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Phthalate esters (PAEs) are the most widely used plasticizers worldwide and are considered as ubiquitous environmental contaminants. Due to both their ubiquity and potential health and environmental risks, their determination is a matter of worldwide concern. In the present study, an efficient method based on ultrasonic-assisted solvent extraction followed by gas chromatography-mass spectrometry is proposed for the simultaneous determination of PAEs and di(2-ethylhexyl) adipate in estuarine sediments and shells. Method optimization was successfully carried out according to Quality by Design principles. Shaking time, ultrasonic time, extractant volume, and solvent type were selected as Critical Method Parameters. Validation proved method reliability for the determination of the investigated analytes, achieving detection limits in the 0.1–0.7 ng g–1 and 0.1–0.5 ng g–1 range for sediments and shells, respectively. A good precision was obtained with RSD < 20% and trueness (recovery) in the 73(±7)–120(±10)% and 70(±10)–111(±3)% range, for sediments and shells, respectively. Finally, the method was applied to analyze sediment samples and mollusc shells, collected from the Curonian Lagoon (Southeast Baltic Sea). Di(2-ethylhexyl) phthalate was present in all the analyzed samples, thus pointing out its ubiquity in estuarine environment. PAEs were also found in shell debris or living mussels, highlighting them as a hotspot of organic contaminants, especially in transitional environments, where accumulation of organic rich deposits is limited.