The San Lazaro Basin (SLB) sediment record is highly sensitive to the El Nino-Southern Oscillation (ENSO) and the Pacific Decadal Oscillation (PDO) due to its location vertically underlying the dynamic boundary between the northern, cooler and fresher waters of the California Current System (CCS) and the southern, warmer and saltier surface waters from the subtropics and tropics. Warm sea surface temperatures (SSTs) and the ensuing stratified surface water column favor carbonate productivity, mostly dominated by the export of coccolithophorids as observed during El Nino events, while cool SSTs and a less stratified water column favor a relatively higher export of organic carbon. Here we show how during the last two millennia, the mechanisms that drive the organic carbon and carbonate export depend on the time scale considered. The organic carbon and carbonate records show opposite trends for the past 2000years. On multicentennial periodicities, their variability is probably a result of precessional forcing and associated decreasing Northern Hemisphere insolation, which has been shown to affect the migration of the Intertropical Convergence Zone and the polar jet stream. On shorter time scales, interannual to centennial, the SLB records exhibit an ENSO-like variability; similarly, decadal to multidecadal variability is correlated with instrumental and reconstructed PDO records. We further show how interannual variance seems to have increased during the Little Ice Age, most likely related to large ENSO events, in contrast with an apparent reduction in this type of variability between 400 and 1350 Common Era, suggesting a changing sensitivity of the ENSO teleconnection in the southern CCS for the past two millennia.