Groundwater vulnerability assessment is critical for the effective groundwater management, particularly in areas with significant anthropogenic activities, such as agriculture. In this study, seven different methods, namely, DRASTIC, Pesticide DRASTIC, SINTACS, Nitrate SINTACS, GOD, AVI, and SI, were implemented using Geographical Information System techniques in Nea Moudania aquifer, Chalkidiki, Greece, to evaluate and identify groundwater vulnerability zones. The study area was classified into five categories: very low, low, moderate, high, and very high vulnerability. The southern and south-western parts of the study area had the highest pollution potential; the corresponding potential is lower in the northern part. Furthermore, single-parameter sensitivity analysis has revealed that the vadose zone and the topography were the most influential parameters of the vulnerability indexes, while the hydraulic conductivity exhibited the lowest effective weight. Finally, nitrate concentrations, taken from 23 observation wells, were employed for the validation of the aforementioned seven methods, using the coefficient of determination (R²). Results showed that Pesticide DRASTIC and Nitrate SINTACS were the most accurate and efficient methods for the present study area, which is characterized by intense agricultural activities.