Microfluidic processes which are accompanied with structural changes at the solid–liquid interface are monitored with in situ grazing incidence small angle X-ray scattering (GISAXS) using a micro-focused X-ray beam. Changes of the nanostructure of a film of nanospheres dispersed in a matrix of sodium alginate of algal origin and its cross-linked analogue are followed during flow of water through a microfluidic channel. The initial structural changes caused by the laminar flow in the microfluidic channel are traced and demonstrate the high sensitivity and the possibilities of the in situ GISAXS technique.