Comprehensive, multi-year studies of microbial processes in an ecosystem context are important in understanding microbial regulation of ecosystem structure, function and variability. A 3 yr study on microbial community was carried out in a coastal area in the northern Adriatic Sea (Gulf of Trieste). It is a semi-enclosed shallow system, mostly controlled by pulsed external inputs, which determine a high variability of plankton communities. Samples were collected monthly at 2 stations from January 1999 to December 2001. Data illustrate remarkable inter- and intra-annual variability in parameters relevant to carbon biogeochemistry and ecosystem energy flow patterns. Integrated primary production (PP; 135 g C m–2 yr–1) in 1999 tripled (414 g C m–2 yr–1) in 2000, returning to a low level (150 g C m–2 yr–1) in 2001. Bacterial production (by 3H-leucine incorporation) accounted, on average, for 35.3% of net PP in 1999, 9.5% in 2000 and 29.4% in 2001. Flux into the microbial loop via bacterial