This study assessed black carbon (BC) dynamics, concentrations, and the organic matter (OM) isotopic carbon composition in northeastern South America drainage basin coastal sediments. Paraíba do Sul (PSR; Atlantic Rainforest, Brazil) coastal sediments displayed more 13C-enriched values (−22.6 ± 1.3 ‰ [n = 13]) than Amazon and Sinnamary (Amazon Rainforest in French Guiana and Brazil) sediments (−25.0 ± 3.1 ‰ [n = 14] and − 26.1 ± 1.0 ‰ [n = 6], respectively), indicating that local land-use basin changes have altered the OM composition, i.e., from natural C3 plant to C4 plants contributions. BC contents normalized to total organic carbon (TOC) content were 0.32 ± 0.24 (n = 8), 0.73 ± 0.67 (n = 6), and 0.95 ± 0.74 (n = 13) mg g−1 TOC for Amazon, Sinnamary and PSR samples, respectively, with BC sources appearing to differ according to different drainage basin vegetation covers. With increasing distance from the river mouths, BC contents exhibited different trends between the coastal zones, with values increasing for the PSR and decreasing values for the Amazon samples. BC distribution in Sinnamary coastal sediments did not display specific patterns. Regarding the Amazon coastal zone, BC contents decreased while the B6CA:B5CA ratios did not show a pattern, which could indicate that BC in the area originates from river transport (aged BC) and that the hydrophobic component of dissolved BC is removed. The BC content mostly increased in the PSR coastal zone, while the B6CA:B5CA ratios were not altered for the entire gradient, indicating the BC stability and possible atmospheric deposition of soot. Our findings indicate that different sources, transformation processes, and hydrological conditions affect BC contents within coastal zones. Continuous land cover changes in both the Amazon and Atlantic Rainforests may result in large-scale marine carbon cycling impacts.