Predicting ecosystem response to chemicals is a complex problem in ecotoxicology and a challenge for risk assessors. The variables potentially influencing chemical fate and exposure define the exposure scenario while the variables determining effects at the ecosystem level define the ecological scenario. In absence of any empirical data, the objective of this paper is to present simulations by a fugacity-based fate model and a differential equation-based ecosystem model to theoretically explore how direct and indirect effects on invertebrate shallow pond communities vary with changing ecological and exposure scenarios. These simulations suggest that direct and indirect effects are larger in mesotrophic systems than in oligotrophic systems. In both trophic states, interaction strength (quantified using grazing rates) was suggested a more important driver for the size and recovery from direct and indirect effects than immigration rate. In general, weak interactions led to smaller direct and indirect effects. For chemicals targeting mesozooplankton only, indirect effects were common in (simple) food-chains but rare in (complex) food-webs. For chemicals directly affecting microzooplankton, the dominant zooplankton group in the modelled community, indirect effects occurred both in food-chains and food-webs. We conclude that the choice of the ecological and exposure scenarios in ecotoxicological modelling efforts needs to be justified because of its influence on the prevalence and magnitude of the predicted effects. Overall, more work needs to be done to empirically test the theoretical expectations formulated here.