A river exhibits strong upstream erosion and rapid downstream accumulation. Dredging is one of the methods that is most commonly adopted by the Taiwan Water Resources Agency (WRA) to ensure the smooth flow of rivers and their ability to discharge water, protecting lives and property from flood disasters. However, dredging projects are large, involving very many stakeholders, leading to high uncertainty in the implementation of the project. The WRA also lacks relevant risk management methods and countermeasures owing to the periodical brain drain and retirement within the organisation. In order to enhance risk management for dredging engineers, river management offices across the country were visited, and knowledge and experience of dredging engineering were obtained using expert meetings and scientific methods. Work was carried out with the WRA to identify six major risk categories for dredging projects, covering 30 risks. An Analytic Hierarchy Process (AHP) questionnaire was developed using the Risk Breakdown Structure (RBS), and a Risk Impact/Frequency Analysis (RIFA) questionnaire was developed using the Important/Performance Analysis (IPA) method; these were answered by 69 engineers with experience in river dredging. Finally, critical risk factors are identified and ranked by combining the responses to the questionnaires and in the interviews, helping engineers with risk management in the future. Research results demonstrate that most of the engineering management experience in practice is communicated by word of mouth, with no effective and systematic method of knowledge management. Therefore, a knowledge‐based system is created, covering 170 risk events and solutions for various dredging projects, and a graphical user information system is built in a programming language, to enable the WRA to save engineering experience systematically for future exploitation.