Knowledge of the movement patterns of threatened fishes aids their conservation management and informs sustainable development of natural resources including freshwater. Prior to the expansion of a temperate upland reservoir in Australia, we used radio telemetry to compare seasonal differences in the diel movements of adult endangered Macquarie perch (Macquaria australasica) (235–414 mm total length) in Cotter Reservoir, Australian Capital Territory. Macquarie perch exhibited a diel range of 389 ± 46 m, a diel mobility of 769 ± 93 m and diel area use of 24008 ± 5595 m2 among four seasons. Diel range was significantly higher in winter compared with other seasons, and diel mobility was negatively correlated with fish size among four seasons. Macquarie perch inhabited deeper water in summer across the diel cycle (7.2 ± 0.5 m) in comparison with other seasons (spring: 3.8 ± 0.3 m, autumn: 3.0 ± 0.2 m, winter: 3.0 ± 0.3 m). Within seasons, both remote and manual telemetry identified that diel activity was predominantly crepuscular. Prey availability and the threat of avian predation represent the most likely explanations for the differences in seasonal movements. In a reservoir where expansion will likely result in a loss of critical habitat (emergent macrophytes) for this endangered species, we use site-specific knowledge of the spatial ecology of Macquarie perch to inform the placement of shelter habitat prior to filling the enlarged reservoir.