Mesoscale eddies play a key role in regulating oceanic physical and biogeochemical environments. However, their influence on vertical oxygen distribution remains poorly constrained by observations. Using 32 years (1993–2024) of oxygen observations from the Bermuda Atlantic Time-series Study (BATS) site combined with satellite-tracked eddies, we show that eddy-induced oxygen anomalies are substantially stronger in the mesopelagic than at the surface. Anticyclonic eddies deepen the oxygen minimum layer (OML) by ~100 m and reduce its thickness by ~30%, with increases of ~3–6% in mean and minimum oxygen. Cyclonic eddies induce a similar but weaker thinning, accompanied by an upward displacement of about 100 m. More than 80% of the variance is explained by isopycnal heaving, with additional contributions from biogeochemical processes. Our results underscore that both eddy types systematically alleviate low-oxygen conditions within the OML, with important implications for subsurface oxygen habitat variability.