Pollution of soils, sediments and especially ground- and surface water by a wide variety of chemicals, including emerging micropollutants necessitates the development of new, powerful strategies of mitigation, restoration and sustainable environmental protection. Micropollutants such as endocrine disruptor chemicals (EDC) represent an increasing concern which is only partially addressed by the use of physicochemical nonspecific approaches such as ozonation. An attractive and ‘greener’ alternative is the use of enzymatic biocatalysis for the removal and detoxification of micropollutants. In addition to the ease and reliability of enzyme usage, the biocatalytic properties of enzymes can be manipulated thanks to protein engineering, enzyme immobilization and bioreactor design. The ligninolytic enzymes of white-rot fungi (WRF) such as peroxidases and laccases are particularly suited to the degradation of micropollutants such as EDC, pharmaceuticals and personal care products. Thanks to their relatively low substrate specificity, these oxidoreductases can oxidize various micropollutants of phenol-like structure plus several non-phenolic substrates indirectly via the oxidized form of mediator molecules. The re-usability of enzymes and their separability from reactants and products is ensured by support-based immobilization or by formation of cross-linked enzyme aggregates (CLEA). These techniques are illustrated by several new technical developments facilitating enzyme retention in reactor systems. Although of high interest for biotechnological applications, reported CLEA conversion efficiencies for oxidative enzymes are still far from fulfilling these needs. Thus, we have identified relevant factors for the production of CLEA of laccases alone or in combination with other oxidoreductases and improved them by applying rational experimental design and optimization methodologies. The resulting CLEA were considerably more robust than their free counterparts. A uniform size distribution of the CLEA was shown using light microscopy, environmental scanning electron microscopy and dynamic light scattering. The results are exploited in continuous membrane reactors for the biotransformation of micropollutants such as bisphenol A or nonylphenol.