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Abstract Interior marsh pond formation has been commonly observed in tidal marshes affected by high rates of relative sea level rise (RSLR). However, it is difficult to conclude whether an accretion deficit (accretion which does not keep pace with RSLR) or natural ice and wrack disturbance has driven pond formation. We propose that marsh deterioration caused by accretion deficit can be differentiated from that caused by other disturbances based upon temporal vegetation changes and the spatial configuration of vegetation zones relative to tidal creeks and the marsh platform. We tested this hypothesis in six newly ponded sites within RSLR‐affected marshes in Deal Island, Chesapeake Bay. At each site, we used field surveys and remote sensing to study spatiotemporal dynamics of marsh vegetation, marsh topography, and tidal creek incision. We found flood tolerant plants displaced flood intolerant species over time in the landward direction, or upslope, of ponds. A reverse species transition was observed seaward of ponds because tidal creek incision alleviated interior marsh inundation. The landscape‐scale biogeographic pattern we have recognized sheds light on how plants adapt to chronically reshaped geomorphological configurations of the marsh platform, which differentiates ponding caused by accretion deficit from ponding caused by natural and artificial disturbances. Furthermore, our results point to vegetation patterns that can be used as early warning signals of interior marsh loss to ponding. As ponding has been a major driver of tidal marsh habitat loss in microtidal marshes around the world, early indicators of decline are sorely needed to direct conservation activities.