St.-Petersburg model of eutrophication (SPBEM) has been modified for improving description of organic matter as a part of the nutrient biogeochemical cycles. The dynamics of labile and refractory fractions of dissolved organic nitrogen
and phosphorus are now described with four additional equations. The modification was tested at the Gulf of Finland in a numerical experiment made with plausible initial and actual boundary conditions for the years 2009—2014. Comparison of simulation with the available field observations indicates quite reasonable reproducibility of seasonal and inter-annual variations of spatial distribution of hydrophysical and biogeochemical characteristics, including almost a perfect match between simulated and observed dynamic of organic nutrients. The most important distinction from natural prototypes is the overestimated total amounts of inorganic nitrogen and phosphorus, which can be caused by the deficiencies in the prescription of initial and boundary conditions as well as in the current parameterizations of pathways and rates of
mineralization fluxes. The finer tuning of SPBEM-2 requires more extensive sensitivity analysis.