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Spatial and seasonal distribution patterns of suspended particulate matter, particulate organic carbon (POC), particulate nitrogen, chlorophyll a and phytoplankton abundance and biomass were analysed along two transects in the southern Adriatic and northern Ionian Seas. Moreover, 2 years of samples collected by sediment traps at one selected station for each transect are used to assess the variability of fluxes of biogenic (organic carbon, total nitrogen, carbonates, biogenic silica) and lithogenic constituents. According to the low suspended matter concentration, the two study areas can be considered as representative of oligotrophic systems. The availability of diverse nutrient forms (inorganic or organic), due to the different water column structure and circulation dynamics, affected the structure of phytoplankton communities. Along the Adriatic transect, the influence of waters coming from the northern Adriatic was evident at the surface of the western stations. The phytoplankton community was mainly represented by diatoms and nanoflagellates. In the northern Ionian, particulate matter concentration decreases with respect to the Adriatic stations (st. A1) and the community was dominated by nanoflagellates (54% in cell number), and coccolithophorids (26%). In the southern Adriatic, the vertical mixing convection related to the climatic variability, supplying inorganic nutrients in the upper layers from the deep, represents the dominant process, increasing primary production and downward fluxes of particulate matter in early spring. Higher mass fluxes measured at the bottom are likely due to horizontal and advective contributions of material originated in the shelf area and transported into the basin by mesoscale circulation. Vertical fluxes in the Ionian mainly depend on production processes occurring in the photic layer, such as spring and autumn blooms, controlled by the seasonal mixing and dynamics of the water column. Fluxes are characterised by discontinuous and short-time events correlated with the end phase of micro-phytoplankton blooms. At both stations, the low carbon export (less than 4% of primary productivity) indicates high carbon utilisation and/or high degradation efficiencies of particulate organic matter, i.e. fast recycling in the upper water column.