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The evolution of the bottom water in Amvrakikos Gulf in Ionian Sea at western Greece for a 50-year timespan was assessed by benthic foraminifera assemblages. The degradation of the bottom water of Amvrakikos has been a catalyst for the surface water degradation. The east basin has shown permanent low environmental quality in bottom waters since 1980, while the west basin has been under seasonal hypoxic regime since 2000. The most adverse environmental conditions occurred in 1990-2000 and 2005-2010 coinciding with the recorded fish mortality events. The major cause of the environmental quality improvement of the bottom water is the intrusion of seawater. In western areas of the gulf, where the influence of the seawater is high, the decreased temperature improves the environmental conditions, while in the areas influenced by river discharges (east and northern), the environmental conditions are depended on multiple causes like organic matter input and surface salinity.