Adaptive management of river systems assumes uncertainty and makes provision for system variability. Inherent within this management approach is that perceived limits of ‘acceptable’ system variability are regarded not only as testable hypotheses, but also as playing a central role in maintaining biodiversity. While the Kruger National Park currently functions as a flagship conservation area in South Africa, projected increases in air temperatures as a consequence of global climate change present challenges in conserving this biodiversity inside the established land boundaries. Within the rivers of the Kruger National Park, a management goal of maintaining biodiversity requires a clearer understanding of system variability. One component of this is water temperature, an important water quality parameter defining the distribution patterns of aquatic organisms. In this study, Chiloglanis anoterus Crass (1960) (Pisces: Mochokidae) was selected as a biological indicator of changes in annual water temperatures within the Sabie River in the southern Kruger National Park. Relative abundances of C. anoterus were determined using standard electro-fishing surveys. The presence or absence of C. anoterus was linked to cumulative annual heat units using a logistic regression model, and a critical annual cumulative water temperature threshold estimated. A correlative relationship between this temperature threshold and a biological index using a C. anoterus condition factor provides river ecologists with a tool to assess ecologically significant warming trends in Sabie River water temperatures. A similar approach could be applied with relative ease to other Southern African river systems. Further testing of this hypothesis is suggested, as part of the adaptive management cycle.