Sea level rise and uncertainty in its projections pose a major challenge to flood risk management and adaptation investments in coastal mega cities. This study presents a comparative economic evaluation method for flood adaptation measures, which couples a cost–benefit analysis with the concept of adaptation pathways. Our approach accounts for uncertainty in sea level rise projections by allowing for flexibility of adaptation strategies over time. Our method is illustrated for Los Angeles County which is vulnerable to flooding and sea level rise. Results for different sea level rise scenarios show that applying adaptation pathways can result in higher economic efficiency (up to 10%) than individual adaptation strategies, despite the loss of efficiency of the initial strategy. However, we identified ‘investment tipping points’ after which a transition could decrease the economic efficiencies of a pathway significantly. Overall, we recommend that studies evaluating adaptation strategies should integrate cost–benefit analysis frameworks with adaptation pathways since this allows for better informing decision makers about the robustness and economic desirability of their investment choices.