Fish invasions are a key driver of change in freshwater systems, impacting biodiversity and economies. The use of barriers to mitigate invasions, isolation management, has been increasingly reported as a protection strategy. However, negative impacts of deliberate fragmentation include stochastic extinction, extirpation through sink population formation and prevention of native biota dispersal. In Aotearoa New Zealand native non-migratory (NMG) fish are a group dominated by species at risk of extinction. NMG continue to decline in density and range, despite 30 years of evidence that introduced salmonids (trout) are a key factor in this trend. We conducted a qualitative review of barriers protecting NMG in the South Island of Aotearoa, illustrating implementation with case studies. We found a range of barrier types across a variety of habitats in the Canterbury and Otago regions. NMG species protected by fragmentation had threat statuses encompassing “declining” to “nationally critical”. We assessed these barrier populations applying metacommunity theory and life history traits. We found that barriers have a large impact on dispersal, but some NMG co-occur with trout at low densities as sink populations, potentially reliant on a secure source population above a barrier. We found evidence of at least four new invasions, where trout were identified in previously secure NMG populations, highlighting the need for robust surveillance of such populations. We suggest the use of this tool requires managers to assess extinction risk of individual populations by isolation or invasion, often based on incomplete data. We go on to identify key research gaps such as viable population analysis for NMG, feasibility of trout removal and the physical characteristics required of instream structures to prevent incursion by introduced salmonids.