Coastal agricultural systems in Southeast Asia are vulnerable to climate change. The combination of rising sea levels and extreme rainfall events is eroding fragile coastlines that protect emblematic “rice bowls” across the region. A series of recent damaging floods in Southeastern Thailand has raised concerns about their increased frequency. Local and regional trends in rainfall variables relevant to farming were investigated using the resampling-based Mann–Kendall test applied to four rainfall stations of the Songkhla lagoon basin during the period 1957–2019. Using the findings from long-term and multi-scale agrarian change surveys based on Mazoyer and Roudard's methodology, a vulnerability framework was used to assess the sensitivity and response capacity to these trends of the great Songkhla spit agroecosystem. Significant positive trends in the rainfall depth, number of rainy days, and maximum daily rainfall were observed in January at individual stations and across the region, especially since the early 1980s. Moreover, the annual frequency of extreme rainfall events consistently increased over the same period. The impacts on the unstable coastal main sandbar that protects the flood plain are discussed, while the effects on rice production are analyzed. The coping responses of the cultural rice and sugar palm-based agroforestry system, and the lack of adaptation of recent land-use changes are examined. The agro-ecological, economic, and social importance of the dense hedges of sugar palms to mitigate climatic risks and maintain the resilience of local livelihood systems is underlined. Propositions for short and longer-term measures to adapt water management, diversify cropping systems, and foster participatory disaster risk management are made.