For fish species with a planktonic larval stage, transport from the spawning ground to juvenile habitat is a critical aspect of their life history. While the upper estuary may provide higher turbidity and food supplies, which can be beneficial to early larval survival, larvae must also disperse to suitable recruitment habitat. Hydrodynamics, egg buoyancy, and larval behaviour may all influence dispersal. In estuaries, especially where strong stratification is present, variation in currents may occur over scales of centimetres to metres. Vertical variation in salinity can cause large velocity variations over short vertical distances. For small organisms in aquatic environments, hydrodynamics provides a large physical influence on their transport. Larvae, however, are not passive particles and may behave in ways which alter their location in the water column. The dominant research paradigm frames behaviour as an important feature in determining larval dispersal patterns, despite the magnitude of hydrodynamic influences. This study examined the balance between hydrodynamics and larval behaviour in determining the dispersal patterns of larvae of black bream (Acanthopagrus butcheri), an estuarine dependent species endemic to southern Australia. The study utilised a biophysical modelling approach, informed by empirical studies in both the field and the laboratory, to explore the dispersal of black bream larvae in the Mitchell River sub-estuary, part of the Gippsland Lakes in South-eastern Australia.