There is a strong need to understand sources of organic matter in coastal lagoons because these systems often have long water residence times, are susceptible to eutrophication, and display symptoms such as low-oxygen conditions. We found that integrated dissolved oxygen (DO) consumption in the water column accounted for 67-73% of total DO consumption in two eutrophic coastal lagoons (Baffin Bay and Oso Bay) in the northwestern Gulf of Mexico. The d13C of particulate organic carbon (d13CPOC) showed temporal variations that corresponded with hydrological condition changes in Baffin Bay but fewer temporal changes in Oso Bay, whereas the lower d15NPON values in Baffin Bay indicated more agricultural influence than in Oso Bay, where urban sewage influences dominated. Based on closed-system incubation experiments, water-column respiration in Baffin Bay was driven by the respiration of a combination of phytoplankton, carbon from near-shore and benthic macrophytes, and other allochthonous organic carbon sources depending on hydrological conditions. However, respiration of algal carbon dominated DO consumption in Baffin Bay sediments. In comparison, Oso Bay water-column respiration was largely attributed to the degradation of phytoplankton, the growth of which was sustained by nutrient discharge from wastewater treatment plants in the watershed. In contrast to the water column, seagrass and saltmarsh carbon appeared to be the primary organic carbon source that drove DO consumption in Oso Bay sediments. These observations highlight the complexity of organic carbon sources that contribute to DO consumption in estuaries affected by human activities, especially in systems with long water residence times that can retain both organic matter and nutrients for extended periods of time.