A microcosm experiment that addressed the interaction between eutrophication processes and contaminants was analyzed using a food web model. Both direct and indirect effects of nutrient additions and a single insecticide application (chlorpyrifos) on biomass dynamics and recovery of functional groups were modeled. Direct toxicant effects on sensitive arthropods could be predicted reasonably well using concentration-response relationships from the laboratory with representative species. Model predictions showed that nutrient additions alone caused only small effects on toxicant fate and effects probably due to the relatively high dissipation rate of chlorpyrifos. Enhancement of eutrophication effects by the insecticide was relatively small and seemed to be additive. The recovery of some affected functional groups was hampered in the indoor microcosms due to their isolation from outdoor seed populations. Introducing recolonization scenarios in the model simulated dose-dependent recovery. Recolonization increased the recovering rate after exposure to the pesticide. Modeling can extend the use of microcosms as a link between laboratory and field as this allows the prediction of effects and recovery of ecosystems for concentrations that have not been experimentally tested.