Coastal fisheries contributed substantially to population growth and complex forms of social organisation in eastern South America in pre-European times. In the Atlantic Forest coast of Brazil, these societies produced shell mounds (locally known as sambaquis) and shallow archaeological sites with abundant fish and shellfish remains that offer snapshots of past species diversity and distribution. Babitonga Bay hosts the largest concentration of coastal archaeological sites in Brazil, playing a prominent role in our understanding of long-term human-ocean interaction in subtropical and tropical South America. In this paper, we reviewed pre-European fish catch composition and associated fishing artefacts from archaeological sites in this region spanning the last 6000 years. Our results reveal changes in fishing practices and an increased capture of pelagic and high trophic level species from 2000 to 1500 years ago. This “fishing up the marine food web” coincided with the appearance of single-piece baited fish hooks and evidence for the colonisation of oceanic islands. The results indicate an expansion of fishing to deep waters and invite us to reconsider the antiquity of the human footprint on ocean ecosystems in the region.