Understanding the interactive effects of non-native species and alterations to flow regimes is important to combat threats to freshwater communities. Low-flow conditions may either exacerbate or offset influences of non-natives but the mechanisms determining the direction are poorly understood. We evaluated how stream drying affected interactions between vulnerable native non-migratory galaxiids and non-native trout in Aotearoa - New Zealand. We electrofished (December – March) paired perennial and drying reaches containing galaxiids ( Galaxias vulgaris and G. paucispondylus) to compare abundance and growth rates in streams with high abundance (n=2), low abundance (n=2) or no brown trout (n=3; Salmo trutta). Low flows greatly reduced trout abundance and size, likely reducing predatory threats to galaxiids since risk is size-related. Galaxiid densities were consistently lower in drying compared to perennial reaches of troutless streams. However, galaxiids were less affected by low flows than trout, setting the scene for an interaction between trout and low flow. In streams with high numbers of trout, galaxiid numbers were very low in perennial reaches, whereas they were moderate in drying reaches. That meant galaxiid numbers increased with decreasing flow in streams with many trout, an indirect positive effect, although their abundance never reached the high levels of trout-free perennial reaches. In low-density trout streams, there were no clear differences in galaxiid abundance between reaches of different flow type. Thus, the effects of trout on galaxiids depended on the flow regime, likely driven by harsh low-flow conditions suppressing large trout, which were more sensitive to low flow than galaxiids. Growth advantages for galaxiids possibly enhanced this interaction because galaxiids grew fastest when trout were present at low densities. Overall, although low-flow conditions likely reduced predatory effects of non-natives, populations of natives were also suppressed by low flow. Such interactive effects of flow reduction are likely common and appear controlled by relative vulnerability and size-structured interactions. Balancing maintenance of natural flows with minimising effects of non-native sports fish poses a difficult challenge, but managers should aim to both protect natural flow regimes to maintain suitable fish habitat, and actively manage non-native species in harmful situations to conserve native fish.