The emerging eco-industrial parks are established in an attempt to use shared infrastructure efficiently in industrial communities, while the concentrated discharge of wastewater in eco-industrial parks causes great pressure on the water ecosystem. The modern environmental challenges require updated systematic approaches to assess the water risk in eco-industrial parks. This research established a comprehensive index evaluation system with Analytic Hierarchy Process (AHP) and fuzzy theory to evaluate the risk of the water ecosystem in eco-industrial parks. Geographic Information System is combined with pollutant diffusion model to analyze the risk status of water ecosystem and provide early warning of water pollution. The model is applied to a case of Shenzhen Eco-industrial Park. The result showed that the concentrations of TN, suspended solids and coliforms in Longgang River at the entrance to the eco-park were 11.71 mg/L, 29.01 mg/L and 8.65 x 10(4) CFU/L, respectively, which exceeded the 5th class of environmental quality standard for surface water. The concentration of coliforms at the exit of Chunzi River reached 15.5x10(4) CFU/L, reaching the inferior 5th class standard. The early warning result shows that the ecological hazards caused by the same amount of pollutants in the dry season present much higher risks than those in the wet season. Stringent pollutants discharge regulations in dry season are suggested to effectively manage water risks in eco-industrial parks. (C) 2019 Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.