Little is known on the El Niño-related impacts affecting the CO 2 dynamic and fluxes in productive Eastern Boundary Upwelling Systems (EBUS). Through 35 oceanographic campaigns conducted between January 2015 and April 2016 in the Humboldt EBUS (23°S), intraseasonal (i.e., daily-to-bimonthly) hydrographic variations and nearshore changes in surface carbonates system were assessed during the 2015 El Niño event. Collected hydrographic and carbonates system data (sea surface temperature (SST), subsurface temperature, salinity, oxygen, chlorophyll a, pH, total alkalinity (A T) and pCO 2), were analyzed and interpreted considering local (i.e., satellite winds and tide gauge sea level) and remote (i.e., equatorial Kelvin waves) forcing. Permanent alongshore wind conditions prompted a relatively deep mixed layer favoring elevated acidity (7.8-7.9 pH T) and CO 2 saturated (>450 μatm) conditions throughout most of the study period. Between austral summer-fall and fall-winter transitions, intermittent warm events increased water temperature (SST) above the long-term climatological state (2000-2010), and gave rise to high acidity-warm conditions. However, despite warm water particularly high in salinity (>35) and A T (>2,300 μmol kg −1) associated with downwelling Kelvin waves activity observed during the developing phase of the 2015 El Niño event, phytoplankton production and CO 2 uptake were favored because of the maintenance of mean upwelling conditions. These results are discussed in terms of data limitations, coastal processes adding variability to carbonates system variability, and requirements for a better understanding of hydrographic forcing and responses in the Humboldt EBUS. Plain Language Summary Little is known of the El Niño-related variations affecting the CO 2 fluxes in productive upwelling ecosystems. Through 35 oceanographic campaigns conducted between 2015 and April 2016 in a Humboldt upwelling system (23°S), we evaluated daily-to-bimonthly hydrographic variations and coastal changes in the carbonates system during the 2015 El Niño event. Collected hydrographic and carbonates system data were analyzed and interpreted considering local (i.e., satellite winds and tide gauge sea level) and remote (i.e., equatorial Kelvin waves) forcing. Wind mixed the upper layer, favoring elevated acidity (7.8-7.9 pH) and CO 2 saturated (>450 μatm) levels in the surface layer during most of the study period. Between austral summer-fall and fall-winter transitions, intermittent warm events increased water temperature above the long-term climatological state (2000-2010), and gave rise to high acidity-warm conditions. However, despite the developing El Niño conditions yielding to surface waters particularly high in salinity (>35) and alkalinity (>2,300 μmol kg −1), phytoplankton production and CO 2 uptake were favored due to persistent mean upwelling conditions. We discussed limitations of our approach and how our study can contribute to a better understanding of hydrographic forcing and responses in productive upwelling ecosys...