Saline intrusion (SI) is increasing at an accelerating rate in the coastal zones of the Vietnamese Mekong Delta (VMD). This challenges various crop production practices in these areas. Using ecological and social approaches, this paper aims to explore farmers’ perceptions of SI occurring in Tra Vinh and Kien Giang provinces, and their adaptation measures to deal with the situation. A mixed-method approach was used, including in-depth interviews, focus group discussions, and household surveys. The results demonstrated that farmers have implemented various adaptation measures in tackling SI impacts. High market demand for shrimp also contributed to farmers’ decisions in shifting farming practices. The study underscores the important role of the integrated shrimp-rice system as a more comparatively sustainable model to the intensive shrimp culture in the face of SI. Qualitative analysis revealed water conflicts occurring in mixed rice and shrimp farming areas driven by the poor performance of combined irrigation and drainage systems together with the undefined water demarcation zones between rice and shrimp farmers. The paper provides better insights into how farmers’ adaptation strategies could facilitate decision-making processes with regard to water management and adaptation policies in the coastal areas. It calls for local governments’ attention to modifying water infrastructure to better address water-related issues.