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We reconstructed the palaeoenvironmental conditions of Cartagena Bay during the Holocene after a multidisciplinary study to identify natural variations and the anthropic processes of this coastal area. A total of 119 samples were recovered for amino acid racemization dating, 3 for radiocarbon dating (14C), and four sets of 80 samples for sedimentological and palaeontological determination, mineralogical content, biomarker and trace elements quantification. Two natural scenarios were identified from the variations of n -alkane indices and palaeobiological content. The first period (6650–5750 yr cal BP) was marked by the development of euhaline marine conditions with strong inputs from aquatic macrophytes and high biodiversity. After a hiatus, the area underwent a profound change, becoming a paucispecific brackish marsh environment with increasing inputs from land plants, with possible episodes of emersion with a greater presence from terrestrial gastropods (3600–300 cal yr BP). By combining trace element abundance and stanol distributions, our study also provides a novel approach to identify the predominant influence of anthropogenic factors in the last three millennia in the coastal record of Cartagena Bay. Findings confirmed that Pb mining and metallurgy began during the Bronze Age, with considerable inputs of this heavy metal into the atmosphere during Phoenician, Punic and particularly Roman times compared to the Middle Ages. Pollution by Cu and Zn was also observed during Punic and Roman times, and was first documented in the Middle Ages. In addition, faecal stanols, such as coprostanol, derived mainly from humans, and 24-ethylcoprostanol from herbivores were present, thereby indicating for the first time a continuous presence of human populations and significant pollution input since 3600 yr cal BP, this being greater in the late Bronze Age and Phoenician, Punic and Roman times than during Late Antiquity and the Middle Ages, when the city was in decline. [Display omitted] • Euhaline marine conditions and high biodiversity occurred at 6650–5750 yr. • A paucispecific brackish marsh environment occurred at 3400–300 yr after an hiatus. • Faecal sterols revealed pollution from herbivores and humans since Bronze Age. • Pb–Zn–Cu linked to regional mining-metallurgy since Bronze Age to Middle Ages. [ABSTRACT FROM AUTHOR]