This research aims to provide an overview of the seawater encroachment threat on agriculture in lowland areas and potential solutions for better practices. It was found that the Mekong river delta experiences severe impacts from climate change with more than 75% of provinces affected by seawater intrusion, of which Kien Giang, Ca Mau and Ben Tre provinces are the most influenced with 70% affected areas. The salinity of river water was observed in the range of 15–30 g/L in 2015; meanwhile, the strongest tolerated rice species reached ceiling values of 3–4 g/L. Emerging challenges were identified due to the uncertain upstream hydrological regime coupled with high levels of tide, field evaporation and water withdrawal. The development strategies of affected provinces are given on the modification of rice tolerant capacity, and modification to aquaculture in areas with high salinity, in which water purification is in urgent demand. Desalination technologies have been proposed with various innovations which are still not practical on a large scale. The desalination of seawater and brackish water by reverse osmosis, nano-filtration, electro-dialysis, ion-exchange resins, electrochemical processes and thermal distillation has been applied to agriculture. The advance reverse osmosis shows most potential because of its advances in treating performance, cost effectiveness and effective rejection of brine.