Reports concerning the quantitative analysis of pharmaceuticals in marine ecosystems are somewhat limited. It is necessary to determine pharmaceutical fate and assess any potential risk of exposure to aquatic species and ultimately, seafood consumers. However, in Ireland very little research has been carried out to determine the presence of pharmaceutical residues in the aquatic environment. The research carried out investigates the occurrence of pharmaceuticals in the Irish aquatic environment and their potential to bioaccumulate in aquatic organisms and pose a risk to human health via dietary intake. Pharmaceutical residues were determined in liquid matrices, such as wastewater effluent, marine surface water (MSW) and artificial seawater (ASW), using solid phase extraction (SPE) in combination with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Pharmaceutical extraction from marine mussels and fish tissues required an additional pressurised liquid extraction (PLE) step prior to SPE and LC-MS/MS. The results of an in situ study, in which caged Mytilus spp. were deployed at three sites on the Irish coastline over a 1-year period are presented. All of the selected pharmaceuticals were quantified in wastewater effluent and marine surface waters and three out of the five monitored pharmaceuticals were detected in environmentally exposed mussel tissue. The potential for pharmaceutical bioaccumulation in fish via trophic level transfer was investigated. A 28-day in vivo experiment was carried out in a flow-through system in which rainbow trout were fed wild marine mussels sampled from one of the most contaminated sites in Ireland. Although low-level residues of trimethoprim were detected in the mussel tissues, no bioaccumulation was reported for this drug or any of the other selected compounds in the liver of the exposed fish. The effect of steaming on the concentrations of five pharmaceutical residues in exposed mussel tissue was investigated in an attempt to assess the potential risk of exposure to humans via ingestion of contaminated seafood. An in vivo experiment was carried out exposing marine mussels to pharmaceutical concentrations via direct injection and water uptake. A selection of water-exposed mussels were cooked (via steaming) resulting in a significant increase of parent pharmaceutical concentrations in the bivalves.