Abstract Flow cells (or ‘transparent micromodels’) are widely used to observe complex processes in two dimensional (2D) porous media. The objective of this study is to design, develop, and apply a wet-etched glass micromodel suitable for the observation of biofilm formation, transport of microorganisms and flow measurements using Particle Image Velocimetry (PIV). PIV in this case can be used for the visualisation and quantification of flow diversion. The wet-etching technique applied here is relatively straightforward. The paper addresses all aspects involved necessary to perform these experiments. The chosen etching depth of around 25 μm proved to be well suited for transport experiments with microorganisms. We show that the micromodel containing a wet-etched cell (wafer) provides a high quality image of transport and growth of microorganisms in porous media. The microorganism Pseudomonas chlororaphis was used as a model strain to perform the experiments on biofilm formation and transport. In the transparent cell, we could clearly observe biofilm formation. Moreover, we showed that PIV techniques can indeed visualize the change in flow pattern caused by biofilm presence.