Coastal wetlands play an important role in the global water and biogeochemical cycles. Climate change makes it more difficult for these ecosystems to adapt to the fluctuation in sea levels and other environmental changes. Given the importance of eco-geomorphological processes for coastal wetland resilience, many eco-geomorphology models differing in complexity and numerical schemes have been developed in recent decades. However, their divergent estimates of the response of coastal wetlands to climate change indicate that substantial structural uncertainties exist in these models. To investigate the structural uncertainty of coastal wetland eco-geomorphology models, we developed a multi-algorithm model framework of eco-geomorphological processes, such as mineral accretion and organic matter accretion, within a single hydrodynamics model. The framework is designed to explore possible ways to represent coastal wetland eco-geomorphology in Earth system models and reduce the related uncertainties in global applications. We tested this model framework at three representative coastal wetland sites: two saltmarsh wetlands (Venice Lagoon and Plum Island Estuary) and a mangrove wetland (Hunter Estuary). Through the model–data comparison, we showed the importance of using a multi-algorithm ensemble approach for more robust predictions of the evolution of coastal wetlands. We also found that more observations of mineral and organic matter accretion at different elevations of coastal wetlands and evaluation of the coastal wetland models at different sites in diverse environments can help reduce the model uncertainty.