Anguillid eel populations are under threat globally. A particularly vulnerable life‐cycle stage is the migration of mature adult eels downstream from freshwater habitats through estuaries into the sea to spawn. This study investigated the factors associated with downstream migration of the short‐finned eel Anguilla australis (Richardson 1841) from a coastal wetland (Lake Condah) in south‐east Australia, using acoustic telemetry. Migration was associated with time of the year, higher water level and river flows, decreasing water temperature, and darker moon phases. Larger individuals and those in better condition were more likely to migrate from the wetland. Downstream migration peaked in spring, in contrast to the typical autumn migration period for other temperate anguillids. Variable responses, in comparison to other studies, highlight how migration cues may not be universal. In south‐east Australia, short‐finned eels may have evolved to migrate in multiple phases by first migrating to the estuary during typical seasonal spring flow pulses (e.g., to avoid being stranded in upland reaches during dry summer periods) and then migrating into the ocean in autumn. More research is needed to unravel these processes and causes, especially considering that the relationship between migration and hydrology may be complex and confounded (e.g., by human‐induced disruptions to migratory pathways).