Contrasting organic matter signatures reveal the vulnerability of carbon storage in semiarid mangroves

• Two semiarid mangroves show contrasting organic matter sources and carbon stocks. • Organic matter in impacted mangrove is C-depleted, N- and O-rich, driven by allochthonous river inputs. • Organic matter in preserved mangrove is C- and H-rich, driven by autochthonous mangroves inputs. • Carbon stocks are higher and carbon is more stable in preserved mangrove. We analyzed sediment organic matter (OM) and carbon stocks in two semiarid mangroves in northeastern Brazil, Pacoti and Jaguaribe, along a river gradient. Pacoti, a protected site, contrasts with Jaguaribe, impacted by human activities – shrimp farming, agriculture, and urban effluents. Sediments cores were characterized for granulometry, OM (%LOI), carbon (C) and nitrogen (N) content, UV–Vis and 3D fluorescence spectroscopy, and Rock-Eval pyrolysis (HI, OI -Hydrogen and Oxygen Index, I, R indices). Pacoti exhibits higher mean C content (2.16%; 0.44–5.80), higher C/N ratios (21.75; 13.6–28.7), high HI, and low OI, consistent with predominantly autochthonous OM from mangrove vegetation. Jaguaribe sediments have lower C content (1.2%; 0.02–2.46) despite similar OM levels, lower C/N ratios (15.1; 10.7–29.8), low HI, and high OI, reflecting carbon-depleted, river-derived OM influenced by anthropogenic inputs and a higher river-to-mangrove area ratio. Rock-Eval I and R ratios and 3D fluorescence indicate greater OM stability and humification with depth in Pacoti than in Jaguaribe. Consequently, Pacoti stores up to five times more carbon than Jaguaribe (85.8 vs. 16.4 MgC ha −1 ), with more persistent storage over time, challenging Jaguaribe’s role as a carbon sink. Jaguaribe carbon accumulates downstream in finer sediments, making it vulnerable to erosion. These results emphasize the critical role of OM source, stability, and sediment granulometry in determining carbon stocks. Accurate blue carbon assessments in mangrove sediments must integrate OM stability and granulometry analysis in addition to carbon content.