Pharmaceuticals are present in water (river, estuaries, coastal waters) and sediment. The available information about their levels in the coastal ecosystems is scarce. In this chapter, a review is carried out about the ecotoxicity of pharmaceuticals focused on marine environment, in organisms from different trophic levels—from bacteria to fish. The biomarker approach and new omic technologies are considered as tools for environmental risk assessment of these compounds. In fact, the –omic technologies is a promising tool for evaluation of global molecular and cellular responses of an organisms to pharmaceuticals exposure. Nevertheless, their employment in marine organisms are scarce because of limited genomic resources.