Emergent herbaceous wetlands are characterized by complex salt marsh ecosystems that play a key role in diverse coastal processes including carbon storage, nutrient cycling, flood attenuation and shoreline protection. Surface elevation characterization and spatiotemporal distribution of these ecosystems are commonly obtained from LiDAR measurements as this low-cost airborne technique has a wide range of applicability and usefulness in coastal environments. LiDAR techniques, despite significant advantages, show poor performance in generation of digital elevation models (DEMs) in tidal salt marshes due to large vertical errors. In this study, we present a methodology to (i) update emergent herbaceous wetlands (i.e., the ones delineated in the 2016 National Land Cover Database) to present-day conditions; and (ii) automate salt marsh elevation correction in estuarine systems. We integrate object-based image analysis and random forest technique with surface reflectance Landsat imagery to map three emergent U.S. wetlands in Weeks Bay, Alabama, Savannah Estuary, Georgia and Fire Island, New York. Conducting a hyperparameter tuning of random forest and following a hierarchical approach with three nomenclature levels for land cover classification, we are able to better map wetlands and improve overall accuracies in Weeks Bay (0.91), Savannah Estuary (0.97) and Fire Island (0.95). We then develop a tool in ArcGIS to automate salt marsh elevation correction. We use this ‘DEM-correction’ tool to modify an existing DEM (model input) with the calculated elevation correction over salt marsh regions. Our method and tool are validated with real-time kinematic elevation data and helps correct overestimated salt marsh elevation up to 0.50 m in the studied estuaries. The proposed tool can be easily adapted to different vegetation species in wetlands, and thus help provide accurate DEMs for flood inundation mapping in estuarine systems.