The emergence of plant-based economies have dominated evolutionary models of Middle and Late Holocene pre-Columbian societies in South America. Comparatively, the use of aquatic resources and the circumstances for intensifying their exploitation have received little attention. Here we reviewed the stable carbon and nitrogen isotope composition of 390 human individuals from Middle and Late Holocene coastal sambaquis, a long-lasting shell mound culture that flourished for nearly 7000 years along the Atlantic Forest coast of Brazil. Using a newly generated faunal isotopic baseline and Bayesian Isotope Mixing Models we quantified the relative contribution of marine resources to the diet of some of these groups. Through the analysis of more than 400 radiocarbon dates we show that fishing sustained large and resilient populations during most of the Late Holocene. A sharp decline was observed in the frequency of sambaqui sites and radiocarbon dates from ca. 2200 years ago, possibly reflecting the dissolution of several nucleated groups into smaller social units, coinciding with substantial changes in coastal environments. The spread of ceramics from ca. 1200 years ago is marked by innovation and intensification of fishing practices, in a context of increasing social and ecological instability in the Late Holocene.