Simulation models are well-known informatic tools to manage environmental knowledge. Current approaches to ecosystems modelling are theoretically based on information theory, thermodynamics, topology, or systems theory. Water quality models are used for managing eutrophication problems. In the past, the Cottbus Eutrophication Simulator (CEUS) has been designed on the base of MATLAB and SIMULINK, which enables an user to couple the simulator with different software tools. To quantify these relations differential equations, some site constants and model specific parameters have to be specified. The fine tuning of parameters of an ecological model can be considered from the perspective of a suitable optimization procedure. Especially the commercial optimization software ISSOP realised different optimization algorithms which are traced back to one standard form of discrete optimization. In the paper, results of parameter optimisation will be presented for important water quality indicators. The results of parameter fine tuning and possibilities of parameter optimisation are discussed.