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Marinas are semi-enclosed environments characterised by reduced hydrodynamic energy, high sedimentation rates, and reduced oxygen levels. The ongoing development of activities and infrastructure construction are leading to deterioration in the quality of coastal aquatic environments, creating environmental risks. Trace metal elements (TMEs) and organotins are significant contaminants, prompting this study to evaluate the added value of spatiotemporal monitoring compared to one-time sediment assessments. Two Mediterranean harbours, Port Camargue (PC) and Port Carnon (C), differing in morphology and size, were monitored for a year with regular water sampling, focusing on TMEs and organotins. Sediment contamination, notably in the technical zone, revealed concentrations of Cu (309 and 1210 mg kg−1 for C and PC, respectively), Zn (242 and 425 mg kg−1 for C and PC, respectively), and tributyltin (TBT) (198 and 4678 µg (Sn) kg−1 for C and PC, respectively) surpassing the effect range medium (ERM), while other marina stations generally stayed below this threshold. Spatiotemporal water monitoring highlighted concentrations above environmental quality standards (EQS) at all stations of the larger marina. This exceedance was systematic for Cu and Zn in all samples, ranging respectively between 2.54 and 37.56 µg (Sn) L−1 and 0.63 and 33.48 µg (Sn) L−1. A notable temporal dynamic for TBT and Cu was also observed. Conversely, the open marina, connected to the open sea, rarely exhibited concentrations above EQS in water, despite sediment concentrations occasionally exceeding ERM values. This underscores that risk assessment in these ecosystems cannot rely solely on sediment characterisation. [ABSTRACT FROM AUTHOR]