A horizontally integrated, time-dependent physical-biogeochemical model of high vertical resolution has been developed for the Baltic Sea proper. A seasonal pycnocline model computes the physical state of the mixed surface layer. Below this is an advective-diffusive model. The vertical advection is caused by a time-dependent, entraining bottom current which transports dense seawater into the system. The vertical distributions of volumes and sediment areas are accounted for by the use of the hypsographic function of the system. The chemical/biological processes controlling the distributions of nitrogen and oxygen are modelled as follows: Primary production is controlled by light, temperature, nutrients and density stratification (critical depth). Nutrient recycling, nitrification and sedimentation are accounted for using simple, rather general process descriptions. Organic matter is broken down both in the water column and at the bottom. Denitrification in the water and sediment is controlled by the concentrations of oxygen, nitrate and organic substrate and by temperature. Sulphate reduction to hydrogen sulphide occurs during anaerobic conditions once nitrate has been depleted. The daily meteorological forcing of the model is synthetic and randomly selected from monthly statistical distributions of observed weather components. The dense water inflow from the sea used in the model is synthetic as well. Loadings of biologically active nitrogen compounds from rivers and atmospheric fall-out, representative of contemporary conditions, are used. We have run the model for a 20 year period. When compared to the field data the computed dynamics of the mixed layer and the patterns of primary production, nutrients and oxygen appear quite realistic. Due to the effect of intermittent convection in early spring nutrients are utilized down to the perennial halocline (at about 65 m depth). The conditions in the deep water, below the perennial halocline, are also well reproduced by the model, possibly except for too high ammonia concentrations during anoxic conditions. Since the dense bottom current usually is interleaved in or just below the perennial halocline the upper deep water is well oxygenated. The renewal of the lower deep water, below about 130 m, is a discontinuous process and this water may be stagnant for several years. During such periods the water becomes anoxic and high concentrations of ammonia and hydrogen sulphide may eventually result. Denitrification at the sediment redoxcline is quantitatively much more important than denitrification in the water column. Primarily since the lower deep water holds only 5% of the total volume, the influence of processes in this water mass upon the total nitrogen budget is found to be negligible.