In densely populated urban areas, the pressure on water resources is considerable and will tend to intensify over the next decades. Preserving water resources therefore seems fundamental, but many questions remain as to the transfer of contaminants to subsurface waters in these largely sealed areas. Because of their toxicity and persistence in the environment, this work focused on the study of polycyclic aromatic hydrocarbons (PAHs), ubiquitous pollutants mainly produced by human activities. To better understand the main factors leading to the retention or transport of these pollutants in urban environments, vertical transects, from the surface to several meters down, were established on three study sites in or near Paris (France), selected according to an urbanization gradient. Soil samples collected at the surface and urban secondary carbonate deposits (USCD), similar to cave speleothems, sampled underground in quarries and aqueducts were analyzed. As the hydrophobic properties of PAHs favor their sorption onto organic matter, the latter was also studied using organic carbon analysis and UV fluorescence spectroscopy. The USCD located closest to the urbanized surface contained high concentrations of PAHs (76.8 ± 5.3 ng g−1), while the USCD located at greater depth with organic soil on the surface contained the lowest amount of PAHs (2.9 ± 0.4 ng g−1), and no PAHs with log KOC > 5. The results highlight the predominant role played by the presence of organic topsoil at the surface in retaining and storing large amounts of PAHs (1914–2595 ng. gsoil−1), particularly the most hydrophobic ones (i.e. 60% of the 15 PAHs are characterized by a Log KOC >5), which are also the most toxic. The lithology and thickness of the bedrock (between the surface and the USCD) also play an important role in the retention of PAHs, particularly those adsorbed on the particulate phase.