The present study assesses the vulnerability of groundwater seawater intrusion using the GALDIT method in the rural and coastal Almyros basin, in Thessaly, Greece. Excessive groundwater abstractions, mainly for irrigation, have degraded the quality and quantity of Almyros basin’s aquifer. Seawater intrusion vulnerability indices have been estimated for the period 1992-2015 using the original GALDIT method and the modified GALDIT method with the weights being estimated through the Analytical Hierarchy Process (AHP) (GALDIT-AHP). The weights in the modified GALDIT-AHP have been estimated based on the pairwise table responses of 15 experts. The average, median and the mode of the 15 experts have been used to find the final weights in the modified GALDIT-AHP method and three variations of the method have been applied (i.e. GALDIT-AHP (Average), GALDIT-AHP(Median), and GALDIT-AHP (Mode)). The GALDIT and modified GALDIT-AHP results have been validated against observed Cl concentration measurements in the Almyros basin aquifer, using the Spearman's rank correlation coefficient. The results indicate that the weights of the original GALDIT index and the modified GALDIT-AHP indices differ affecting the estimated vulnerability in seawater intrusion. All indices's values range from low to high vulnerability at the Almyros aquifer and the coastal area, respectively, for all the studied periods. The original GALDIT index, the modified GALDIT-AHP (Average) and the modified GALDIT-AHP (Median) present similar results. It seems that the most appropriate method for the estimation of the vulnerability in seawater intrusion is the modified GALDIT-AHP (Mode) index because it exhibits the highest correlation to the observed Cl concentrations.