Spawning migration by freshwater eels to their marine spawning grounds is widely considered to be direct and rapid; however, emerging evidence suggests that eel migratory behaviour is more complex than previously thought, with potential implications for eel conservation and management. Over a 5-year period, we tagged 97 yellow-phase short-finned eels Anguilla australis with acoustic transmitters in the freshwater reaches of a south-eastern Australian river to: (i) examine environmental correlates associated with seaward migration; (ii) test the hypothesis that migration is rapid and direct once initiated and (iii) assess individual variation in behaviour associated with seaward migration. Twenty-three of the tagged eels migrated from fresh water into the estuary, whilst the remainder stayed within fresh water. Movement was detected primarily at night and eels entered the estuary throughout the year, with an increase in frequency over summer and following high river flows. Time in the estuary ranged from 1 to 305 days (median: 77 days). Movement into the sea was influenced primarily by the lunar phase, and to a lesser degree by water temperature, and occurred from late summer to early autumn. The extended residence and complex movements of migrating eels in the estuary suggest that they are considerably more vulnerable to exploitation than would be predicted by the generalised eel migration model of direct movement out to sea.