The increasing number of pharmaceuticals in the environment and their difficult biodegradation, can lead to bioaccumulation in different trophic compartments. Their bioaccumulation can have negative consequences, especially in the generation of bacterial resistance by antibiotics, but also in the impairment of plant and animal metabolism. The Tejo estuary in Portugal is the habitat for many plant and animal species, which are also prone to this type of contamination. Therefore, in the present study different classes of emerging pollutants (EPs) were surveyed in water samples in the Tejo estuary, including antibiotics, anticonvulsants, antidepressants, lipid-lowering drugs, anti-inflammatory drugs, beta-blockers and analgesics. According to the results, only four compounds were detected in water samples collected at the three selected salt marshes, including carbamazepine, fluoxetine hydrochloride, venlafaxine hydrochloride and acetaminophen. Having the detected substances as a basis, a subsequent study was performed aiming to investigate the uptake and biodegradation capacity of halophytes, using Tripolium pannonicum as a model plant cultivated under controlled conditions with different concentrations of the found EPs. This experimental approach showed that T. pannonicum was able to uptake and degrade xenobiotics. Moreover, the application of sulfamethazine, as a model antibiotic, showed also that this species can uptake and degrade this compound, although the degradation rate and process proved to be compound-specific. This was also confirmed using crude plant extracts spiked with the different EPs. Thus this species is a potential candidate for the remediation of marine water and sediments contaminated with environmentally-significant EPs.