Modern diatom samples were collected from 43 sites across the Strømness Bay area of South Georgia. From 115 taxa belonging to 22 six diatom assemblages were distinguished. A CCA-analysis indicated that the assemblages are linked to pH and conductivity ranges, and habitat structure. The Eunotia paludosa var. paludosa - Eunotia subarcuatoides assemblage occurs in small acid water bodies. Samples of the Fragilaria germainii - Pinnularia aff. anglica assemblage are found in pools with a relatively high conductivity. The Fragilaria neoproducta assemblage and the Achnanthes subatomoides - Navicula vitabunda assemblage are mainly found in larger pools and lakes. This relationship between the assemblages and pH was comparable with results found in the testate amoebae fauna of South Georgia.