In-stream barriers are used to mitigate invasions in freshwaters and protect indigenous biodiversity is known as isolation management. Barriers are used for securing vulnerable populations of native river resident galaxiids (RRG) threatened by non-native salmonids (trout) but the success and risks, such as risk stochastic extirpation, of this strategy have not been fully assessed. We quantified fish abundance, and habitat size and complexity above barriers preventing trout incursion for four species of RRG, with upstream population limits determined by electrofishing and environmental DNA. Across all habitats above barriers, habitat extent varied from 152 m to 2.2 km. Thus, habitats above barriers are generally small, making populations vulnerable. We also found evidence of severe RRG population declines, and even local extinction, above barriers due to both recent trout invasion and stochastic events, including floods and drought. Total estimated population sizes of barrier populations were variable among species, location and time, but were never large and many have undergone dramatic fluctuations as indicated above. Overall, our study indicates that barriers play a key role in vulnerable population protection, but careful planning and post-intervention monitoring are required to achieve optimal outcomes. Moreover, barriers alone are unlikely capable of reversing population trends and need to be considered as part of more holistic management actions such as habitat restoration and manipulation, trout removal, captive breeding, translocations and increased protection of all types.