The freshwater sponge Ephydatia fluviatilis (Linnaeus, 1759) is cosmopolitan, yet it is poorly documented in South Africa. We report a new record from Lake Sibaya in the iSimangaliso Wetland Park, representing the first modern integrative record from the east coast of South Africa. Morphological analyses using light and scanning electron microscopy revealed a skeleton dominated by smooth oxeas, with rare styles and tylostyles. Megascleres lacked microspination and fell within the known global range of variation. Only a few birotulate gemmuloscleres were observed, and no intact gemmules were found. Following recent molecular and taxonomic revisions that treated Ephydatia syriaca, Cortispongilla barroisi, and Ephydatia cooperensis as junior synonyms of Ephydatia fluviatilis, sequences originally assigned to these names were treated as E. fluviatilis throughout the molecular analyses and comparative assessments. The COI and ITS phylogenetic trees recovered sequences originally identified as E. syriaca, C. barroisi, and E. cooperensis within the E. fluviatilis lineage, supporting their treatment as conspecific with E. fluviatilis. The South African sequence was also recovered within this lineage and, together with the established synonymy of these taxa, these results support its assignment to E. fluviatilis. A median-joining network based on ITS sequences reveals limited genetic differentiation and extensive genotype sharing within the Ephydatia fluviatilis group across much of its cosmopolitan distribution, particularly among African, European, and Asian specimens. A comparative analysis demonstrated substantial overlap in spicule morphology among specimens from different regions, highlighting the limitations of morphology alone for species delineation and the need for complementary molecular data. The lack of visible gemmules is interpreted as resulting from seasonal sampling or environmentally driven reduction in gemmulation, rather than species level differentiation. This study expands the established distribution of E. fluviatilis in South Africa and highlights the importance of integrative approaches that combine morphological and molecular data in freshwater sponge taxonomy.