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. In the work presented herein, analytical methods were optimised and validated for the quantification of pharmaceutical residues in wastewater effluent, receiving marine waters and marine mussels (Mytilus spp.). Selected pharmaceuticals included two non-steroidal anti-inflammatory drugs (NSAIDs) (diclofenac and mefenamic acid), an antibiotic (trimethoprim), an antiepileptic (carbamazepine) and a lipid regulator (gemfibrozil). This paper also presents 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. In water samples, pharmaceutical residues were determined using solid phase extraction (SPE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). The extraction of pharmaceuticals from mussel tissues used an additional pressurised liquid extraction (PLE) step prior to SPE and LC-MS/MS. Limits of quantification between 15 and 225ng·L(-1) were achieved in wastewater effluent, between 3 and 38ng·L(-1) in marine surface water and between 4 and 29ng·g(-1) dry weight in marine mussels. Method linearity was achieved for pharmaceuticals in each matrix with correlation coefficients of R(2)≥0.976. All five selected pharmaceuticals were quantified in wastewater effluent and marine surface waters. This work has demonstrated the susceptibility of the Mytilus spp. to pharmaceutical exposure following the detection of pharmaceutical residues in the tissues of this mussel species at measurable concentrations.