Agriculture is exposed to climatic impacts, especially in developing countries. Adaptation is the predominant practice that farming communities undertake to deal with these climate-induced challenges. While significant attention has been devoted to farmers’ adaptation strategies, little is known about how innovative practices are associated with the improvement of rural livelihoods. To address this gap, the paper attempts to investigate how farmers lead the process of rural innovations that constitute successful forms of adaptation to address the mixed impacts of dyke policies and climate change in two distinct agro-ecological zones (i.e. flooding and salinity) in the Vietnamese Mekong Delta (VMD). Drawing on qualitative information collected from focus group discussions and interviews across the case studies, the paper argues that farmers are the key innovation actors who contribute to improving rural farming and water management practices. The study suggests that the evolution of farmer-led innovations is mainly attributed to the operation of various informal learning networks that provide important platforms for the generation and diffusion of effective innovative practices across farming communities. It also highlights how farmers contribute their innovative knowledge to local adaptation policies. From the policy perspective, this study sees the development of rural innovation systems as the best practices of farmers’ adaptation, which needs to be scaled out to better support agricultural water management in the delta.