Coastal winds transport larval fish towards the coast and estuaries where they ultimately recruit, yet our understanding of the mechanism of how different coastal winds interact to influence estuarine recruitment is incomplete. Here, we first demonstrate a two-stage recruitment mechanism showing that larvae of coastally spawned species increased in abundance with moderately strong upwelling favourable winds 14 days prior to sampling, reflecting increased nutrient and plankton availability for larval fish. The larvae of coastally spawned species increased in abundance with onshore (downwelling favourable) winds three days prior to sampling, which retain larvae near the coast, facilitating estuarine recruitment through onshore transport. Secondly, we show that effects of wind during the spawning period can be detected 2–8 years later (depending on the species) in estuarine commercial fisheries catch rates. Finally, we show in the southeast Australian region, upwelling favourable winds have increased while downwelling favourable winds have decreased since 1850, potentially reducing larval recruitment to estuaries. The two-stage wind mechanism identified in this study is likely applicable to other regions where wind driven upwelling occurs and influences onshore and offshore transport. Future research should incorporate coastal winds into predictions of estuarine catch rates.