Climate‐driven environmental change is increasingly impacting global fisheries and marine resource use. Fisheries provide a broad range of economic, social and cultural benefits while delivering essential contributions to nutrient security and human health. Despite this, little is known about how climate change will impact the availability and quality of seafood‐derived nutrients. Here, we quantified spatial and temporal changes in the nutritional quality of the commercially harvested eastern school whiting, Sillago flindersi, sampled throughout the south‐east Australian ocean warming hotspot. Several nutrients measured in S. flindersi, including protein, ash, polyunsaturated fatty acids (PUFA) and the omega‐3 PUFA–docosahexaenoic acid (DHA, 22:6ɷ3), were related to one or more environmental factors (sea bottom temperature, depth and chlorophyll). We also detected seasonal variability in DHA and ash composition throughout the species' commercially harvested distribution. Historical and future spatial modelling predicted a decrease in DHA of up to 6% with increasing ocean temperature under future Representative Concentration Pathway (RCP) 4.5 and 8.5 emission scenarios. Overall, our results identified S. flindersi as a rich source of protein and essential PUFAs for human consumers and supported emerging evidence that reductions in seafood‐derived essential nutrients may occur under future ocean warming, specifically reductions in omega‐3 fatty acids. The development of nutritional quality forecasting tools for seafood holds the potential to inform fishers and managers of locations and times of the year to target species with optimal nutritional quality.