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The distribution, composition and activity of phytoplankton, and accompanying changes in specific activities of bacterioplankton and copepods, were related to variahons in the vertical structure of the water column along a transect through the Skagerrak in May 1987. The Skagerrak is charactenzed by a doming of the pycnocline, with a deep mixed layer along the periphery and a very shallow pycnochne in central parts Average phytoplankton size increased with the depth of the upper mixed layer, and the central stratified area was characterized by small flagellates while large and chainforming diatoms dominated along the periphery. In situ fecundities of 2 copepod species (Ternora long~cornis and Acarha c l a u s ~) increased linearly with the concentration of phytoplankton (chl a ) > 8 pm and were, therefore, highest along the Skagerrak margin. Specific growth rates of bactenoplankton appeared to depend on particle surface area rather than particle volume or chla, and showed a distributional pattern that was nearly the inverse of the distribution of copepod activity. That is, peak bacterial growth rates occurred in central, stratified parts and lower rates were found along the margin with a deep mixed layer. Thus a 'microbial loop' type of food web seemed to be evolving in the central, strongly stratified parts of the Skagerrak, while a shorter 'classical' type of food web appeared to dominate along the margin. The relation between food web structure and verucal mixing processes observed on oceanwide scales, e.g. between oligotrophic ocean gyres and the major upwelling systems, thus seems to recur on much smaller honzontal scales.