This dataset includes the spectral absorption and fluorescence characteristics of colored dissolved organic matter (CDOM) and coincident field measurements of hyperspectral water remote sensing reflectance collected in coastal and inland waters around South Africa's Greater Cape Floristic Region (GCFR) as part of NASA's Biodiversity Survey of the Cape (BioSCape) field campaign in 2023. Samples cover three ecologically distinct but socio-economically vital coastal bays: St. Helena Bay, Walker Bay, and Algoa Bay, as well as four contrasting inland aquatic systems: Rietvlei wetland, Zeekoevlei lake, Theewaterskloof dam, and the Klein River estuary. Data from this and other elements of the BioSCape project can be found via the NASA Earthdata portal (https://search.earthdata.nasa.gov).