The Southern Ocean is rich in highly dynamic mesoscale eddies and substantially modulates global biogeochemical cycles. However, the overall surface and subsurface effects of eddies on the Southern Ocean biogeochemistry have not been quantified observationally at a large scale. Here, we co-locate eddies, identified in the Meta3.2DT satellite altimeter-based product, with biogeochemical Argo floats to determine the effects of eddies on the dissolved inorganic carbon (DIC), nitrate, and dissolved oxygen concentrations in the upper 1,500 m of the ice-free Southern Ocean, as well as the eddy effects on the carbon fluxes in this region. DIC and nitrate concentrations are lower in anticyclonic eddies (AEs) and increased in cyclonic eddies (CEs), while dissolved oxygen anomalies switch signs above (CEs: positive, AEs: negative) and below the mixed layer (CEs: negative, AEs: positive). We attribute these anomalies primarily to eddy pumping (isopycnal heave), as well as eddy trapping for oxygen. Maximum anomalies in all tracers occur at greater depths in the subduction zone north of the Antarctic Circumpolar Current (ACC) compared to the upwelling region in the ACC, reflecting differences in background vertical structures. Eddy effects on air-sea CO2 exchange have significant seasonal variability, with additional outgassing in CEs in fall (physical process) and additional oceanic uptake in AEs and CEs in spring (biological and physical process). Integrated over the Southern Ocean, AEs contribute ∼0.03± 0.01 Pg C yr-1 (7 ±2% ) to the Southern Ocean carbon uptake, and CEs offset this by ∼0.01± 0.01 Pg C yr-1 (2 ±2% ). These findings underscore the importance of considering eddy impacts in observing networks and climate models.