<p>Wing dams, used in rivers like the Mississippi and Danube, improve navigation by increasing water depth during low flow. Their hydromorphological effects are complex, and their influence on flood risk remains debated. Here we developed an approach that identifies local physical patterns from detailed numerical calculations, enabling extension to larger river sections and longer time scales previously difficult to study. We apply this numerical method to assess wing dam impacts on water and bed levels over decades to centuries. Our results show that rivers with bed materials prone to armouring tend to experience long-term water level increases due to wing dams, while others may see decreases. Adjustments to new stable conditions take decades, with temporary water level rises even in uniform beds. For the Mississippi River, wing dams likely caused initial water level increases, but effects declined over time, indicating evolving riverbed responses. These findings help design flood risk–optimal wing dam configurations.</p>