ABSTRACTUnderstanding ecosystem dynamics is essential for ecological research and resource management. Bioenergetic or allometric trophic network models are effective in elucidating these interactions. However, aligning them accurately with empirical data remains challenging. Our present study contributes to such efforts by developing a trophic network model to describe population dynamics at Lake Võrtsjärv, Estonia, with a focus on predator–prey relationships and energy considerations. We calibrate this model to empirical biomass time series data using numerical optimization methods, a process previously applied to bionergetic models with considerably fewer guilds and/or parameters. Our approach emphasizes aligning the model closely with empirical time series and yields 77%–81% similarity between the modeled average dynamics and recorded biomasses. Despite relatively high similarity, the models we tested for noise—those assuming observation noise, as well as those incorporating environmental noise through stochastic differential equations—could not describe the annual variation of biomasses realistically. Overall, our tentative results demonstrate both the potential and the challenges involved in calibrating bioenergetic models to empirical data from large food webs.