This focus of the study was on system dynamic models that could be useful for modelling environmental processes in Lake Engure. The paper considers the system dynamic model development principles, the most important elements and structure. The aim of the study was to describe possible methods of ecosystem process modelling that allow to represent the actual state of ecosystems and provide opportunities to predict further processes. The methods of ecosystem modelling considered in the paper reveal interactive factors of anthropogenic and environmental processes that influence changes in ecosystems. System dynamic models indicate not only interactions between various factors in the environment but also the most important driving forces. These models are based on flowchart and algorithm systems, which represent changes using mathematical functions in a graphic or tabular form. In the case study of Lake Engure, connections between factors that influence ecosystems in the study area were identified. Specialised software, PowerSim Studio Academic 9.0, was used for modelling. The model consists of qualitative and multifactor data of Lake Engure ecosystems, such as water chemical, physical and hydrological parameters, biological, ornithological and other data collected in the study area. Development of this modelling method will make it possible to evaluate the impact of various processes on biological diversity changes in the study area and to identify the most important problems. Furthermore, this method could improve environmental management practice in the surrounding municipalities, and it will also be possible to make similar models of ecosystem quality in other regions.