The mergence of microfluidics and nanocomposite materials and their in situ structuring leads to a higher integration level within microsystems technology. Nanoparticles (Cu and Ag) produced via laser radiation were suspended in Poly(dimethylsiloxane) to permanently modify surface material. A microstructuring process was implemented which allows the incorporation of these nanomaterials globally or partially at defined locations within a microbioreactor (MBR) for the determination of their antiseptic and toxic effects on the growth of biomass.