Invasive species are an important contributor to global biodiversity loss. This is particularly true in freshwater ecosystems, where introduced species have contributed to native fish extinctions, altered native fish communities and modified aquatic ecosystem structure and function. Native species can potentially mitigate the impact of invasive predators and competitors by altering their behaviour, for example by reducing activity such as foraging or by increasing their use of shelter. This study investigated interactions between an introduced salmonid, the rainbow trout (Oncorhynchus mykiss), and a native fish, the riffle galaxiid (Galaxias arcanus), that currently co-inhabit streams in parts of south-eastern Australia. We used three separate sets of behavioural experiments to test whether riffle galaxiids avoided trout under different substrate conditions. We hypothesised that habitat selection in the presence of a predator could be an important factor in facilitating galaxiid and trout co-existence. We found that interactions between the two fish differed depending on substrate. Galaxiids avoided trout when only sand substrate was available, but did not avoid trout when cobble substrate was available. The complex structure of cobbles may afford riffle galaxiids protection from trout, thereby facilitating their current existence in trout-inhabited streams.