Depending on climate conditions, bathymetry, basin morphology, management practices and other factors, some reservoirs are more or less prone to stratification, which can strongly affect both chemical and biological status of water. In the Goczalkowice Reservoir (the biggest dam reservoir in the south of Poland), water quality parameters, such as chlorophyll a concentration, change very dynamically. In the presented study, the Estuary, Lake and Coastal Ocean Model (ELCOM) was applied to simulate water thermodynamics in a period of summer and autumn when the highest concentrations of chlorophyll a were observed, based on the continuous water monitoring in the ZiZOZap project (Łaszczyca et al., 2011). The purpose of the application of ELCOM was to simulate the thermal stratification in the reservoir and to prepare a basis for analyses of the relationship between water thermodynamics and quality. Simulations allowed the identification of several short water mixing events in summer and the final mixing event at the end of summer. The study also included the first application of model results to analyse the relation of changes in water temperature with observed concentration of chlorophyll a (ChlA). Analysis confirmed that each water mixing event was followed by a significant increase in ChlA concentration.