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Introduced rainbow trout Oncorhynchus mykiss have invaded many headwater streams in South Africa’s Cape Fold Ecoregion (CFE) and pose arguably the greatest threat to several species of threatened native fishes. Trout impacts in these systems appear to be density-dependent; we hypothesized that temperature is a key factor determining trout density and corresponding impacts on native fishes. We took advantage of natural spatial and temporal thermal heterogeneity in two CFE headwater streams to investigate the influence of temperature and other environmental factors on trout density and impacts on native fish assemblages. Temperature limited trout density (negative relationship) during summer surveys (hottest months), but not during spring and autumn (cooler months). During summer, the highest trout densities were recorded at sites that remained relatively cool (7-day moving average of the daily maximum temperature (Max_7) < 27 °C), while trout were generally absent from relatively warm sites (Max_7 > 27 °C). Native fish density was best explained by trout density (inverse relationship) during summer, but by other environmental variables such as habitat complexity and current flow velocity during autumn and spring. Trout distributions expand during cooler seasons when thermal heterogeneity and maximum temperatures are relatively low, but contract into thermal refugia (habitat patches that remain relatively cool) as temperatures and thermal heterogeneity increase over summer, leaving warmer habitat patches vacant and able to function as predation refugia for native fish. We hypothesize that climate warming could reduce trout density and distribution, and associated impacts on native fish, in CFE headwater streams, but may increase the potential for invasions by other warm-adapted non-native predatory fish already established in downstream river reaches in the region. [ABSTRACT FROM AUTHOR]