We characterized the transport pathways of pharmaceuticals released from wastewater outfalls in one ofEurope’s largest estuarine systems (Tagus estuary, Portugal), to identify areas of ecological relevance prone toenvironmental degradation due to increased exposure to these emerging contaminants. Particle source,Lagrangian trajectories and arrivals over time (1, 6, and 10 days) were used as a proxy to determine the exposurepotential and vulnerability of different habitats to an array of pharmaceuticals with different environmentaldegradation rates and half-lives. Then, exposure potential was combined with information on sensitive habitatsto identify vulnerable areas in the estuary. Three different freshwater inflow scenarios were considered simu-lating Mediumflow, Noflow andflood conditions (Highflow). Model results for areas with higher particledensity were concordant with concentration hotspots of pharmaceuticals. Higher potential exposure in a largerarea of the estuary was observed for the High freshwaterflow; yet reduced particles export to adjacent coastalareas highlights the potential of estuaries and bays as particle sinks. In all modeled scenarios, vulnerable areaswere predominantly located in the southern bays up to day 6, and later in eastern areas, which include a naturereserve. These areas are largely composed of intertidal soft substratum and salt marshes habitats, and thuswarrant prioritization for monitoring and risk assessment of pharmaceuticals exposure in the Tagus estuary dueto the higher risk of exposure of a wealth of vertebrate and invertebrate species that use them. This frameworkallowed the identification of vulnerable areas to pharmaceutical contamination and can be a valuable instrumentto plan the location for wastewater treatment plants (WWTPs) in estuaries and coastal areas.