Along with rapid population growth in Vietnam, there is an increasing dependence on groundwater for various activities. An Giang province is known to be one of the agricultural intensification areas of The Vietnamese Mekong Delta (VMD). This study aimed to evaluate the spatiotemporal variation of groundwater quality for a period of ten years from 2009 to 2018 in An Giang. The weighted groundwater quality index (GWQI) was developed based on the fuzzy analytic hierarchy process (Fuzzy-AHP) for assigning weighted parameters. The results show that that shallow wells in the Northeast and Southeast regions of An Giang were mostly categorized under “bad water” quality with high arsenic (As) concentration over the years partly due to huge amounts of sediment deposition in monsoon season. Overall, the reason for the poor groundwater quality in An Giang was the combined effect of both natural and human activities. On the other hand, we detected high values of GWQI links with high As concentration in areas where people extract more groundwater for irrigation. Temporal variation of GWQI suggested that groundwater quality at eight wells has improved from 2009 to 2018 in the wet season as compared to the dry season. The reason behind the improvement of groundwater quality during wet season was the decrease in river discharge, which causes less deposition of suspended solids near the flood plains. Moreover, the filling of unused wells can reduce the movement of pollutants from unused wells to groundwater aquifers. Although there was not sufficient evidence to show the relationship between As and sediment concentration, the temporal reduction trend in river discharge and suspended solids was detected in An Giang. The understanding of groundwater quality can help policymakers protect and manage limited water resources in the long-term.