Elevation gradients including abrupt barriers such as cascades and waterfalls, are known to shape the composition of amphidromous fish assemblages in tropical Pacific streams. We aimed to describe the structuring of fish assemblages in short-steep-coastal-streams (SSCS) of the Australian Wet Tropics by snorkeling continuous lengths of three streams from the upper tidal limit to the source. Greatest species richness consistently occurred in the lower course of streams, and while elevational generalists were observed (Sicyopterus lagocephalus, Anguilla spp.) a number of elevational specialists, primarily sicydiine gobies, were exclusively found in the mid to upper course. Subsequently, species assemblages were identified and used to disentangle elevation and barrier effects on faunal distribution based on natural differences in stream profile. We also provide preliminary evidence that the stream profile dictates the upstream limits of keystone diurnal predators capable of ascending cascades and a subset of waterfalls, and that in turn this has implications for top-down effects on prawns and shrimps. We conclude that the detection and mapping of sicydiine gobies poses a challenge for comprehensive conservation planning and protection of regional fish diversity in SSCS of the Australian Wet Tropics.