This study investigated the range-wide phylogenetics and biogeography of the Cape Kurper Sandelia capensis, a primary freshwater fish endemic to, and widespread within, the Cape Floristic Region (CFR) of South Africa. Maximum likelihood, Bayesian phylogenetic, and haplotype network analyses, based on two mitochondrial and two nuclear genes, revealed the existence of three reciprocally monophyletic, deeply divergent and allopatric clades that likely represent cryptic species. The West Coast Clade is largely confined to the Langvlei, Verlorenvlei, Berg, and Diep rivers, the Klein River Clade is endemic to the Klein River, and the South Coast Clade is found everywhere else in the range of S. capensis sensu lato. It was hypothesized that divergences within S. capensis sensu lato likely occurred because of (1) isolation of coastal drainages by persistent drainage divides and/or (2) vicariance of current tributaries by the drowning of their confluences by high sea levels. The current distribution of lineages could be due to historical range expansion and gene flow via (1) river capture or some other mode of transdivide dispersal, and/or (2) dispersal during periods of low sea level via paleoriver confluences of currently isolated coastal rivers. Comparison of BEAST2 estimated divergence times with the timing of climatic, geological, and geomorphological events supported long-term coastal drainage isolation, punctuated by rare transdivide dispersal events and limited paleoriver dispersal, as the best explanation of current phylogeographic and divergence patterns in S. capensis. Hydrological barriers that block upstream passage in palaeotributaries could hypothetically explain why S. capensis failed to disperse through certain palaeoriver confluences. There were several sites where biogeographic patterns have likely been confounded by human translocation of S. capensis. Alien fish predators and water extraction may threaten the three cryptic species more severely than previously realized, due to their smaller population sizes and inhabitation of only a portion of the range previously ascribed to S. capensis sensu lato. The preponderance of cryptic diversity and endemism in the CFR suggests that additional undescribed cryptic species of obligate freshwater fishes may be found in short coastal river systems around the world, especially in regions with a history of geological stability and a narrow continental shelf.