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In the rural and coastal Almyros basin in Magnesia, Greece, the objective of the current study is the assessment of aquifer vulnerability to seawater intrusion using the GALDIT approach. The Almyros aquifer system’s quality and quantity have declined as a result of unsustainable groundwater abstraction for irrigation. The Analytical Hierarchy Process (AHP) of Multicriteria Analysis has been used for the modification of the GALDIT index based on the statistics of experts’s responses to questionnaires on the influence of hydrological, hydrogeological, and other parameters. For all methodologies and time periods, the aquifer’s coastline section had high susceptibility levels, whereas the northeast and southeast had lower values. The most vulnerable area of the aquifer changes over the various time periods of analysis.