Six different soil food webs, assembled from a bacterium, a bacterial-feeding nematode, a fungus and a fungal-feeding nematode, were established in replicated laboratory microcosms. Glucose was supplied as the sole carbon source for the microbes. Biomasses of the organisms and the concentration of dissolved organic carbon (DOC) were measured ten times during 20 weeks. A discrete dynamic model based on the material flow between system components was fitted to the experimental data. Bacterial-based food chains were largely inactive in the absence of fungi, but mutual facilitation was observed in the systems with both fungus and bacterium. The population dynamics of a fungal-feeding nematode was adequately described by the models, but the model failed to describe DOC dynamics. The quality of fungal biomass appeared to be a key parameter in the system. Model performance was improved by letting fungal parameters vary with time and food web structure. Because fungal dynamics could not be explained by a trophic-dynamic model with rigid parameters, it is suggested that non-trophic effects of fungal-feeding nematodes on fungi may be more important in microcosms.