To improve estimates of the long-term response of the marine carbon system to climate change a better understanding of the seasonal and interannual variability is needed. We use high-frequency multi-year data at three locations identified as climate change hotspots: two sites located close to South Pacific boundary currents and one in the Subantarctic Zone (SAZ). We investigate and identify the main drivers involved in the seasonal an interannual (2012–2016) variability of the carbon system. The seasonal variability at boundary current sites is temporally different and highly controlled by sea surface temperature. Advection processes also play a significant role on the monthly changes of the carbon system at the western boundary current site. The interannual variability at these sites most likely responds to long-term variability in oceanic circulation ultimately related to climatic indices such as the El Niño Southern Oscillation, the Pacific Decadal Oscillation and the Southern Annular Mode (SAM). In the SAZ, advection and entrainment processes drive most of the seasonality, augmented by the action of biological processes in spring. Given the relevance of advection and entrainment processes at SAZ, the interannual variability is most probably modulated by changes in the regional winds linked to the variability of the SAM.
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