An internal “gap” layer of deteriorated sea ice is co-located with a significant microbial biological community in late first year and second year Antarctic sea ice in summer. We modeled gap layer formation using a thermal flux model based on the summer reversal in thermal gradient and the thermal conductivity found in the upper ice column. The conductive model gives internal sea ice melt rates (gap layer formation rates) between 0.1 to 0.75cm/day. The cumulative melted layer thicknesses during summer computed from these rates agree with field observations. Since the processes for forming these structures act in the vertical direction only and over a significant range of expected conditions, they are commonly formed in the Antarctic sea ice zone during summer, supporting a significant contribution of gap layers to the ice mass balance and productivity on a circumpolar basis.