Given the potential for a projected acceleration in sea-level rise to impact wetland sustainability over the next century, a better understanding is needed of climate-related drivers that influence the processes controlling wetland elevation. Changes in local hydrology and groundwater conditions can cause short-term perturbations to marsh elevation trends through shrink–swell of marsh soils. To better understand the magnitude of these perturbations and their impacts on marsh elevation trends, we measured vertical accretion and elevation dynamics in microtidal marshes in Texas and Louisiana during and after the extreme drought conditions that existed there from 1998 to 2000. In a Louisiana marsh, elevation was controlled by subsurface hydrologic fluxes occurring below the root zone but above the 4 m depth (i.e., the base of the surface elevation table benchmark) that were related to regional drought and local meteorological conditions, with marsh elevation tracking water level variations closely. In Texas, a rapid decline in marsh elevation was related to severe drought conditions, which lowered local groundwater levels. Unfragmented marshes experienced smaller water level drawdowns and more rapid marsh elevation recovery than fragmented marshes. It appears that extended drawdowns lead to increased substrate consolidation making it less resilient to respond to future favorable conditions. Overall, changes in water storage lead to rapid and large short-term impacts on marsh elevation that are as much as five times greater than the long-term elevation trend, indicating the importance of long-term, high-resolution elevation data sets to understand the prolonged effects of water deficits on marsh elevation change.