The coastal aquifers and inland waters of the Long Xuyen Quadrangle and Ca Mau Peninsula of southern Vietnam have been significantly impacted by sea water intrusion (SI) as a result of recent anthropogenic activities. This study identified the evolution and spatial distribution of hydrochemical conditions in coastal aquifers at this region using Hydrochemical Facies Evolution Diagram (HFE‐D) and Geographical Information System mapping. Hydraulic heads and water chemistry were measured at 31 observation wells in four layered aquifers during dry and rainy seasons in early (2005), and more recent (2016), stages of agricultural development. Hydrochemical facies associated with intrusion or freshening stages were mapped in each aquifer after assigning mixing index values to each facies. The position of groundwater freshening and SI phases differed in Holocene, Upper Pleistocene, Middle Pleistocene, and Lower Pleistocene aquifers. The geographic position of freshening and intrusion fronts differ in dry and rainy seasons, and shifted after 11 years of groundwater abstraction in all four aquifers. The spatial and temporal differences in hydrochemical facies distributions according to HFE‐D reflect the relative impact of SI in the four aquifers. The study results provide a better understanding of the evolution of groundwater quality associated with SI in a peninsular coastal aquifer system, and highlight the need for improving groundwater quality and management in similar coastal regions.