We present a high-resolution spatial study of ocean surface carbon dioxide partial pressure (pCO2), temperature and salinity coupled with a seismic survey performed in subpolar waters with a variable presence of glaciers along the coastal margins of Admiralty Bay and the Bransfield Strait, northern Antarctic Peninsula, during the late spring season. Three zones were identified in this bay. The shallow and relatively fresh SHALLOW GLACIER THAW zone in the inner portion of the bay had high freshwater inputs from active glacial meltwater channels, representing higher pCO2 levels (median ~438 μatm) than the shallow and relatively salty SHALLOW zone without glaciers along the margins and dominated by macroalgae communities at the bottom, which showed relatively low pCO2 levels (median ~371 μatm). The deep and relatively salty CENTRE zone was highly influenced by seawater intrusions from the Bransfield Strait, representing intermediate pCO2 levels (median ~397 μatm). The net sea-air CO2 fluxes in late spring obtained from the high-resolution surface survey in Admiralty Bay indicate a condition of near neutral air-sea CO2 flux, with a median (25–75% interquartile range) value of -0.07 mmol m-2 day-1 (ranging from -12.21 to +4.33 mmol m-2 day-1), contrasting with the slight source to the atmosphere estimated from measurements only in the CENTRE zone. This finding suggests that temperature-sensitive metabolic and physical-chemical processes may cause significant variability in the ocean surface distribution of CO2 over short shoreline distances in the northern Antarctic Peninsula.