Karst springs are considered among the most vulnerable groundwater-dependent ecosystems. Despite their ecological value and importance as strategic water sources, Mediterranean karst springs are still poorly investigated. The aim of this study was to analyse the epilithic diatom assemblages and to test their usefulness as indicators of environmental quality on the Su Gologone spring (central-eastern Sardinia, Italy), a biotope of great natural value and a precious source of drinking water. A total of 89 diatom taxa were found with 25 new records for Sardinian running waters. Species richness, Shannon-Wiener and Pielou indices showed good biotic integrity. The dominant taxa were alkaliphilous, halophobous-oligohalobous exigent, xeno- oligosaprobic and characteristic of oligotrophic waters. The eutrophication/pollution index − diatom based (EPI-D) and the Navicula Nitzschia Surirella indices indicated respectively an excellent/good biological water quality and a low physical disturbance. However, the biological and chemical oxygen demand, and the microbiological variables (E. coli, fecal and total coliforms) revealed an organic contamination of the water, although moderate. The judgment provided by the EPI-D should be verified after updating of the index. In fact, 10 taxa found in this study are not currently considered by the EPI-D method.