This taxon is threatened by loss of habitat and the impacts of alien invasive fishes. The main causes of habitat loss are complete surface water abstraction, inadequate management of alien invasive vegetation in riparian zones and damage to instream river structure as a result of poor land-use practices (instream bulldozing and poor management of bank erosion). There is extensive bulldozing of the Huis River upstream of the town of Barrydale up to the causeway. The area above the causeway is unimpacted by bulldozing and has been identified as an ideal sanctuary that needs to be protected to secure the Barrydale Redfin from imminent extinction. However, the town's water extraction point is above the upper limit of this taxon's current distribution. Complete water abstraction has left much of the upper Huis completely dry, with the exception of a few isolated pools below the waterfall. The deep pools in the Tradouw’s Pass provide more stable habitat for this taxon.
The lower Tradouw River below Barrydale has however been severely affected by nutrient enrichment through sewage effluent discharge from the town and potential agrichemical pollution from the upper Tradouw River. This is exacerbated by extensive water abstraction for agricultural purposes in the upper Tradouw River. The impact of pollution on the Barrydale Redfin has however not yet been studied or documented. The pools in the gorge have also been heavily invaded by three alien fish species; Largemouth Bass (Micropterus salmoides), Banded Tilapia (Tilapia sparrmanii) and Bluegill Sunfish (Lepomis macrochirus) which have become established in the Tradouw catchment. Preliminary results from ongoing surveys indicate that Barrydale Redfins have been locally extirpated in pools that have been invaded by Largemouth Bass and Bluegill Sunfish (Jordaan et al. unpublished data). Banded Tilapia is likely to impact the Barrydale Redfins through competition, but this needs to be established through dedicated studies that compare the trophic ecology and habitat use of the two species. Other threats include invasion of the Tradouw catchment by alien vegetation, mainly Black Wattle (Acacia mearnsii) and pines (Pinus spp.).