Abstract Variation in river flow is a strong behavioural determinant for the movement of many freshwater fish species and often is linked to key aspects of their life cycle. The alteration of natural flow regimes to meet human water demands can result in changes to this variability, and cause declines in water‐dependent biota. Environmental flows are used as a remediation tool in some regulated rivers with the intention of restoring aspects of the natural flow regime to benefit riverine species, although empirical data are required to inform the efficacy of these interventions. Using acoustic telemetry, we quantified the movement responses of two large‐bodied native fish species (freshwater catfish, Tandanus tandanus and Murray cod, Maccullochella peelii) to variations in river flow over 4 years in two intermittent regulated rivers in the northern Murray–Darling Basin, Australia. Both rivers received periodic environmental flow releases and also there were several large natural flow events during the study period. Both species displayed a range of intra‐specific movement behaviours. Analysis of individuals' movements revealed five distinct functional groups, which were represented in both species. We found that periods of environmental flow delivery played an important role in the movement behaviour of both species. Murray cod were more likely to move during periods of environmental flow releases, whereas freshwater catfish were less likely to move on an environmental release following higher antecedent flows. No large‐scale philopatric movements were observed, yet Murray cod were more likely to move during the breeding period, indicative of nest site selection. We also found that the likelihood of movement in both species was higher in the smaller of the two rivers for a given magnitude of flow. Our results suggest that environmental flows may benefit certain fish species by facilitating, rather than cueing breeding behaviours, allowing individuals improved access to, and provision of, higher‐quality nesting habitats. These findings will aid water managers in creating economical and targeted environmental flow releases, timing larger flow pulses for the species with flow‐cued reproductive strategies, and providing a continuity of smaller baseflows for species whose reproduction is not dependent on flow cues but may be enhanced by greater connectivity.