The designs of stream channel naturalization, rehabilitation, and restoration projects are inherently fraught with uncertainty. Although a systematic approach to design can be described, the likelihood of success or failure of the design is unknown due to uncertainties within the design and implementation process. In this paper, a method for incorporating uncertainty in decision‐making during the design phase is presented that uses a decision analysis method known as Failure Modes and Effects Analysis (FMEA). The approach is applied to a channel rehabilitation project in north‐central Pennsylvania. FMEA considers risk in terms of the likelihood of a component failure, the consequences of failure, and the level of difficulty required to detect failure. Ratings developed as part of the FMEA can provide justification for decision making in determining design components that require particular attention to prevent failure of the project and the appropriate compensating actions to be taken.