Sedimentation arising from agricultural run-offs, riparian habitat fragmentation and channel bank erosion has long been known to impair the structure and ecological functioning of stream and river ecosystems. This study examined the effects of fine sediment grain sizes on the functional feeding group structure of Ephemeroptera, Plecoptera and Trichoptera (EPT) in the Tsitsa River catchment in the Eastern Cape Province of South Africa. Fine sediments and EPT were sampled between August 2016 and April 2017 from eight selected sampling sites. The eight sites were classified into four groups in terms of fine sediments and turbidity to represent a gradient of sediment stress, with site groups 4 and 3 being less influenced and groups 2 and 1 as the highly influenced groups. EPT genera/species were assigned to five functional feeding groups (FFGs) and their responses to sediment stress assessed. The results of the study showed that of the five FFGs, four (i.e. collector-filterer, collector-gatherer, scraper/grazer and shredder) were significantly different between the four groups, separating the impacted groups from the less impacted groups. Redundancy analysis (RDA) showed that FFGs such as scraper/grazer, collector-gatherer and shredder were tolerant to fine sediment, especially during the dry season. Collector-filterers and predators were the most sensitive FFGs observed in the studied river systems. The RDA results showed that the coarser grain size fractions (very coarse and coarse silt, very fine sand and turbidity) displayed more severe negative effects on EPT FFGs when compared with the finer grain size fractions such as very fine and fine silt. The results obtained in this study provided more insights into the response patterns and functional dynamics of EPTs in the Tsitsa River systems, a knowledge that can contribute to trait-based biomonitoring in South Africa.