Maliakos Gulf is a semi enclosed embayment influenced by the Spercheios River, with high human activity both in the marine environment and the surrounding land. The existing information concerning its biological processes is very limited. Three stations, from the river mouth to the outer gulf, were sampled monthly at standard depths during two periods of investigation. Measurements in the pelagic included temperature, salinity, dissolved oxygen, depth of euphotic zone, nutrients, suspended particulate matter (SPM), chlorophyll a, primary productivity, abundance and biomass of mesozooplankton, sedimentation of SPM, dissolved organic carbon (DOC), bacterial abundance, river discharge of nutrients and suspended matter. In the sediment, granulometry and organic matter, carbon and chlorophyll at three layers were measured. Spercheios river is a source of nutrients and suspended matter. Most of the introduced SPM is low in organic carbon. Neither typical thermocline nor halocline is observed in the pelagic while most of the parameters measured show no depth variation. Nutrient concentrations are higher than those of the open Aegean decreasing, however, after the winter phytoplankton bloom. Chlorophyll is high with a decreasing gradient from the inner to the outer gulf. Bacterial abundance is coupled with chlorophyll. Conversely, the mesozooplankton growth shows a time lag of 2-4 months from the phytoplankton bloom. Copepods are the dominant zooplankton group but the presence of larvae of benthic invertebrates is important in November and June. Sedimentation of particulate matter is higher in the inner gulf especially in winter. Most of the particle flux is inorganic. The fate of the winter phytoplankton bloom is sedimentation. The sediment is mud with high content of organic matter and carbon compared with similar ecosystems. Higher concentrations are found in the outer part and lower in the inner with no difference between the three layers. Sediment chlorophyll is higher, especially in the summer and in the top layer, in the inner gulf where the smaller depth allows penetrating light to reach the bottom. Concentrations of phaeopigments are higher than chlorophyll, indicating continuous environmental pressure that the microphytobenthos is under mostly because of the increased turbidity in the water column which regulates the light available at the sediment surface. The winter phytoplankton bloom is influenced by the river since the former occurs when the river input starts to increase. The riverine in inorganic particles is reflected to the uniformity of the bottom, the high sedimentation of inorganic matter and the high concentrations of SPM in the gulf. The trophic web in the gulf seems to oscillate between an eutrophic and an oligotrophic period. The eutrophic period -winter- is followed by rapid sedimentation of phytoplanktonic cells due to the large size of the dominant diatoms and the lack of grazing by the zooplankton, and by the decrease of nutrients due to the consumption by the phytoplankton. These events lead to the dominance of pico- and nanoplankton which excrete larger quantities of labile DOC, the most suitable substratum for bacterial growth. Thus, in the spring and summer there is a closer relationship between bacteria and phytoplankton. The increase of bacteria is followed by an increase of the microzooplankton the most important grazers of bacteria, which turn is grazed effectively by the mesozooplankton; the latter peaks the spring.