Author summary Many coastal marine ecosystems are threatened by anthropogenic activities, but often, the best way to restore and protect these important ecosystems is unclear. Conventional wisdom suggests that the 2 most effective conservation actions to benefit coastal marine ecosystems are implementation of marine protected areas or, alternatively, reduction of land-based threats. Active marine restoration is typically considered a low-priority option, in part due to high costs and low success rates. But does this conventional wisdom hold up to closer scrutiny? We developed a model to ask: should we restore or protect, on either the land or in the ocean, to maximise the extent of coastal marine ecosystems? We based the model on seagrass meadows and adjacent catchments in Queensland, Australia. Surprisingly, we found that direct, active marine restoration can be the most cost-effective approach to maximising extent of marine ecosystems over longer (decades-long) timescales. There is, however, substantial uncertainty in our understanding of the dynamics of complex linked land–sea ecosystems. Further, geomorphological and ecological conditions vary geographically. Therefore, we also used the model to investigate how uncertainty in key parameters affects decision-making outcomes. Our results can be used to guide investment into coastal marine conservation in the absence of complex, region-specific modelling.