Experimental enclosures were used to follow responses of the plankton~c microbial food web to varying short-tern~ (5 d) perturbations induced by adding inorganic nutrients ( N and P) and a top predator (fish) during a 21 d period in late summer, on the coastal area of the Baltic Sea. Biomass, production, growth and grazing of pico-and nanoplankton assemblages were estimated, and a carbon budget for the microbial loop during the experiment was constructed. The microbial food web was a highly dynamic system. Varying perturbations due to nutrient loading and the top predator provoked eutrophication in the enclosures, but they affected the microbial loop only slightly. The amplitudes of oscillation in abundance of coupled communities were amplified, but the frequencies of oscillations in the microbial loop were not affected by the perturbations. Changes in the route of carbon flow through the microbial food web occurred In relatively short time scales. These changes seemed to be dependent on the phasing of the coupled oscillations between the communities, and the structure within the different communities. Ciliates were only loosely connected to the microbial loop: although ciliates and heterotrophic nanoflagellates (HNF) showed predator-prey-like coupled oscillations, the ciliates gained most of their carbon from other sources, and most of the HNF carbon loss was due to factors other than ciliates. HNF were the most important consumers of picoplankton during the HNF maximum, but they were also dependent on other sources of nutrition.