Rice intensification programs target poverty reduction and improved food availability in Asia. Vietnam adopted a rice intensification policy aimed at a rice surplus for export by the 1990s. The intensification policy replaced an annual wet season crop with two to three High Yielding Variety (HYV) rice crops a year. These multiple annual crops required changes in hydraulic systems in areas such as the Mekong Delta (MD) with the introduction of low and high dikes for wet season flood control and dry season irrigation. This study examines the impacts of rice intensification and hydraulic changes in the MD between the 1990s and 2000s on rural household food sources, both wild and cultivated. Across study sites representing three flood management regimes, 165 households were sampled for data on household demographics, the collection and consumption of fish, other aquatic animals, wild and cultivated vegetables and fruit, and other food sources. The results indicate that rice intensification programs and dike construction have significantly increased rice production. However, farm household catch, collection and consumption of wild foods has decreased. Household use of wild fish, other aquatic animals, and wild vegetables was reduced significantly over the period. Significant wet and dry season variation in food availability emerged. Poor households experienced most loss. Overall household food security was affected. This study suggests that rice intensification policies aimed at global food security need to balance wider population access to a food staple with the need for rice farming communities to maintain access to high quality wild foods obtained from the fields and waterways of rice farming landscapes.