The Amundsen Sea polynya (ASP) is reportedly the most productive among the coastal polynyas around Antarctica. However, observational constraints limit our understanding of the biological pump and carbon cycle in the ASP. We measured various carbon‐related parameters such as primary production, bacterial production, sinking flux of particulate organic carbon (POC), and accumulation of organic carbon in the sediment as well as hydrographic parameters during field observations and by instrument moorings. Over 95% of the photosynthetically produced POC was converted to suspended POC and/or dissolved carbon forms in the upper ~400 m layer. We postulate that most of the carbon transported to the water column by the biological pump in the ASP was flushed out of the shelf without being sequestered for long‐term storage in sediments. Lack of bottom water formation due to intrusion of Circumpolar Deep Water in the lower layer reduces carbon sequestration efficiency.