In the 21st century, humans are facing a high risk of exposure to emerging pollutants. Water contamination has become a major threat due to its devastating impacts on the entire ecosystem. Relatively great danger for aquatic microorganisms is posed by organic micropollutants, which are a consequence of progressing urbanization and industrialization. This review focuses on laccase of mainly fungal and bacterial origin, which provides an eco-friendly strategy for the transformation of these harmful pollutants to less or non-toxic compounds, as it acts oxidatively on the aromatic ring of a wide range of compounds, releasing water as the only by-product. Laccase alone or with the use of mediators has been used successfully to remove micropollutants from wastewater, including pharmaceuticals and personal care products, biocides, endocrine disrupting agents, steroid hormones, and microplastics. Even though the potential of an LMS (laccase–mediator system) is tremendous, the selection of an appropriate mediator and the persistent monitoring of toxicity after treatment are critical and should be performed routinely. Hence, further research is still needed for the optimization of degradation processes to improve our understanding of the different interactions of laccase with the substrate and to develop sustainable advanced water treatment systems.