Spatial and temporal variations in pelagic carbon fluxes were examined by means of a large-scale and long-term monitoring data set from the Kattegat, a shallow marginal sea impacted by man-induced eutrophication. Flows of carbon, nitrogen and phosphorus in the upper mixed layer (0 to 10 m) were estimated from a simple descriptive model using measurements of primary production, temperature, and phytoplankton/zooplankton biomass as input variables. For all years combined, annual primary production at coastal stations (171 g C m(-2) yr(-1); 8 stations) was almost twice that at the deeper open-water stations (105 g C m(-2) yr 1; 5 stations), which resulted in an annual primary production of 116 g C m(-2) yr(-1) for the region as a whole during the entire study period (1989 to 1997). Interannual variation in primary production was substantially smaller than the between-station variation. The phytoplankton spring bloom contributed substantially to annual production (10 to 20 %), but the magnitude and timing were highly variable between years. Respiration accounted for on average 12 % of the measured primary production. Annual sedimentation was estimated at 55 g C m(-2) yr(-1), equivalent to 54 % of net primary production. The estimated new production was significantly related to nitrogen loading from the land and atmosphere, and a regression analysis predicted declines of between 20 and 47 % in annual net primary production from a 50 % reduction in nitrogen loading. Carbon and nutrient fluxes are consistent with those of earlier studies from the Kattegat based on small-scale and short-term data sets. However, combining monitoring data with a budget model greatly improved data resolution in both time and space. Estimated C/N/P fluxes from the model can act as reliable indicators for assessing the state of eutrophication in the Kattegat and other inland seas impacted by man-induced nutrient loading.