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Abstract Ponds influence global carbon (C) cycling due to high rates of organic C (OC) burial and carbon dioxide (CO₂) and methane (CH₄) emissions. Here, we quantified OC burial rates and CO₂and CH₄concentrations and fluxes in two ponds that were similar in size and gross primary production, but differed in depth and dominant primary producers. The deeper (3.9 m) Texas Hollow Pond was phytoplankton dominated with stronger and longer (143 d) stratification compared to the shallower (2.7 m) macrophyte‐dominated Mud Pond (85 d). Both ponds exhibited high CO₂and CH₄emissions and high OC burial, yet C pathways differed. Strong stratification in Texas Hollow Pond led to anoxic bottom waters, benthic CO₂and CH₄accumulation, and limited OC decomposition, whereas Mud Pond remained oxygenated with similar gas concentrations across the water column. Texas Hollow Pond had 2.6 times higher CO₂emissions than Mud Pond, perhaps related to greater wetland C inputs in Texas Hollow. Despite similar diffusive CH₄emissions between ponds, the weakly stratified Mud Pond had twice as much CH₄ebullition, likely due to warmer waters and macrophyte‐derived OC fueling methanogenesis. In summary, slight differences in depth and light attenuation can regulate stratification, plant communities, oxygen availability, and C processing in ponds. Given that ponds are hotspots for C cycling and are sensitive to climate‐driven changes in stratification, understanding the mechanisms behind C processing is critical for local management and predicting global C budgets.