The conditions of eutrophication are described in three lagoon systems differing by their structure, their catchment area and their connection with the sea : the Bassin d'Arcachon on the Atlantic coast, SW France, the semi-artificial fish ponds of the Bassin d'Arcachon, and the Etang du Prevost on the Mediterranean . The Bassin d'Arcachon is a shallow semi-enclosed bay, strongly influenced by climatic factors and tidal currents . The Bassin receives significant inflow of freshwater and the waters are only partially renewed . The greatest part of the primary production is due to the seagrass Zostera noltii . Although the ecosystem remains on the whole in steady state, some evidence of potential eutrophication are visible . For instance, the flux of nitrogen into the Bassin d'Arcachon has increased by more than 50% during the last 25 years . The most significant change among primary producers is the massive development since 1988 of the green alga Monostroma obscurum . The fish `reservoirs' of the Bassin d'Arcachon are man-made enclosures designed for extensive aquaculture and where the water renewal is only possible during certain periods of time . Thus, because of the shallowness and the confined nature of these fish ponds, acute eutrophication is sometimes observed in summer . The Etang du Prevost is extremely eutrophic due to agricultural and urban run-off . Red waters occur periodically during the warm summer months as a consequence of ecological events beginning in the early spring with a bloom of green macroalgae (Ulva sp.) . In summer, the algal biomass is degraded by aerobic heterotrophic bacteria ; the oxygen demand encompasses the oxygen production, leading to the predominence of anaerobic processes and dystrophic crisis . From the comparison of the selected sites, three stages of eutrophication are recognized according to the conceptual model of Nienhuis (1992) describing the relation between the relative dominance of primary producers connected to the availability of nutrients . Such macroscopic observations should, now, be explained by the study of microbiological processes including meiofauna, protozoa, bacteria and all the components of the microbial loop .