Abstract X-ray fluorescence scanners, such as the Itrax™ Core Scanner (Itrax) (Cox Analytical Systems, Mölndal, Sweden), provide high-resolution geochemical data within several hours. However, the semi-quantitative nature of these analysers has hampered their use to study pollution. This study explores Itrax’s capabilities to detect trace metals, such as Hg and Cd, in the Ría de Pontevedra harbour (NW Spain). A set of Itrax detection levels were proposed for each metal after comparison with quantitative measurements obtained from Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES) and Vapour Atomic Absorption Spectrometry (CVAAS) analyses. These quantitative data obtained after a sequential extraction were used to evaluate pollutant bioavailability and to determine metal pollution levels exhibiting Hg pollution. The reliability of inc/coh and Br/Cl ratios to assess the total organic matter variability was also evaluated. The results indicated that the Itrax is an efficient and fast option to monitor contamination, thereby avoiding laborious discrete analyses and reducing analytical cost and time.