Although the long-term geomorphic evolution of an estuarine tidal flat consequent to flow alteration and erosion has been widely documented, the short-term ecological responses of such ecosystems to multiple stressors remain poorly understood. We combined a mechanism-based ecomorphodynamic model with a hydrodynamic and sediment numerical model to examine the ecological response of an estuarine tidal flat ecosystem to different magnitudes of flow discharge and erosion conditions in the Yellow River Estuary (YRE) of China. The ecological benefits of flow discharge and erosion are reported in terms of the state of the tidal flat system: (1) a patterned state with high primary production and strong sediment stabilization; and (2) a homogeneous state with low primary production and severe erosion. We focused on the nonlinear flow-ecology relationship and identified the minimum threshold of flow discharge at which a patterned state occurs. Both flow discharge and erosion rates were shown to be important determinants of the state of the estuarine tidal flat ecosystem. We showed that a change in flow discharge altered the sediment deposition rate S in and induced a state transition of the tidal flat ecosystem. Erosion increased the minimum threshold value of flow discharge at which a patterned state occurred. Our model framework provides an insightful method with a strong mechanistic basis to determine thresholds of flow discharge at which ecological benefits change dramatically, thereby providing a tool to make decisions regarding flow allocation in estuarine tidal flat ecosystems that are suffering from degradation caused by restricted flow and sediment load.