Bioremediation involves the exposure of a whole mixture of chemical structures to an intricate multispecies metabolic network present in a polluted scenario. The complexity involved in such events is growingly amenable to the conceptual frame and the tools of systems biology. The availability of genes, genomes, and metagenomes of biodegradative micro-organisms make it possible to model and even predict the fate of chemicals through the global metabolic network that results from connecting all known biochemical transactions. Microbial communities thus embody a landscape of pan-enzymes that is shaped by the freely diffusible metabolic pool (epimetabolome). Recent computational resources increasingly help the design of superior biocatalysts for biodegradation and biotransformations of desired chemicals, an objective that capitalizes on the new field of synthetic biology.