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The hydrologic nonstationarity and uncertainty associated with climate change requires new decision-making methods to incorporate climate change impacts into flood frequency and flood risk analyses. To aid decision-making under climate change, we developed a bottom-up approach for assessing the performance of flood management systems under climate uncertainty and nonstationarity. The developed bottom-up approach was applied to the American River, CA, USA flood management system by first identifying the sensitivity and vulnerability of the system to different climates. To do this, we developed a climate response surface by calculating and plotting Expected Annual Damages (EAD, $/year) under different flood regimes. Next, we determined a range of plausible future climate change and flood frequency scenarios by applying Bayesian statistical methods to projected future flows derived from a Variable Infiltration Capacity (VIC) model forced with Global Circulation Model (GCM) output. We measured system robustness as the portion of plausible future scenarios under which the current flood system could meet its performance goal. Using this approach, we then evaluated the robustness of four proposed management strategies in the 2012 Central Valley Flood Protection Plan in terms of both flood risk and cost-effectiveness, to assess the performance of the strategies in the face of climate risks. Results indicated that the high sensitivity of the expected damages to changes in flood regimes makes the system extremely vulnerable to a large portion of the plausible range of future flood conditions. The management strategy that includes a combination of nature-based flood management actions along with engineered structures yields the greatest potential to increase system robustness in terms of maintaining EAD below an acceptable risk threshold. However, this strategy still leaves the system vulnerable to a wide range of plausible future conditions. As flood frequency regimes increase in intensity from the current conditions, the cost-effectiveness of the management strategies increases, to a point, before decreasing. This bottom up analysis demonstrated a viable decision-making approach for water managers in the face of uncertain and changing future conditions. Neglecting to use such an approach and omitting climate considerations from water resource planning could lead to strategies that do not perform as expected or which actually lead to mal-adaptations, increasing vulnerability to climate change.