Marine ecosystems and associated fisheries support lifestyles, livelihoods and economic activities in the Torres Strait but are increasingly at risk from climate change. Understanding the nature and extent of climate change impacts on key species in this tropical marine socio-ecological system will help prepare Traditional Owners, communities and stakeholders to navigate the changes, manage risks and adapt. We analysed trends in ocean and atmospheric variables and synthesised changes that have taken place in key Torres Strait marine habitats and resources since the 1970s. We found increasing trends in temperature, marine heatwaves, sea level and dry-season wind run. Other variables including solar exposure, rainfall, Fly River (Papua New Guinea) discharge and net primary productivity show variability but no trend, and are typically aligned with large El Niño Southern Oscillation (ENSO) events. Habitats such as mangroves, seagrass meadows and coral reefs are naturally variable, but sensitive to compounding climate extremes, including ENSO-related anomalies and sustained ocean warming. Our study further explores the dependence of commercial and cultural fisheries on these foundation habitats, highlighting that habitat fluctuations combined with ocean warming are already impacting some fisheries (e.g. tropical rock lobster). Cultural totemic species such as dugongs and green turtle are also under pressure from climate change. Our synthesis informs efforts to respond and adapt to climate change. We discuss progress on ocean and ecosystem models to investigate the impacts of future climate change on key fisheries. We provide examples of current adaptation measures and discuss potential new ones. This work builds on inclusive and trusted partnerships with Indigenous peoples and stakeholders living in a changing system.