Introduced predators with patchy distributions can create demographic sinks within native prey populations. Such invasions may give rise to source–sink metapopulations if there are still sources of native species colonists in the landscape. In New Zealand, introduced brown trout (Salmo trutta) and rainbow trout (Oncorhychus mykiss) are linked with declines in native non-diadromous galaxiids but co-occur with these galaxiids in some locations. We investigated whether trout create sinks in Galaxias vulgaris populations, and whether trout-free reaches could act as sources, allowing persistence in the sink habitat. We conducted quantitative seasonal monitoring of G. vulgaris population structure across two subcatchments of the Waimakariri River, South Island. Two trout-free and seven trout-invaded sites in the Porter River catchment and two trout-free and five trout-invaded sites in the Broken River catchment were monitored over two winters and the adjoining summer. Spatially continuous monitoring of young-of-the-year (YOY) galaxiid distributions and apparent survival across the Broken River catchment was also undertaken. Galaxias vulgaris YOY recruitment was high in trout-free reaches, indicating positive population growth. Galaxias vulgaris was absent from three trout-invaded sites, and the remaining invaded sites had significantly depleted juvenile recruitment. Information-theoretic model selection indicated that trout, rather than habitat, drove recruitment failure. Trout-invaded sites could be divided into “sinks” that retained no YOY galaxiids, indicating no local recruitment, and “pseudosinks,” which had very few recruits. Absence of small G. vulgaris at sink sites suggested population maintenance through immigration of adults from sources, whereas pseudosink sites appear capable of self-recruitment at low carrying capacities. Trout-free reaches appear to act as sources in a river network but are susceptible to future invasions by trout. Thus, not only may invasive species cause source–sink metapopulations in native species, but also the potential of refugia for natives (sources) to become future sinks highlights the vulnerability of these metapopulations when invasive predators are the principal demographic driver.