International agreements increasingly mandate restoration at landscape scales. Restoration actions are expanding for coastal seascapes globally, but planning is challenging because they are comprised of a heterogeneous and highly connected mosaic of ecosystems. This requires that seascape-scale coastal restoration programs prioritise actions both spatially (i.e. which ecosystems to restore, and where?) and temporally (i.e. should ecosystems be restored in a particular sequence?), and to what level of ecosystem condition. We surveyed fish assemblages, and the condition and context of six coastal ecosystems, including mangroves, seagrass, and oyster reefs, in 13 southeast Queensland estuaries over multiple years and used this data to prioritise restoration. Fishing is a key socio-economic driver of restoration in the region, so the abundance of common harvestable fish is the focus of this prioritisation. Results show that co-restoration of multiple coastal ecosystems has synergistic benefits for fish within this region. We use temporally dynamic spatial models to show that the choice of ‘starting’ ecosystem/s in restoration programs has implications for subsequent choices. Finally, we show how progressive change in the distribution of ecosystems across seascapes as they are restored proliferates into change in fish abundance. Consideration of both time and space is crucial in optimising the outcomes of seascape-scale restoration for key restoration objectives.