Human activities are increasingly altering ecosystems, and are especially severe in streams where flow modification can affect environments far downstream and can interact with other pressures, such as species invasions. This has led to a disproportionately high number of threatened species in streams (e.g., native galaxiid fishes in New Zealand). I investigated how threatened bignose galaxias (Galaxias macronasus) and upland longjaw galaxias (Galaxias prognathus) were affected by flow-related influences in their habitats. A survey of sub-catchments in the Mackenzie Basin showed that flow regulation played a strong role in influencing fish occurrence; native fishes dominated unregulated rivers and introduced species dominated regulated rivers. Upland longjaw galaxias (ULG) were sparsely distributed and only found in unmodified braided rivers. Targeted surveys in these rivers indicated their habitat selection was weak, and although habitat availability was high, individual habitats were only occupied for short periods because floods frequently reconfigured the river bed. Thus, disturbances played a major role in ULG populations, forcing a strategy of weak habitat selection and frequent movement. This also makes them vulnerable to large-scale flow changes making the habitat more benign and potentially increasing competition (e.g., from invasive trout). Bignose galaxias were only locally abundant in very low discharge habitats lacking other fishes, so were restricted to very small parts of the river network. An experiment manipulating flows showed bignose galaxias moved into slower habitats over the short-term, suggesting a slow-flow preference, but not excluding the competitive influences of other fish like trout. Overall, this work shows these threatened fishes are susceptible to many of the current and future global changes affecting freshwaters like habitat alteration and invaders, but the above knowledge should allow targeted management of these influences for these highly threatened endemic fish.