Dispersal is the process in which individuals are transferred between populations, and is essential for population sustainability and longevity. In estuarine soft sediment communities, dispersal often occurs as the interaction between the individual and tidal flows. Many coastal benthic marine invertebrate populations have been considered open because of the dispersal potential of a pelagic larval phase, with populations maintained by an external supply of recruits. However, for estuarine populations, recent evidence has suggested that populations may be more closed because of local hydrodynamic conditions causing larval retention within the source estuary. In this thesis, field observations and numerical simulations were used to investigate the effect of estuary morphology on the transport and retention of benthic invertebrate larvae in Tauranga Harbour, a large (218 km2), shallow (mean depth = 2.8 m) meso-tidal estuary. Previous studies indicate that residence times extracted from hydrodynamic modelling vary throughout the harbour, due to residual circulation patterns caused by complex channel morphology. Field observations indicate increased abundance and differing community composition of invertebrate larvae in the upper harbour compared to the lower. Tidal circulation is asymmetrical, with transport through a seaward channel during flood tides, and in a landward channel during ebb, suggesting that larval retention in the upper harbour may provide a source of larvae for the lower harbour. Larval transport pathways were evaluated by a coupled hydrodynamic-transport model and confirmed those observed in the field. Modelled larvae, released under different stages of spring-neap tidal cycle in the upper harbour, were retained for up to 16 d whereas retention for larvae released in other harbour locations was much more variable and depended on the timing of release and direction of initial transport. Results of this study highlight the impact of complex channel morphology (particularly at a scale of 10s to 100s of meters) on the large scale circulation and subsequent transport and retention of benthic invertebrate larvae. Understanding these influences on the transportation of benthic invertebrate larvae and the identification of retentive regions, will aid future population management or conservation efforts