Wastewater reuse could provide a substantial relief from water scarcity, particularly for agricultural and industrial purposes. To meet future legislation and environmental standards in this regard, organic micropollutants must be efficiently eliminated in the treated effluent. Innovative water treatment technologies can contribute to achieve this goal, but their environmental consequences must be controlled. The objective of this study is to assess the environmental hotspots of an enzyme-based wastewater treatment system for the removal of sulfamethoxazole (SMX) as a model pollutant. For this purpose, the Life Cycle Assessment and Product Environmental Footprint methodologies have been applied to a conceptual process design based on laboratory-scale data. In addition, we addressed the relevant process parameters (i.e., the stability and reuse of the enzyme and the impacts associated with its immobilization), the comparison with consolidated technologies (membrane and ozonation systems) and the geographical situation (such as the electricity mix and the water stress level). The main hotspot of the analyzed treatment process is the production of the unspecific peroxygenase used within the magnetic biocatalyst, contributing more than 36 % to all impact categories considered. Focusing on the magnetic biocatalyst synthesis, the enzyme production phase and the functionalization of the immobilization support are the most problematic (with percentages of up to 75 % in stratospheric ozone depletion and 65 % in terrestrial ecotoxicity, respectively). In relation to resource consumption, water demand has been estimated at 0.02 m3 per cubic meter of treated water, but water deprivation can be much higher depending on the country (∼0.5 m3). Therefore, the use of reclaimed water can offset the indirect effects of its treatment. This study serves as a roadmap for future research to achieve reduced emissions by reduction of energy requirements, the use of renewable energy but also by increasing the enzyme stability. Furthermore, the background environmental impacts of the production of the biocatalyst must be reduced to improve the competitiveness against implemented alternatives based on physical (membranes) and chemical (ozonation) processes.