Identifying what, when, and how much adaptation is needed to account for increased pluvial flood risk is inherently uncertain. This presents a challenge to decision makers when trying to identify robust measures. This paper presents an integrated uncertainty analysis to quantify not only the overall uncertainty of individual adaptation scenarios, but also the net uncertainty between adaptation alternatives for a direct comparison of their efficiency. Further, a sensitivity analysis is used to assess the relative contribution of inherent uncertainties in the assessment. A Danish case study shows that the uncertainties in relation to assessing the present hazards and vulnerabilities (e.g., input runoff volume, threshold for damage, and costing of floods) are important to the overall uncertainty, thus contributing substantially to the overall uncertainty in relation to decisions on action or in-action. Once a decision of action has been taken, the uncertainty of the hazards under the current climate, and also the magnitude of future climate change, are less important than other uncertainties such as discount rate and the cost of implementing the adaptation measures. The proposed methodology is an important tool for achieving an explicit uncertainty description of climate adaptation strategies and provides a guide for further efforts (e.g., field data collection) to improve decision-making in relation to climate change.