AbstractScientific visualization is proving very promising for the study of biological interactions at the organismal level in porous opaque media. We present our research in visualizing and modelling fungal and plant root development and interactions in the soil. Because the dynamic biological properties of the soil ecosystem can be observed in only the crudest fashion, we emphasize the fundamental link between visualization and modelling. Our research focuses along the parallel lines of imaging actual phenomena and of modelling these same phenomena. Many soil organisms, such as plants and fungi, exist predominately in a vegetative state which is highly branched, non‐random and non‐homogeneous. This structure itself is important to dynamic process such as parasitism of one organism by another, yet due to the opacity of soil, structure is difficult to observe and dynamic interactions are impossible to observe. The modelling of growth patterns and interactions of fungi and plant roots with the concomitant use of visualization and rigorous model validation provides the best method to build a working concept, which is faithful to the spatial organization of the real world. We hypothesize that the genetic determinants controlling growth and interactions operate both inside and outside the soil environment. We conclude that visualization provides a means by which spatial extrapolation of laboratory observations may be made to the real world, providing both model validation and a means to build mechanistically‐based hypotheses about different types of dynamic phenomena in the soil ecosystem, which can be tested in the