We examine intensified rice-based agriculture facilitated by dyke heightening in Vietnam’s Mekong Delta (VMD). Heightening prevents floodwaters entering fields so three rice crops can be grown annually rather than two. However, the high dykes have changed the annual connectivity in the floodplain and increased the rice cropping intensity inside high dykes. Hence dyke heightening may come at the costs of the ecological sustainability necessary to maintain rice productivity. By estimating the difference in rice profit between two areas with the assumption of the same natural condition and social characteristics before dyke heightening, the results showed that the longer term productivity loss of rice resulting from 10-year dyke heightening was about USD 196 per hectare per crop or 21.6 percent of rice profit per crop in year 2012 alone.