The impacts of mine contaminants on ecological connectivity in rivers and streams are poorly documented globally. We used acoustic telemetry to evaluate and refine conceptual models of fish movement in Magela Creek, a stream in the wet-dry tropics of Australia. This creek receives wastewater discharge from a nearby uranium mine, and a secondary objective was to describe behavioural responses of fish to one such discharge event. Of 55 fish (black bream Hephaestus fuliginosus, saratoga Scleropages jardinii, sharp-nose grunter Syncomistes butleri) tagged in dry season refuge pools 18 km upstream of the mine lease area (RPA [Ranger Project Area]), 16 (29%) moved downstream after the first wet season flows, using the RPA as habitat for 3–5 months before moving upstream to their previous locations as flows receded. Of 39 fish (spangled perch Leiopotherapon unicolor, barred grunter Amniataba percoides, black catfish Neosilurus ater) tagged ~ 8–12 km downstream of the RPA in the late wet season, only two were subsequently detected in the RPA. Direct and camera-based observations of 12 species of upstream-migrating fish during mine-water discharge in the late wet season showed no evidence of mine-water avoidance. Our results demonstrate that Magela Creek provides wet season habitat for fish within the RPA and acts as a migration pathway that connects lowland reaches and floodplains to upstream dry season refuges. Use by fish of waterbodies within the RPA highlights the need to manage the site to ensure that future contaminant egress and water quality do not adversely affect fish migration and habitat suitability.