Coastal ecosystems are increasingly impacted by expanding and diversifying human impacts, leading to reductions in valuable ecosystem services like fisheries. Many coastal restoration programs therefore include fish biodiversity and fisheries recovery as key and stated goals. However, few studies have appropriately used quantitative information regarding the drivers of fish assemblage structure and distribution across seascapes to identify preferred actions and sites. Fewer still have continued this quantitative approach through to using key fish species as success indicators. We used data describing fish assemblages and habitat condition and extent collected for 13 estuaries and six coastal habitats in southeast Queensland over three years to illustrate 1) that fish assemblages can be used to optimise the quantitative selection of target/reference ecosystem conditions, 2) how spatial modelling approaches can be used for individual indicator species to optimise planning, and 3) how landscape scale restoration that accounts for the positioning of both remnant habitat patches and newly restored sites can result in synergistic improvements in the abundance of key fisheries species. We finish by introducing a new collaborative project between UniSC and OzFish seeking to test these modelled spatial patterns quantitatively across Moreton Bay for shellfish reef restoration.