The outcomes of negative interactions between introduced and native species can be complex, ranging from complete elimination of one group, through temporally unstable co-occurrence, to stable coexistence. Furthermore, coexistence patterns vary spatially depending on environmental conditions. In the streams of Aotearoa | New Zealand, introduced trout compete with native river-resident galaxiids (RRG) for resources, and prey heavily on smaller RRG. While some RRG populations go extinct after invasion, others seem to persist in sympatry with trout. This pattern is likely caused by a combination of interspecific differences between RRG species, environmental heterogeneity, disturbance, and the proximity of trout-free refuges. However, a more mechanistic understanding of these processes is needed to predict future dynamics under global change, and to help guide management. We used a structural equation modelling approach and data from 25 years of fish surveys in the Waimakariri catchment, Canterbury, to quantify relationships between environmental gradients, trout population structure, and galaxiid demography. We expected trout to be more susceptible to flood disturbance than RRG, which could suppress trout populations, especially large individuals, reducing pressure on RRG. Ultimately, we anticipated the presence of local RRG recruitment to be the key indicator of stable coexistence. We found evidence of context-dependent co-occurrence along disturbance gradients with negative impacts of increasing disturbance on both species. However, there was relatively little evidence of local recruitment in trout-invaded systems. An ongoing experiment reducing trout densities in natural systems supports these findings, with fewer RRG at higher trout densities and few RRG larvae at any site with trout present. Our results highlight the potential for stable coexistence in habitats with environmental trout suppression but indicate it is rare. Further investigation of coexistence drivers will advance our ability to project future interactions between trout and RRG under changing environmental conditions, and guide galaxiid conservation management in areas with galaxiid-trout co-occurrence.