As in other fields of science and engineering, the need to understand and predict biofilm systems both on a physical and on a technical scale results in an increasing demand for reliable and efficient numerical simulations of the different processes that take place within biofilms. For that, the expertise of biofilm specialists on the one hand and modern computational techniques on the other hand have to be brought together. In this paper, we present results of a combined and interdisciplinary attempt to simulate fluid flow and transport in defined pure-culture biofilms at the level of continuum mechanics. In order to provide a realistic setup for the simulation and to offer possibilities for a validation of the obtained results, our approach is embedded into state-of-the-art confocal laser scanning microscopy including automated image acquisition and semi-automated image analysis within extended 3D-regions of biofilm structures, which allow both the generation of real-life starting geometries for simulation purposes and the direct comparison of computed and experimental data. An important issue of our approach is flexibility, and the used code NaSt++ offers extensions for taking into account biomass growth or EPS as well as for dealing with more than one substrate.

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