The São Francisco River forms one of the main Brazilian hydrographic basins of ca. 645,000 km2. The Pandeiros River is a tributary situated on the left margin of the São Francisco and is considered a strategic component for conservation of biodiversity of that hydrographic basin. An inventory of the aquatic macrophyte flora of the Pandeiros River Wildlife Sanctuary was carried out, using collections of botanical samples and examination of specimens at the BHCB Herbarium. Aquatic environments in the study area were classified as follows: the Pandeiros riverbed, floodplains, oxbow lakes, and swamps. A total of 101 species was inventoried, distributed in 37 families (1 charophytes, 1 liverworts, 3 ferns and 32 angiosperms) and 71 genera. The species were classified into seven life forms, with the amphibian and rafted plants the more representative. The area shows a high diversity in its aquatic macrophytes and has an important role in the conservation of biodiversity of the region.