A model (DALIS 1.0) of pelagic zone trophic interactions was developed using long-term, comprehensive data sets of the Sulejow Reservoir. We calibrated the model using observations from the pelagic zone of the Sulejow Reservoir made between 1999 and 2001. The model performed well in the description of Daphnia sp. – L. kindtii interactions when hydrological conditions were stable. A discrepancy between observed and simulated results was found when water inflows were high, which washed out the biota. We suggested that the hydrological impacts should be coupled in the updated DALIS model. Using DALIS, we also tested two scenarios: the food web model (A) without Leptodora; and (B) without YOY fish, under both good and bad food conditions for Daphnia. Results indicated that Leptodora would have a more significant impact on the reduction of Daphnia biomass than juvenile fish during some periods. As the maintenance of high Daphnia densities is recognised as a key factor in top-down effects, the DALIS model may provide frameworks that support ongoing empirical work. It is therefore recommended that the model be incorporated into the programme of the Sulejow Reservoir restoration.