Identifying and conserving sites with consistently high settlement is necessary for protecting recruitment of coastal fish populations. We investigated the initial settlement patterns of coastally spawned juvenile fish entering 4 temperate estuaries with narrow entrances (<500 m wide) on the eastern coast of Australia. Habitat structure (seagrass cover, blade length and syngnathid density), landscape (patch isolation, perimeter to area ratio and distance to ocean) and hydrological factors (maximum current speed, tidal volume and modelled delivery of passive particles) were investigated as possible explanations for settlement patterns into seagrass beds. One site within Lake Macquarie and 1 site within Smiths Lake were found to have consistently high settlement of 9 coastally spawned taxa over different months and were therefore identified as settlement ‘hotspots’. The magnitude of tidal volume, the modelled delivery of passive particles and patch isolation together explained 70% of variation in settlement. Sites of high settlement were characterised as (1) being near to a high-volume channel supplying an abundance of larvae and (2) being isolated from other seagrass patches to concentrate settlement. Monthly variation in settlement, while affecting species composition and total fish abundance, did not alter the relative importance of the identified hotspots, suggesting that these common factors were driving settlement across different species.