Integrated rice-shrimp ponds (IRSPs) are common in areas of Southeast Asia where saltwater intrudes into rice fields in the dry season, enabling rice production in the wet season, and shrimp farming in the dry season or throughout the year. Previous research has highlighted that IRSPs have periods of low dissolved oxygen concentrations which may have a critical effect on shrimp survival. To understand the causes of low dissolved oxygen, this study examined oxygen fluxes at two IRSPs in Ca Mau Province, Vietnam during a two-year period (two wet seasons and two dry seasons). Sediment oxygen demand (SOD) incubations and whole-system oxygen flux measurements were conducted and compared with a range of water and sediment parameters to explain drivers for low oxygen concentrations. A high percentage of oxygen demand at a whole pond scale was from the sediment; hence SOD drove low oxygen concentrations in the water column. SOD rates were significantly positively correlated with chlorophyll a concentrations in the water column. These findings suggested that algal production in the water column, rather than benthic algal production, or other organic loading, provided an organic carbon source driving SOD. Oxygen demand was much higher than oxygen production within the IRSPs, indicating high bacterial activity and low algal production. This study has shed new light on the importance of SOD in driving oxygen drawdown in IRSPs and improving shrimp survival requires new management approaches to reduce the negative effect of SOD.