Coastal backwaters are created by elevated sea levels that can cause upstream propagation of flood waves and the attenuation of the spatial and temporal water stage fluctuations. Such effects have crucial impacts on coastal and fluvial flooding but have not been well represented in large-scale river models used in Earth system models (ESMs), partly due to model mesh deficiency and oversimplifications of river hydrodynamics. Using two mid-Atlantic river basins as a testbed, we perform the first attempt to simulate the backwater effects over a coastal region using the river transport model under E3SM configured on a regionally refined unstructured mesh, with a focus on understanding the backwater drivers and their long-term variations. The model performance in capturing backwaters is greatly improved by including sea level variations at the river downstream boundary. The results show that the influence of extreme discharge cannot be neglected, particularly when the river drains to a narrow river-like estuary. The backwater effects show an increasing strength due to sea level rise and more frequent storm surges during the past 40 years and have to be properly represented in ESMs to improve the predictive understanding of coastal flooding.