power University, Beijing 102206, China e-mail: yongping.li@iseis.org