The article describes the general structure of the simulation model, the most important principles for describing the processes of bio-hydrochemical transformation of nutrient (C, N, P, Si) compounds, and the dynamics of dissolved oxygen in the ecosystem of the Vistula Lagoon (VL), Baltic Sea. Based on the results of long-term observations, tuning of the model parameters was performed, its adequacy and sensitivity to changes in parameter values were checked, within-year variations of nutrient compounds, components of the planktic and benthic parts of the VL ecosystem, turnover periods, as well as fluxes (balances) of dissolved and suspended solids between the selected components of the model were calculated and analyzed. Model calculations showed fairly good qualitative and quantitative correspondence of the simulated results to observed data for all variables of the simulation model. Practical implementation of computational procedures for model tuning proves that with the proposed algorithms for finding the parameters for the bio-hydrochemical block of the simulation model the
optimization problem can be solved effectively even where the amount of observed data is insufficient and their variance is rather high. Attention should be given to statistically significant among-year variations in the values of the empirical parameters of the model. One should be cautious using the same values of model parameters in running computational experiments for different years of observations and in predicting VL ecosystem development in response to changes in external conditions. We quantified turnover times for the model components of the VL ecosystem. In a vast majority of cases there existed significant among-year variations in the turnover times for the model variables. Calculations of the balances of dissolved organic substances, as well as detrital nitrogen, phosphorus, and silicon have led us to an important conclusion that heterotrophic bacterioplankton and protozoa play a significant role in the processes of nutrient compound transformation in the lagoon ecosystem.