The construction of dams and weirs, and associated changes to hydrological and hydraulic (e.g., water level and velocity) characteristics of rivers is a key environmental threat for fish. These multiple stressors potentially can affect fish in a variety of ways, including by causing changes in their movement, habitat use and activity. Understanding how and why these changes occur can inform management efforts to ameliorate these threats. In this context, we used acoustic telemetry to examine habitat use, longitudinal movement and activity of two lowland river fishes, Murray cod Maccullochella peelii and golden perch Macquaria ambigua, in a weir pool environment in south‐eastern Australia. We compared our results to published studies on riverine populations to determine if their behaviours are similar (or not). We show that M. peelii and M. ambigua in a weir pool exhibited some similar behaviours to conspecific riverine populations, such as strong site fidelity and use of woody habitat for M. ambigua. However, some behaviours, such as large‐scale (tens–hundreds of kilometres) movements documented for riverine populations, were rarely observed. These differences potentially reflect flow regulation (e.g., stable water levels, loss of hydraulic cues) in the weir pool. The two species also exhibited contrasting responses to dissolved oxygen conditions in the weir pool, which may reflect differences in their life history. Overall, this study shows that although some aspects of these two native fishes' life history can continue despite flow regulation, other aspects may change in weir pools, potentially impacting on long‐term population persistence.