The Berg River system in the southwestern Cape South Africa was historically populated by at least four species of highly endemic fish species. A litany of anthropogenic changes, including large-scale land transformation, invasion by alien plant species, modification of the natural flow regime of the river, changes to water chemistry, siltation, and introduction of alien fish species, has transformed the system to the extent that some of these species were believed to have been completely eradicated from the system while others had become severely restricted in terms of the ranges they now occupy. This paper pulls together all available data and information (mostly anecdotal) on historical abundance and distribution patterns of indigenous fish species in the system and on the introduction and spread of alien fish species through the system. It also presents results of a series of surveys undertaken in recent years which provide a snapshot of present day abundances and distributions patterns of both the indigenous and alien fish species in the system. These recent surveys are focussed mostly on the main stem of the system but cover the full length of the river from the upper reaches to the estuary. Methods employed in the recent surveys included beach seine netting, gill netting, electrofishing and snorkelling. These surveys have revealed the presence of only three indigenous fish species in the system—the Berg River redfin, Pseudobarbus burgi, the Cape kurper, Sandelia capensis, and the Cape galaxias, Galaxias zebratus. In spite of once being abundant and widespread in the system these species are now confined to the extreme upper reaches of the mainstem and in the upper tributaries where alien species have not yet managed to penetrate and water quality remains pristine. A fourth indigenous species, once reported as being widespread through the system, the witvis, Barbus andrewi, appears to have been extirpated from the system in its entirety. At least ten species of alien species are present in the system and include rainbow trout, Onchorhynchus mykiss, smallmouth bass, Micropterus dolomieu, spotted bass, M. punctulatus, large mouth bass, M. salmoides, Mozambique tilapia, Oreochromis mossambicus, banded tilapia, Tilapia sparrmanii, sharptooth catfish, C. gariepinus, bluegill sunfish, Lepomis macrochirus, carp, Cyprinus carpio, and mosquito fish, Gambusia affinis. These species are most abundant in the mainstem of the river and lower portions of the tributaries, being prevented from penetrating further upstream by a combination of physical barriers, low winter temperature, and turbulent flow patterns which characterise the upper reaches of the Berg River system. Historical surveys of freshwater fish populations in the Berg River system relied mostly on surface observations and angling as survey methods, and thus most of the results of these studies are of an anecdotal nature. However, using these as a base, it has been possible to pinpoint with a reasonable degree of accuracy the time at which most of the alien species were originally introduced into the Berg River system as well as their spread through the system, and the simultaneous decline of indigenous species in the river. We conclude from this analysis that the strong correlation between the spread of alien species through the Berg River system and the concomitant decline of indigenous species is strongly suggestive of a causative relationship. The paper concludes with some speculation on the prognosis for both indigenous and alien fish species in the Berg River system, focusing on the impacts that the newly constructed Berg River Dam may have on these fauna, as well as potential opportunities this may present for their conservation.