Human and veterinary pharmaceuticals have been recognized as ubiquitous water microcontaminants with potential subtle detrimental effects on aquatic organisms. The majority of pharmaceutical compounds, after being consumed and excreted, end up in municipal WWTPs, which are not typically designed for complete pharmaceutical removal. Therefore, effluents from WWTPs constitute a low concentration, but continuous source of pharmaceutically active compounds to the aquatic environment. The main objective of the thesis is to acquire and provide with knowledge not only on the occurrence of pharmaceutical compounds in wastewater, but on their biodegradation within WWTPs and their discharge into the receiving media. The obtained results demonstrate conventional wastewater treatment’s variable efficiency when removing the pharmaceutical compounds load and the advance treatment’s contribution to their overall removal. It has also been possible to model the behaviour of a selected pharmaceutical and its transformation products. And it also includes investigation of an antibiotic’s impact on the bacterial community performance, and the antibiotic resistance genes phenomenon. Finally, the role and usefulness of proteomics when investigating the possible proteins involved on the biodegradation pathways of certain pharmaceutical compounds.