This dataset provides vegetation information for 64 coastal wetland plots and coastal wetland extent maps for three habitat classes in 84 estuaries in South Africa. The vegetation plot data include vegetation species occurrence, percent cover, salinity, representative vegetation heights, porewater salinity, and ground temperature. In situ plot data were collected between October 27 and November 10, 2023, in Swartvlei Estuary, Wilderness Lakes, Knynsa Estuary, and Langebaan Lagoon within lands administered by the South African National Parks. The habitat extent maps were created for 84 estuaries across the Greater Cape Floristic Region. The classification is a single point in time representing the growing season when the plot data were collected (December 2023-January 2024). The habitat extent data were created with PlanetScope satellite classified with a U-Net semantic segmentation algorithm. The habitats classified are salt marsh, submerged aquatic vegetation, and reeds & sedges. Plot and habitat data were collected and created to inform analysis of the imaging spectroscopy and LiDAR data collected as part of the BioSCape field campaign. The data are provided in cloud optimized GeoTIFF, comma separated values, and geopackage formats.