Diatoms have a successful history of use in assessments of wetland biological condition. In North America and across Europe, diatom assemblages are used for routine wetland condition assessments to meet the statutory requirements of the European Water Framework Directive and the National Aquatic Resource Survey by the US Environmental Protection Agency. In South Africa, the use of diatom assemblages as indicators of wetland condition may be a promising alternative to the traditional biotic assemblages employed, such as macroinvertebrates or macrophytes, which have proven to be ineffective. We present a preliminary investigation on the feasibility of diatoms in wetland biological assessments in South Africa by evaluating the use of diatoms as indicators of biological condition for depressional wetlands in the Mpumalanga Highveld region of South Africa. Depressional wetlands typically found in this region are either temporary (seasonally inundated) or permanent depressions. Temporary depressional wetlands are expected to be affected by natural environmental disturbances (e.g., seasonal fluctuations in water-level which may cause changes in water chemistry) as compared to relatively stable permanent ones. Establishing whether diatoms are suitable indicators of natural environmental disturbances in temporary depressional wetlands in this region is necessary for further investigations of anthropogenic disturbances. We sampled epiphytic diatoms from three least human-disturbed temporary depressional wetlands during various stages of inundation and showed that the species composition of epiphytic diatom communities were strong indicators of temporally changing environmental conditions. Using the same diatom and physical and chemical data, we also demonstrated that simplifying the taxonomy by using the functional composition (ecological guilds, life-forms) of the epiphytic diatom communities, can assess temporally changing environmental conditions as effectively as the species composition. Moreover, these functional groups provide valuable ecological information that is not available from the species data. Acid mine drainage (AMD) is the predominant stressor in permanent depressional wetlands of the Mpumalanga Highveld region, where coal mines utilise these wetlands for storage of AMD, which has severe impacts on the structure and function of the ecosystem. In order to develop an approach for impact assessment and management of depressional wetlands in the region, we developed an epiphytic diatom multimetric index (MMI) for AMD impacted permanent depressional wetlands. This is also the first diatom index to quantify AMD impacts in wetland habitats. Data collected from 34 sites that represented a range of conditions along an AMD gradient within the Mpumalanga Highveld was used to select responsive diatom metrics which we combined into a multimetric index. We developed separate MMIs for classes of depressional wetland types in order to account for natural variation among diatom assemblages, and compared their performance with an MMI that did not account for natural variation. To account for natural variation, we classified reference sites based on diatom typologies and hypothesised that by using this approach, we would improve MMI performance. Overall, all MMIs performed considerably well, although grouping sites by diatom typology to account for natural variation improved MMI performance, especially the precision, responsiveness and sensitivity to disturbance. We conclude that diatoms have strong potential for use in wetland ecological assessments in South Africa. The experimental and statistical approaches used in this study should expand our knowledge of diatom ecology and further advance the research and development of diatom bioassessment.