Blue carbon ecosystems (BCE) play an essential role in the global carbon cycle by removing atmospheric carbon dioxide and storing it as organic carbon (OC) in biomass and sediments. However, organic matter (OM) deposition and degradation/preservation processes are poorly understood, especially on the long-term and at molecular scales. We analysed sediment samples from six cores collected in tidal marshes, mangroves and seagrasses (up to 150 cm long cores spanning up to 10,000 yrs of OC accumulation) from Spencer Gulf (South Australia), by pyrolysis (Py-GC–MS and THM-GC–MS), and we compared the results with elemental and stable isotope data, to decipher OM provenance and to assess degradation/preservation dynamics. The results showed that: (1) the major biopolymers preserved were polysaccharides, polyphenolic moieties (lignin and tannin) and polymethylenic moieties (e.g. cutin, suberin, chlorophyll) with smaller apportions of proteins and resins; (2) the OM originates predominantly from vascular plant materials (in particular lignocellulose) that have been well-preserved, even in some of the oldest sediments; (3) mangroves were found to be the most efficient OC sinks, partially explained by syringyl lignin preservation; (4) seagrasses were shown to store polysaccharide-enriched OM; (5) large proportions of polycyclic aromatic hydrocarbons (PAHs) in surficial tidal marsh and mangrove sediments probably reflect pyrogenic OM from industrial combustion, and; (6) “ecosystem shifts”, i.e. mangrove encroachment in tidal marsh and transition from seagrass to mangrove, were detected. Deposition environment and source vegetation control OC sequestration and there is no specific recalcitrant form of OM that is selectively preserved. For the first time, we demonstrate how analytical pyrolysis in combination with stable isotope analysis can be used to reconstruct (palaeo-)ecological shifts between different BCE. This study improves our knowledge on OC accumulation dynamics and the response of BCE to environmental change, which can inform the implementation of strategies for climate change mitigation.