Marine fisheries and aquaculture are important contributors to global food security but disturb biogeochemical cycles from local to global scales. In this Review, we summarize how marine fisheries and aquaculture affect biogeochemical cycling of carbon, nitrogen and phosphorus, and discuss differences in the spatial scale, duration and magnitude of their biogeochemical consequences. Globally, marine capture fisheries and aquaculture remove approximately 21.0 Tg C year–1, 4.6 Tg N year–1 and 0.97 Tg P year–1 from the ocean, dominated by fish and shellfish removal. Point-of-harvest activities in marine capture fisheries result in biomass extraction, fishing gear impacts on the sea bed, fuel use and emissions, lost fishing gear and altered trophic structure. Aquaculture involves the addition and subsequent extraction of biomass, and habitat alteration during the introduction of farm structures. These disturbances affect the biogeochemistry of the water column and sediment, influencing the cycling and fate of nutrients over days to centuries and from local to global scales. For example, animals raised in aquaculture excrete 6.5 Tg N year–1 and 1.2 Tg P year–1, contributing to global-scale effects. Better incorporating these biogeochemical effects into environmental footprint assessments of products can guide more sustainable decision-making in the sector.