Pyrolysis coupled with gas chromatography–mass spectrometry (Py–GC–MS) has been previously proved to be an appropriate tool for the screening of organic contaminants in sediments. In this work the double-shoot pyrolysis technique has been applied to assess the contamination degree of sediment samples from Castro Marim Natural Park (South Portugal) and the Ria of Huelva (SW Spain). Compounds released both by thermodesorption at sub-pyrolysis temperatures (250–280°C) and subsequent pyrolysis (300–500°C) revealed information on the origin of the sedimentary organic matter and the occurrence of organic contamination in the sediments. Thermal desorption was found to be effective in releasing organic contaminants from spiked samples. However, in real sediments samples, higher pyrolysis temperatures (>300°C) were necessary to detect the occurrence of organic contaminants. Particularly polycyclic aromatic hydrocarbons (PAHs) and linear alkylbenzenes (LABs) were detected in variable proportions in most sediment samples.