African sharptooth catfish Clarias gariepinus has become established as a non-native invasive species in Eastern Cape, South Africa, where it was translocated primarily through an inter-basin water transfer scheme into the Great Fish and Sundays rivers. This study examined the patterns in catfish distribution and abundance, and compared trophic niches in relation to the ichthyofauna of the two rivers. Correspondence analysis revealed upstream to downstream gradients associated with the spatial distribution in species richness for most species within the mainstream and mainstream to tributary gradients that were associated mostly with the spatial distribution of native minnows in both rivers. Catfish was predicted to occur widely within the mainstream habitats and to decrease progressively from mainstreams to tributaries. Based on classification and regression trees, the physico-chemical environment was found to be a good proxy for predicting the occurrence and abundance of catfish. Although non-significant relationships were observed between catfish and other native fish species abundances, the study suggests potential impact due to predation and interference in habitats where the invader co-occurs with other fishes. Comparisons of trophic niches indicated higher trophic diversity for the mainstream ichthyofauna than the tributary communities in both rivers, suggesting an upstream to downstream continuum in community structure and resource availability. Catfish within the invaded mainstream had comparable trophic niches and similar dispersion patterns among individuals for both rivers, but indicated differences in shapes of scatter. This suggests that the catfish exhibited a differential response, probably in relation to resource availability, that may be indicative of its dietary plasticity. The study suggests the proliferation of catfish and its probable impact within the mainstream flow-altered habitats where invasion resistance was possibly reduced. Comparisons of trophic niches provided information on its probable impact at different scales and the potential risk of invasion of tributaries inhabited by native minnow species. Copyright © 2012 John Wiley & Sons, Ltd.