Given the prevalence of invasive species and high rates of habitat homogenisation across the globe, understanding how these drivers interact to influence native species assemblages is crucial. In river networks, confluences create discontinuities in physical conditions, likely creating hotspots of heterogeneity that influence interactions between native and invasive fish. We examined how spatial configuration of confluences affected the outcome of interactions between native galaxiids and non-native salmonids in New Zealand alpine rivers. Electrofishing in mainstem and tributary branches of twelve replicate confluences revealed highly context-dependent distributions, contingent upon interactions between: (a) the combination of flood disturbance history in confluence branches; (b) distance to the confluence; and (c) the direction of flow, either upstream or downstream, of the confluence. Shifts in native–invasive species relative abundance were determined by the preference of large predatory salmonids for more hydrologically stable conditions, which subsequently limited the abundance of young-of-year galaxiids, and meant galaxiids were more abundant in flood-prone conditions. Distance-from-confluence effects were stronger upstream than downstream, suggesting that flow direction had an important influence on dispersal. Tributary flow regimes also predictably influenced downstream physical conditions, thereby affecting predatory salmonid distribution which likely controlled galaxiid distributions. Overall, our results reveal strong spatial context-dependency in fish assemblages in river networks, and demonstrate how flow regime influences are spatially transferred at confluences, thereby creating areas of influential riverscape heterogeneity. Understanding the influence of such heterogeneity enables ecologically significant locations to be identified, particularly for management of native species vulnerable to invaders.