Pacific Island countries have an extraordinary dependence on fisheries and aquaculture. Maintaining the benefits from the sector is a difficult task, now made more complex by climate change. Here we report how changes to the atmosphere–ocean are likely to affect the food webs, habitats and stocks underpinning fisheries and aquaculture across the region. We found winners and losers—tuna are expected to be more abundant in the east and freshwater aquaculture and fisheries are likely to be more productive. Conversely, coral reef fisheries could decrease by 20% by 2050 and coastal aquaculture may be less efficient. We demonstrate how the economic and social implications can be addressed within the sector—tuna and freshwater aquaculture can help support growing populations as coral reefs, coastal fisheries and mariculture decline.