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• Diatoms in two springs with different surrounding land use in the Karoo compared. • Diatom indices GDI, SPI,BDI and%PTV were used to evaluate water quality. • Diatom species and indices in Great Fish River compared to historical data. • Indices at headwater site reduced ecological classification compared to previous study. This paper examines the efficacy of diatoms as bioindicators of water quality in the upper reaches of the Great Fish River following a period of reduced flow from drought conditions. Of the five sites, three were sampled three times in an 18 month period while the remaining two were sampled once. As a comparison, one headwater site within Mountain Zebra National Park, situated in the same district, was sampled. A total of 166 diatom taxa belonging to 29 genera were identified. Dominant taxa for the Great Fish River were identified as Amphora pediculus; Epithemia sorex; Nitzschia frustulum; Navicula veneta and Craticula buderi. These species, indicative of high nutrient concentrations and moderately saline to brackish conditions can tolerate low flow conditions. The Generic Diatom Index (GDI), the Specific Pollution sensitivity Index (SPI) the Biological Diatom Index (BDI) and the% Pollution Tolerant Valves (%PTV) – part of the UK Trophic Diatom Index (TDI) were used for interpretation of the results. The indices showed that this river is in poor condition. By comparison the headwater site in the Mountain Zebra National Park had Cocconeis placentula var. euglypta, Achnanthidium minutissimum and Cocconeis placentula var. lineata as dominant species and, using the same indices, the river was classified as in moderate to good condition with respect to water quality. When compared to a previous study (2010 – 2012), these sites showed a shift in dominant species indicating a change in water flow conditions and quality. [ABSTRACT FROM AUTHOR]