Several pesticides and pharmaceuticals (PP) have been detected in the effluent of a full-scale Portuguese Wastewater Treatment Plant (WWTP). Their presence contributed to the environmental burdens associated with the existing treatment of the Municipal Wastewater (MWW) in the impact categories of Human Carcinogenicity, Non-Carcinogenicity, and Freshwater toxicities on average by 85%, 60%, and 90%, respectively (ReciPe2016 and USEtox methods). The environmental and economic assessment of the installation of an Anodic Oxidation (AO) unit for PPs’ removal was performed through Life Cycle and Economic Analysis, considering two types of anodes, the Boron-Doped Diamond (BDD) and the Mixed Metal Oxides (MMO). The operation of the AO unit increased the environmental burdens of the system by 95% on average (USEtox), but these impacts can be partially compensated by the avoided the production of non-renewable energy in the Portuguese electricity mix by biogas cogeneration at the WWTP. If the construction of the AO unit and the manufacturing of the electrodes are considered, the Human and Freshwater Toxicities are often higher than the environmental benefits derived from the PPs’ removal. On the economic side, the MMO configuration is clearly more advantageous, whereas BDD is environmentally more favorable. The issue of the presence of PP in MWW effluents has to be addressed as an integrated solution both improving upstream PP’s management and adopting PP’s removal technologies strongly supported by renewable energies. Further insights are needed for the assessment of fate and of the environmental effects of PP in the sludge.