Invasive alien trees along river banks can reduce indigenous biodiversity, while their removal can restore it. We assessed here family-and specieslevel responses of river benthic macroinvertebrate assemblages to three riparian vegetation types (natural, alien trees, cleared of alien trees) in the Cape Floristic Region biodiversity hotspot. High species beta diversity of this highly endemic fauna meant that between-river, as well as seasonal effects, dominated assemblage patterns. SASS5, a qualitative, rapid bioassessment technique, based on the sensitivity of the families present, was used as a measure of river health and, indirectly, of water quality. SASS indicated a decline in water quality conditions after alien clearing, a likely response to the greater insolation and apparent erosion of cleared banks, resulting in elevated temperatures and suspended solids and lowered oxygen levels. Overall, cleared and natural sites were more similar to each other than to alien sites, suggesting some post-clearing recovery. However, many sensitive, endemic taxa survived in alieninvaded sites, and more than in the natural sites. These endemic species made use of shady, cool, highoxygen levels under the alien tree canopy. However, endemics declined in overall abundance in sites cleared of aliens, being replaced by more tolerant, widespread taxa. Clearance of the alien trees opened up the rivers to sunny conditions, which had a major impact on community composition. Vegetation types, oxygen levels and river width were important environmental variables affecting these macroinvertebrate responses. Re-establishment of invertebrate biodiversity matched that of indigenous vegetation, with the most sensitive endemic taxa only recovering after establishment of bushy indigenous and shadeproducing fynbos. Therefore, for biodiversity conservation objectives to be achieved, it is essential that indigenous plants are maintained and encouraged during and after clearing to ensure the recovery of endemic and sensitive taxa.