Compound flooding is generated when two or more flood drivers occur simultaneously or in close succession. Multiple drivers can amplify each other and lead to greater impacts than when they occur in isolation. A better understanding of the interdependence between flood drivers would facilitate a more accurate assessment of compound flood risk in coastal regions. This study employed the D-Flow Flexible Mesh model to simulate the historical peak coastal water level, consisting of the storm surge, astronomical tide, and relative sea level rise (RSLR), in Shanghai over the period 1961–2018. It then applies a copula-based methodology to calculate the joint probability of peak water level and rainfall during historical tropical cyclones (TCs) and to calculate the marginal contribution of each driver. The results indicate that the astronomical tide is the leading driver of peak water level, followed by the contribution of the storm surge. In the longer term, the RSLR has significantly amplified the peak water level. This study investigates the dependency of compound flood events in Shanghai on multiple drivers, which helps us to better understand compound floods and provides scientific references for flood risk management and for further studies. The framework developed in this study could be applied to other coastal cities that face the same constraint of unavailable water level records.