The Smallscale Redfin prefers mainstream and large tributary habitat, making it very vulnerable to a number of anthropogenic threats such as loss of habitat, pollution and over-abstraction of water. These threats are likely to be exacerbated in the future due to the predicted increase in extreme weather conditions in the CFE as a result of climate change (Dallas & Rivers-Moore 2014). Current water abstraction practices often involves the use of diversion weirs located high up in tributary streams which often result in the lower sections of tributaries running dry for extended periods of time as no provision is made for environmental flow allocations (Jordaan et al. unpublished data).
Alien fish invasions are also a major threat to the Smallscale Redfin as a number of non-native fishes are established in the Gouritz and Gamtoos systems. The main threat to this species in the Gamtoos System appears to be the African Sharptooth Catfish but this require further investigation. During a survey in 2000 (E. R. Swartz unpublished), the African Sharptooth Catfish were recorded far upstream in the Gamtoos River System and only a single specimen of the Smallscale Redfin was recorded from three localities during the survey. The continued persistence of this species in this system is therefore highly uncertain. The Gouritz River and its main tributaries have been poorly sampled to date. Recent ad hoc surveys of the mainstream Gouritz River at Vaalhoek Nature Reserve as well as the Olifants and Gamka River tributaries revealed that several alien invasive fish species have become established and are now abundant in these river sections (Black bass species (Micropterus dolomieu and Micropterus salmoides), African Sharptooth Catfish, Common Carp (Cyprinus carpio), Banded Tilapia (Tilapia sparrmanii), Bluegill Sunfish and Smallmouth Yellowfish (Labeobarbus aeneus)). Ongoing decline in the numbers and distribution ranges of native species in the Gouritz and Gamtoos systems is therefore likely due to these multiple impacts.
The mainstem and lowland habitat requirement of this species also means that it is not well represented by the formal protected area network of the CFE. Within the Western Cape, the Touws and Buffels rivers are associated with the Anysberg Nature Reserve, but the protection value of this is low as both rivers have their upstream reaches located outside the formally protected area. This is also the case for the Groot Swartberg Nature Reserve where the upper reaches of the Groot River, which represents one of the most important remaining stronghold population of the Smallscale Redfin are located outside the protected area. A specimen of the highly invasive African Sharptooth Catfish was recently (2017) recorded in the lower Groot River near De Rust (van der Walt, unpublished data) which is a significant cause for concern given the conservation value of this river to the Smallscale Redfin and its sister species the Slender Redfin (Pseudobarbus tenuis). The African Sharptooth Catfish has been illegally introduced into the Floriskraal Dam located on the upper reaches of the Buffels River, thereby posing a significant invasion risk to downstream Smallscale Redfin habitat. The only rivers where both the headwater reaches of the river as well as the preferred habitat for the Smallscale redfin are located inside a protected area, are the Kamma River originating in the Ruitersbos Nature Reserve and the Oshoekshang River in the Gamkaskloof Nature Reserve.