The short-term variability in pelagic-benthic exchange of phytopigments and the response of benthic bacteria to changes in phytopigment input in the bottom were studied in a temperature stratified water column including the sediment surface layer in the Oyster Grounds, North Sea, from 5 to 19 July 1994. The exchange of inorganic nutrients and phytopigments across the thermocline was limited during the cruise, with exception of a single short-lasting event on 14 July. This event resulted in enhancement of pigments throughout the water column and affected the pigment content in the surface mixed layer (SML) more and longer than in the benthic mixed layer (BML). The event did not result in a measurable change of sedimentation in the BML. The temporal variability of phytopigments in the SML was not reflected in the BML, where variations in phytopigments were determined by variations in tidal advection, sedimentation and resuspension. Variations in phytopigment fluxes to the bottom were demonstrated, with pigment sedimentation during slack tide exceeding sedimentation during full tide. The bulk of the phytodetrital material which settled during slack tide was resuspended during full tide. Nevertheless, there was net sedimentation of phytopigments, but insufficient to compensate for the decrease of the pigments in the sediment. The benthic phytopigment inventory gradually decreased during the cruise. Spatial variations in benthic phytopigments were significantly reflected by the spatial variations in bacterial variables, however the temporal decrease in algal pigments in the sediment was not reflected by the temporal variations in the benthic bacterial variables. Spatial relations between primary phytopigments and benthic bacterial production were decoupled in time implying that chlorophyll a and fucoxanthin are poor indicators of the amount of bacterial substrate in the absence of fresh algal input (directly utilizable organic matter). The spatial relations between benthic bacterial variables and benthic phytopigments however indicate that the dominant source of food for bacteria in the Oyster Grounds is phytodetritus.