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The Cape Fold Ecoregion (CFE), a Mediterranean climatic region located at the southern tip of Africa, harbours a unique assemblage of stream fishes found nowhere else in the world. A recent resurgence in field surveys and the use of molecular techniques has led to the discovery of hidden diversity and the description of new species in this region. Knowledge of the distribution and ecology of newly identified lineages and recently described species is a fundamental requirement for informing effective conservation and management of aquatic biodiversity in this region, which is threatened by multiple impacts, including invasion by non-native species, hydrological modifications and habitat degradation. The present study examined the summer habitat associations of three native stream fishes, Pseudobarbus verloreni, Galaxias sp. 'zebratus Verlorenvlei' and Sandelia sp. 'capensis west coast', that are endemic to the Verlorenvlei River system, an intermittent river system in the western CFE. Extensive ecological, fish distribution and abundance data were collected during the summer months in 2015. Although P. verloreni was more widespread in head water sections compared to other species, the maximum likelihood estimates of its population size indicated that its density increased with decreasing altitude. Sandelia sp. 'capensis west coast' appeared to be widespread at sites with course grained substrates, whereas Galaxias sp. 'zebratus Verlorenvlei' was rare. Canonical additive ordination revealed unimodal responses and similar microhabitat optima for P. verloreni and Sandelia sp. 'capensis west coast', together with non-native banded tilapia Tilapia sparrmanii, indicating that these species had similar densities in the remnant pools which form refugia for aquatic taxa during the dry season. Generalised linear models indicated that P. verloreni's abundance was low at sites with high riparian vegetation. In contrast, Sandelia sp. 'capensis west coast' was abundant at sites that had high riparian vegetation cover and course substrates. The summer persistence of these fishes in the Verlorenvlei River system suggests that they may possess physiological and life history traits that allow them to tolerate the extreme environmental conditions often associated with wide hydrological variation in intermittent Mediterranean rivers and streams. The occurrence of non-native species, such as Tilapia sparrmanii, is likely to impose additional pressure on these species during periods of extreme summer conditions.