A methodological approach based on rare earth elements analysis was developed to observe human activities in the stratigraphic sequence of Alagankulam. The site was one of the main ancient ports in south-eastern India and one of the transoceanic connecting points between East and West during the Classical Period. The sampled sediments where collected from vertical profiles, areas with traces of firing activities and filled deposits. Major, minor and trace element concentrations were measured by the means of spectroscopic and spectrometric techniques. Data from multielemental analysis were then cross-referenced together with archaeological evidence to map the variability within the site and its association with the detected anthropic activities. The matching of the interpretation of the archaeological record and the analytical data has allowed a combined mapping of visible and invisible traces of human activities in the site, giving a deeper insight of the Alagankulam occupational history.