The focus of improving fish passage in freshwater systems is largely to allow movement past physical or physiological instream barriers to reinstate catchment-wide connectivity lost through anthropogenic use of rivers since the 1800s, e.g. impoundment, diversion, hydropower, etc. Whilst this mainly benefits migratory fish species and vagile species with widespread distributions, improved fish passage also facilitates the spread of alien invasive species. Understanding situations where maintaining barriers to fish movement can be more beneficial to native species than reinstating historical connectivity is crucial to effective but balanced fish passage programs. In the Southern Hemisphere many small-bodied, non-migratory native fish species now only persist above natural or artificial instream barriers, particularly in small headwater streams at moderate (200 m) to high (> 1000 m) elevations. In Australia these species are primarily galaxiid fishes (Galaxiidae) and are impacted by predatory alien salmonids introduced from the Northern Hemisphere. While the existing or new instream barriers protect the threatened native species from extirpation and extinction some also disrupt historical connectivity across the tributary networks. We discuss the dynamics of headwater persistence of these threatened species in a changed landscape, implications for conservation management, and highlight examples of where construction of new, or preservation of current barriers, to upstream movement of invasive fishes far outweighs improving connectivity, particularly where the latter increases extinction risk. Increased awareness of the smaller, but equally valuable, benefit of barriers to protect biodiversity is crucial to effective conservation management at the catchment-wide scale.