In the framework of the PROOF-PECHE project (http://www.obs-vlfr.fr/proof/vt/op/ec/peche/pec.htm) a multi-disciplinary team performed experiments and collected samples during the DYNAPROC2 cruise aboard the RV Thalassa from September to October in 2004. The cruise provided data on the functioning of the pelagic food web by sampling over a month long period in the NW Mediterranean Sea at a fixed station subject to weak horizontal advection currents during a period of hydrological stability. This paper describes the background of the cruise and provides an overview of the results derived from the campaign which constitute the special section. The major objective of the cruise was to assess the relative importance and variability of the pathways of carbon in the open ocean. Intensive sampling through 4 periods of 5 days each was accomplished at a site near the DYFAMED time-series site. The site was near stable in terms of hydrodynamics as there was some evidence of an intrusion of low-salinity coastal water. The cruise yielded a comprehensive data set acquired by sampling over a vertical spatial dimension (0-1000 m) and at high frequencies ( ranging from every 3, 6, 12 and/or 24 h), unique for the summer to autumn transition in the North Western Mediterranean. Parameters investigated included the biochemical composition of dissolved organic matter ( lipids), and the structure of bacterial communities, phytoplankton and zooplankton community compositions and abundances, as well as zooplankton metabolism, and particulate organic carbon fluxes. Nearly all the parameters described in this section, as well as reports appearing elsewhere, showed time-course variabilities of similar magnitude to those known from a previous study of the spring-summer seasonal transition, a period of marked hydrological change, at the same study site. Remarkably, the least variable characteristic of the system appeared to be the identities of the dominant taxa across several trophic levels (copepods, phytoplankton, ciliates, and bacteria) throughout the study period despite large shifts in stock sizes and fluxes. Thus, the studies of DYNAPROC 2 documented considerable temporal variability of stocks and rates in a system which was, from a hydrological and taxonomic point of view, relatively stable.