A comprehensive knowledge of migratory behaviour is paramount for the effective management and conservation of fishes in coastal drainages. The Australian smelt (Retropinna semoni) is a common fish distributed throughout coastal and inland drainages in south-eastern Australia. Multiple life history patterns (potamodromy, facultative diadromy, estuarine residence) in the southern regions of its geographic distribution have been reported, and it is possible that some of these differences reflect characteristic behaviours of cryptic species within the group. To elucidate the life history patterns of smelt at the northern extent of their range and to identify any differences in migratory behaviour between two genetically distinct lineages (“SEQ-N”, “SEQ-S”) in this region, the movement patterns of Australian smelt were assessed using otolith chemistry. No evidence of marine residence was found based on otolith Sr:Ca and Ba:Ca transects for either group, suggesting that both are non-diadromous. Significant differences in multi-elemental otolith chemistry signatures were found among rivers and between paired sites within some rivers, suggesting no connectivity among drainages and limited dispersal of individuals over large spatial scales within rivers. These findings provide key insights into the migratory patterns of northern Australian smelt populations and, in combination with previous research, suggest that life history variation in the Australian smelt complex may occur primarily at the intra-population level rather than among genetically distinct lineages. Conservation and management strategies for Australian smelt should take limited dispersal and individual life history variation into consideration in order to protect the components of this important species complex.