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Meiobenthos (or meiofauna) are microscopic invertebrates that inhabit biofilms and interstitial spaces in rivers. They are diverse and extremely abundant, and they perform essential ecological functions by linking microbial production to higher trophic levels (e.g. macrobenthic invertebrates and fishes). However, meiobenthic communities remain poorly studied in Africa. Here, we sampled meio- and macrobenthic invertebrate communities associated with biofilms and sediments across an upstream–downstream gradient along the Olifants, Sabie and Crocodile rivers flowing through the Kruger National Park (KNP). We expected to link differences in community structure to environmental gradients as those rivers show different degrees of anthropogenic stress as they enter the park. Both meio- and macrobenthic communities differed across rivers and also structured along an upstream–downstream gradient. The upstream sites, which were the closest to the park borders, consistently showed a lower diversity in all three rivers. There, the invasive snail Tarebia granifera strongly dominated (making up 73% – 87% of the macrobenthos), crowding hard substrates, while concomitantly the abundances of biofilm-dwelling meiobenthos like nematodes and rotifers were substantially reduced. Nevertheless, the diversity and evenness of communities then tended to increase as water flowed downstream through the park, suggesting a beneficial effect of protected river reaches on benthic invertebrate diversity. However, for the Crocodile River, which makes up the southern border of the park, this trend was less conspicuous, suggesting that this river may experience the greatest threats. More generally, benthic invertebrate communities were driven by the concentrations of phosphates, sulphates, ammonium and organic matter and by substrate characteristics. Conservation implications: Meiobenthic organisms are very abundant in KNP rivers and react to environmental gradients; thus, they should be more considered for bio-monitoring or conservation of comprehensive assemblages of animals. Interestingly, protected reaches tended to show a reduced dominance of the invasive T. granifera and a higher diversity of benthic invertebrates.