Environmental flows are applied to regulated rivers, predominantly with the aim of benefiting native fauna. However, the outcomes for biodiversity and the mechanisms that underpin changes due to these manipulations are poorly understood. We examined the effects of elevated water release, of the magnitude used for riffle maintenance, on the movement and habitat use of the locally-threatened two-spined blackfish, Gadopsis bispinosus, in the Cotter River, a regulated upland stream in south-eastern Australia. We compared the behaviour of radio-tagged individuals during baseline flow conditions (0.12 m3 s-1) and during elevated flow releases (1.74 m3 s-1). Eight individuals (196 ᠸ mm TL) were radio-tracked at one site over 22 days, and six individuals (180 ᠵ mm TL) were monitored by fixed telemetry stations at a second site for 1 month. At both the sites, two-spined blackfish were nocturnal and occupied small linear ranges (23 ᠶ m). They preferentially used pools, but also used runs and riffles. Elevated discharge did not significantly affect movement, activity or dispersal of two-spined blackfish. Two individuals utilised inundated vegetation during high flow. Despite a small number of behavioural changes, there was no response to elevated flow at the population level. It is likely that the benthic nature of this species precludes its behaviour being affected by a 15-fold increase in-stream discharge. However, the indirect effects of flows of this magnitude on two-spined blackfish, and their responses to discharges of greater magnitude, remain to be investigated.