The Mekong Delta is the most important rice- and shrimp-producing region for food and economic security in Vietnam. Rice-shrimp farming is practised where salinity fluctuates substantially between wet and dry seasons. Research points to several potential risk factors for rotational systems, but how these link directly to both rice and shrimp production remains poorly quantified for systems that stock and harvest animals year-round. We examined water and soil quality of 18 rice-shrimp-crab ponds, in which shrimp and crab are grown in both wet and dry seasons, in the Cà Mau Province of Vietnam. Multiple lines of evidence indicated that environmental conditions experienced by both rice and shrimp were suboptimal and contributed to low yields and survival. Year-round cropping of shrimp and crab was associated with sustained suboptimal salinity, intensified by drought, for the wet-season cultivation of rice. Although rice seedlings were sown in all 18 ponds, only three had a harvestable crop. Low shrimp production and survival was associated with sustained suboptimal water temperatures (too high), salinity (too high in the dry season and too low in the wet season) and dissolved oxygen concentrations (too low). Food availability and quality may also have affected shrimp production. Improving productivity of rice-shrimp-crab ponds in the study region may require (1) separation of rice and shrimp crops and improving efficiency of soil washing practices such that salinity conditions are more suitable for each when grown, and (2) management intervention to increase oxygenation of water, and the availability and quality of food for shrimp.