We report organic carbon (OC) accumulation rates in three freshwater ecosystems in southern Brazil, along the largest shallow coastal lagoon ecosystem in the world, the Patos-Mirim-Mangueira. After European colonisation in the seventeenth century, regional wetlands started being replaced by agricultural fields (mostly rice). We used excess 210Pb to develop chronologies for lagoon sediment cores and quantify bulk sediment and OC accumulation rates. In the past 120 years, OC accumulation rates in Mirim and Mangueira Lagoons, which are influenced by rice paddies, averaged 14.9 ± 8.5 and 6.4 ± 3.7 g C m−2 year−1, respectively. Greater accumulation rates were estimated for macrophyte-dominated Nicola Lake (69.9 ± 38.5 g C m−2 year−1) located within the protected Taim Wetland with no direct influence of rice plantations. Starting in the early twentieth century, the construction of dams and drainage canals altered regional hydrology. Despite these anthropogenic changes, only a mild increase in OC accumulation was observed in Mirim Lagoon (15% only in site MIR2) after 1970. Mangueira Lagoon experienced the lowest OC burial rates despite increasing sedimentation rate and OC burial after the mid-1970s. This is probably because these large lakes (> 500 km2) have great nutrient-dilution potential, and their well-mixed water columns prevent nutrients from accumulating in the sediments over time.