Iron, which is an essential element for marine photosynthesis, is sparingly soluble in seawater. In consequence, iron bioavailability controls primary productivity in up to 40% of the world’s ocean, including most of the Southern Ocean. Organic ligands are critical to maintaining iron in solution, but their nature is largely unknown. Here, we use a comprehensive dataset of electroactive humics and iron-binding ligands in contrasting regions across the Southern Ocean to show that humic substances are an important part of the iron binding ligand pool, as has been found elsewhere. However, we demonstrate that humics are mostly produced in situ and composed of exopolymeric substances from phytoplankton and bacteria, in contrast to other regions where terrestrially-derived humics are suggested to play a major role. While phytoplankton humics control the biogeochemistry, bioavailability and cycling of iron in surface waters, humics produced or reprocessed by bacteria affect iron cycling and residence time at the scale of the global ocean. Our findings indicate that autochthonous, freshly released organic matter plays a critical role in controlling primary productivity and ocean-climate feedbacks in iron-limited oceanic regions.