Abstract The use of barriers in freshwater systems to mitigate invasions, known as isolation management, has been increasingly implemented as a protection strategy for native fish. Barriers are crucial for securing vulnerable populations, but much remains to be learnt about the drivers of success and the implications of deliberate fragmentation. In Aotearoa‐New Zealand, henceforth Aotearoa, native non‐migratory galaxiid (NMG) fishes are characterized by a disproportionate number of threatened species with introduced salmonids (trout) identified as a key driver of NMG declines. We conducted a qualitative review of barriers protecting NMG in Aotearoa, illustrating varying outcomes and current knowledge gaps with case studies. Barrier types ranged from natural bedrock waterfalls, shallow velocity chutes and drying reaches to deliberately engineered structures (known commonly as exclusion barriers). Barriers were typically located in headwater streams or spring systems. NMG species secured by fragmentation often have high conservation value and barriers are essential for their protection. Despite the critical role of these barriers, the isolated NMG populations above them are at risk of stochastic extirpation, invasion, or re‐invasion. Exclusion barriers may restrict access to habitat for native migratory fish species and can sometimes alter or remove ideal mesohabitat from protected populations. Overall, when using exclusion barriers, managers must assess extinction risk for individual populations by isolation or invasion, balancing benefits and consequences. However, these assessments are frequently based on incomplete data and hindered by lack of general understanding of the underpinning processes. Despite well‐documented benefits to NMG population survival, key knowledge gaps such as long‐term viability of isolated populations, combinations of physical barrier parameters conferring exclusion under all flow regimes and extent of habitat loss to other native species still exist.
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