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Human activities have cumulatively altered natural thermal regimes, with impacts and occurrences of extreme events amplified and exacerbated by global climate change. This leads to cascading ecological impacts in river systems. This paper translates knowledge generated over more than ten years of thermal research in South Africa into a protocol for establishing environmental water temperature guidelines for perennial rivers in South Africa. Tools and protocols for generating thermal guidelines reflecting seasonal variation and daily ranges, setting ecologically relevant thermal targets, and approaches for incorporating water temperature into management plans are presented. Tools include a spatial (thermal) framework within which air-water temperature models are applied and reference thermographs are generated; national maps of system resilience and air-water temperature model accuracy; a database of variables likely to indicate system resilience and model accuracy; innovative tools for generating thermal metrics and thermographs; a screening process to assess thermal risk; and an evaluation process to assess thermal change based on deviation from reference or expected thermal conditions. The importance and value of thermal data was recognised by the freshwater community and collection of water temperature data strongly endorsed. Future rollout of a water temperature-monitoring programme for South Africa needs to be prioritised. [ABSTRACT FROM AUTHOR]