During the last years, there has been a growing interest in the research focused on the pharmaceutical residues in the environment. Those compounds have been recognized as a possible threat to aquatic ecosystems, due to their inherent biological activity and their “pseudo-persistence”. Their presence has been relatively few investigated in the marine environment, though it is the last receiver of the continental contamination. Thus, pharmaceuticals monitoring data in marine waters are necessary to assess water quality and to allow enhancing future regulations and management decisions. A review of the current practices and challenges in monitoring strategies of pharmaceuticals in marine matrices (water, sediment and biota) is provided through the analysis of the available recent scientific literature. Key points are highlighted for the different steps of marine waters monitoring as features to consider for the targeted substance selection, the choice of the marine site configuration and sampling strategies to determine spatio-temporal trends of the contamination. Some marine environment specific features, such as the strong dilution occurring, the complex hydrodynamic and local logistical constraints are making this monitoring a very difficult and demanding task. Thus key knowledge gap priorities for future research are identified and discussed. Suitable passive samplers to monitor pharmaceutical seawater levels need further development and harmonization. Non-target analysis approaches would be promising to understand the fate of the targeted molecules and to enhance the list of substances to analyze. The implementation of integrated monitoring through long-term ecotoxicological tests on sensitive marine species at environmental levels would permit to better assess the ecological risk of these compounds for the marine ecosystems.