Some native fish in New Zealand do not coexist with introduced salmonids. Previous studies of disjunct distributions of exotic brown trout Salmo trutta and native galaxiids demonstrated native extirpation except where major waterfalls prevented upstream migration of trout. In the Manuherikia River system, we predicted that water abstraction might be a further factor controlling the spatial distribution of both the invader and a native fish. We applied multiple discriminant function analyses to test for differences in environmental conditions (catchment and instream scales) at sites with roundhead galaxies Galaxias anomalus and brown trout in sympatry and allopatry. We then used a supervised artificial neural network (ANN) to predict the presence2013absence of G. anomalus and brown trout (135 sites). The quantification of contributions of environmental variables to ANN models allowed us to identify factors controlling their spatial distribution. Brown trout can reach most locations in the Manuherikia catchment, and often occur upstream of G. anomalus. Their largely disjunct distributions in this river are mediated by water abstraction for irrigation, together with pool habitat availability and valley slope. Trout are more susceptible than the native fish to stresses associated with low flows and seem to be prevented from eliminating galaxiid populations from sites in low gradient streams where there is a high level of water abstraction. Synthesis and applications. In contrast to many reports in the literature, our results show that hydrological disturbance associated with human activities benefits a native fish at the expense of an exotic in the Manuherikia River, New Zealand. Water abstraction is also known to have negative impacts on native galaxiids, therefore we recommend restoring natural low flows to maintain sustainable habitats for native galaxiids, implementing artificial barriers in selected tributaries to limit trout predation on native fish, and removing trout upstream. Journal of Applied Ecology (2006) 43, 9302013939doi: 10.1111/j.1365-2664.2006.01201.x