Many communities along urban rivers are trying to reduce future flood risk while also dealing with old infrastructure and limited space to expand. In this study, we look at San Francisquito Creek in California to understand how changes like updating bridges could affect flooding, especially as the climate changes. We used a modeling approach to simulate thousands of possible future flood scenarios, comparing today’s river system with a version that includes planned infrastructure updates. These scenarios also account for increases in river flow and sea level rise. Our results show that looking at only one design past flood when planning infrastructure changes can miss important risks. Changes that reduce the overall flood risk might actually increase it in specific areas. We found that the planned infrastructure updates are the biggest driver of changes in where it floods, rather than sea level rise or higher river flow. Increased river flow, rather than sea level rise, caused the biggest increase in flood risk. This means that focusing only on sea level rise could leave communities unprepared for future flooding. Overall, our study shows that it is important to consider a wide range of possible future conditions when planning for future flood protection.