Subsurface chlorophyll maxima are common phenomena in both the coastal and open ocean. The main objective of this study was to clarify possible differences in the structure and function of the plankton community in subsurface chlorophyll maxima and at the surface. Sampling was performed at seven stations in the Skagerrak, northeast Atlantic, during five cruises in May and August 1992 and April, May and August 1993. Subsurface chlorophyll fluorescence maxima (FM) occurred on 25 out of 32 sampling occasions. The FMs were usually situated below the pycnocline and associated with the nutricline. The ratio of chlorophyll a to particulate carbon and the light-saturated primary production were higher for plankton at the FM than at the surface, although assimilation numbers (primary production rate:chlorophyll a) were not different from surface plankton. The light protective pigment diadinoxanthin occurred in higher concentrations relative to chlorophyll a in surface plankton than in FM plankton. Respiration was higher in the FM than at the surface. This was not related to abundance of bacteria or bacterial production since no differences between surface and FM values were detected for these parameters. FM plankton was characterized by high nutrient uptake rates, but in this study there were no significant differences compared to surface plankton. 'New' production was on average 25%, but up to about 50% in the western Skagerrak in spring. The average nitrogen uptake rates were dominated by the regenerated nutrients ammonium and urea, accounting for about 50 and 25%, respectively. The <3 mu m size fraction contributed significantly to concentrations of total chlorophyll a, particulate carbon, and nitrogen as well as to nitrogen uptake. Its contribution was highest when total values were low. Microscopical investigations and analysis of pigments specific to algal groups showed that diatoms dominated in the FMs in spring and that peridinin-containing dinoflagellates dominated in FMs in August. Autotrophic nanoplankton was dominated by the Prymnesiophyceae contributing about 50% of total cell numbers. Colonies of Phaeocystis sp. were abundant along the NW Danish coast in April and May 1993, Autotrophic eukaryotic picoplankton occurred in cell numbers up to about 30 x 10(6) cells . dm(-3) along the Swedish coast. The highest cell numbers of cyanobacteria of the Synechococcus-type, about 100 x 10(6) cells . dm(-3), were found in the central Skagerrak in August and the abundance of Synechococcus was correlated with nitrogen uptake in the <3 mu m size fraction.