Oxygen minimum zones (OMZs) in the ocean are characterized by enhanced carbon dioxide (CO2) levels and are being further acidified by increasing anthropogenic atmospheric CO2. To investigate how on-going ocean deoxygenation will impact biogeochemical processes, a large-scale mesocosm experiment was conducted offshore Peru in austral summer (Feb-Apr) 2017, coinciding with a rare coastal El Niño event. We deployed eight mesocosms, each with a volume of 55 m3 and a length of 19 m, at the surface water in the coastal area of Callao (12.06° S, 77.23° W). The mesocosm bags were filled by surrounding surface water with daily or every-2nd-day nutrient and CO2 measurements for 10 days to monitor the initial conditions. Deep water masses from two different locations in the nearby OMZs were collected (at a depth of 30 and 70 m, respectively) and added to the mesocosms to simulate upwelling events on day 13 (see Bach et al., 2020 for details). Here we report every-2nd-day measurements of carbonate chemistry parameters in the individual mesocosms and the surrounding Pacific waters over 50 days. Depth-integrated seawater samples were taken from the surface (0-10 m for day 3-28; 0-12.5 m for day 29-50) and bottom layer (10-17 m for day 3-28; 12.5-17 m for day 29-50) of the mesocosms and the surrounding coastal water (named “Pacific”) using a 5-L integrating water sampler. Total alkalinity (TA) was measured by a two-stage open-cell potentiometric titration using a Metrohm 862 Compact Titrosampler, Aquatrode Plus (Pt1000) and a 907 Titrando unit, and pH (total scale) was measured spectrophotometrically by measuring the absorbance ratios after adding the indicator dye m-cresol purple (mCP) on a Varian-Cary 100 double-beam spectrophotometer (Varian). With inputs of the measured TA and pH, other CO2 parameters, such as dissolved inorganic carbon, pCO2, calcite and aragonite saturation state, and CO2 fluxes (FCO2), were calculated using the Excel version of CO2SYS. The performance of pH and TA measurements were also evaluated by examining the standard deviations and range controls of triplicate measurements of samples or reference materials. Our observations showed an acidification of surface water in the mesocosms by the OMZ water addition, followed by a rapid drop in pCO2 to near or below the atmospheric level due to enhance phytoplankton production. The positive CO2 fluxes in the surrounding Pacific waters indicated our study site was a local CO2 source during our study. Nevertheless, our mesocosm experiment suggests this CO2 export to the atmosphere can be largely dampened by biological processes. As a unique dataset that characterized near-shore carbonate chemistry with a high temporal resolution during a rare coastal El Niño event, our study gives important insights into the carbonate chemistry responses to extreme climate events in the Peruvian upwelling system.