We assessed the landscape-scale effect of predation pressure from trout on the population integrity and distributions of non-diadromous galaxiids in high-country streams of the South Island, New Zealand. The effects of trout (brown trout, Salmo trutta, and rainbow trout, Oncorhynchus mykiss) on two widespread species, the Canterbury galaxias (Galaxias vulgaris Stokell) and the alpine galaxias (G. paucispondylus Stokell) were assessed. Experiments confirmed that both species were vulnerable to trout predation and that habitat (size and disturbance regime) may be a factor in local co-occurrence. Quantitative electrofishing surveys indicated that G. paucispondylus distributions were less affected by trout than G. vulgaris distributions and that the species’ range was limited by temperature. Trout created demographic sinks for G. vulgaris across most invaded reaches, while refuge populations in streams above barriers to trout acted as demographic sources for this species. G. vulgaris was consistently absent from small, stable stream reaches far from sources, indicating that trout predation pressure and propagule pressure (driven by immigration from sources) interact to drive local G. vulgaris persistence in trout-invaded reaches. Predation pressure is likely to be highest in areas where infrequent flooding allows high densities of large trout (> 150 mm FL) to occur and where there are few refugia for galaxiids. A spatial model was developed to predict exclusion of galaxiids by trout across invaded networks. If used appropriately, the model could be used to find new refuge populations of non-diadromous galaxiids and to aid planning of active rehabilitation of trout-invaded river networks.