A lot of small and shallow bays that exist along the extended Greek coastline differ significantly from the open sea in the fluctuation of hydrological parameters, the degree of eutrophication and the concentration of pollutants. These characteristics can sometimes create environmental conditions that favour the development of specific ecosystems like the algae mats. The chemical behaviour of dissolved and particulate forms of the most interesting, from the environmental point of view, trace metals along with the variations of salinity and temperature as well as the eutrophication degree in a bay near Athens, Greece was studied in this paper for the period of 1 year (July 2000-June 2001). The results of this study showed that the waters inside the bay are of a higher eutrophication level than the neighbouring open Saronikos gulf. In most cases, the cove's water is enriched in both dissolved and particulate metals in comparison to the neighbouring coastal area and the various parts of Saronikos gulf. The low rate of water renewal, the increased particulate matter, the algal mat and certain human activities (mainly during the warm period of the year) are the main reasons. A good correlation between the fluctuations of the concentrations of some metals inside and outside the cove also occurs. It indicates the contact between the area's water masses and the need for environmental planning covering a wide area around the system.