This paper provides a description of the zooplankton and epiphytic diatom communities of permanent and temporary freshwater pans in the Mpumalanga Highveld region of South Africa. Few studies have investigated the biota of pans in this area, which is seriously threatened by mining and agricultural development. Nineteen pan sites within a 20 km radius covering a wide range of water chemistries were sampled once for zooplankton, epiphytic diatoms and water physico-chemical data in 2009. Collected zooplankton and diatom samples were identified to species or genus level. Many of the zooplankton taxa reported in this study were not recorded in similar pan studies in South Africa and southern Africa. The study revealed a difference among the compositions of zooplankton and diatom communities between temporary pans and permanent pans. Zooplankton found exclusively in freshwater temporary pans included cladocerans (Megafenestra aurita and Scapholeberis kingi), calanoids (Mesocyclops major and Thermodiaptomus mixtus), a cyclopoid (Acanthocyclops vernalis) and a rotifer (Platyias quadricornis). Permanent pans were characterized by taxa such as cladocerans (Ceriodaphnia rigaudi and Dunhevedia crassa), a calanoid (Metadiaptomus transvaalensis), cyclopoids (Paracyclops fimbriatus and Eucyclops gibsoni) and rotifers (Brachionus dimidiatus and Brachionus plicatilis). The most commonly occurring diatom taxa in temporary pans included taxa indicative of slightly acidic to circumneutral, dystrophic and nutrient-poor waters such as Nitzschia acidoclinata, Gomphonema gracile and Eunotia bilunaris. Permanent pan assemblages were characterized by taxa typical of saline waters, including Nitzschia frustulum, Amphora veneta and Planothidium engelbrechtii. Species of the genera Pinnularia and Eunotia were almost totally absent from permanent pans.