In the current paper are presented the results of a multidisciplinary study (stratigraphical, sedimentological, geophysical and geochemical) combined with modern techniques (G.I.S. and remote sensing). This study aims at integrating the natural and anthropogenic factors affecting the Korissia lagoon. It is a shallow coastal lagoon, communicating with the sea via an artificial channel. The area around the lagoon consists of alluvial sediments hosting, in places, newly formed and/or “old” (pre – Holocene) sand-dunes. The broader area constitutes a post- alpine sedimentary basin characterised by smooth morphological relief. The lower stratigraphic unit of the post-alpine sequence is a Pleistocene marly formation, which was detected as the basement (5-15 hm.m) by the geophysical survey. The resistivity-based basement map implies the existence of a “palaeo-gulf” trending E- W. These marls constitute the impermeable basement of a shallow aquifer hosted in the area. The salinity of the lagoon is very high during summer (>40psu) but it does not affect significantly the wells around it. The lagoon is well oxygenated, while the wells have lower D.O. values. Ammonia and nitrates are the main inorganic Nitrogen forms, in the lagoon and the wells, respectively. Phosphorus is the limiting factor for phytoplankton growth. Human activities affect the area that is in need of an environmental management plan in order to prevent ecological degradation.