A high-resolution record of δ18O and δ13C of Uvigerina peregrina (hereinafter: δ18OU and δ13CU) and biogenic opal was used to reconstruct water column conditions in the SW margin of the Baja California peninsula for the last 6–60 kyr. The core was collected from a depth of 700 m in the oxygen deficient zone of the Magdalena margin. Although the δ18OU values showed a large change associated with the passage from glacial conditions to the Holocene, the MIS-3 and MIS-2 were characterized by a low variability. Our results indicated a rapid cooling and/or increase in salinity immediately after H5 that persisted until H1. However, the δ13CU values showed significant variability associated to the incursions of the Antarctic Intermediate Water (AAIW) in the Magdalena margin during the MIS-3 and MIS-2. This agrees with the δ13C composition of water mass end-members at intermediate depths in the Pacific Ocean. Enhanced ventilation during MIS-3 was inferred from the δ13CU values, which were very similar to the δ13C values of the AAIW end-members evidencing the persistence of the AAIW in the region. This conclusion is also supported by the trend of sedimentary δ15N and other dissolved oxygen proxies in the area. A depletion of the δ13CU at a millennial scale suggests intermittent pulses of a water mass richer in nutrients, which generated an increase in exported productivity, and thus, concomitantly depleted the dissolved oxygen levels at intermediate depths. Moreover, exported productivity showed a decreasing long-term trend during the second half of MIS-3, briefly punctuated by millennial-scale increases in exported productivity sustained by nutrient export from the Southern Ocean via the AAIW.