Three parameters must be known to use the thin boundary‐layer model (or other bulk transfer models) for CO2 flux between water and air: the concentration of dissolved CO2, CO2(aq), the concentration of CO2 in the air immediately above the water, CO2(atm), and the wind velocity, which is used to determine the appropriate transfer coefficient. These parameters change hourly and from day to day in a nonlinear fashion, so the frequency of measurements is an important factor in determining the accuracy of flux estimates for any period. To achieve a high frequency measurement, we developed a self‐contained, solar‐powered, in situ sampling system that continuously measures and records CO2(aq), CO2(atm), and windspeed. Unique to this technique is an underwater in situ equilibration chamber (ISEC). The ISEC was tested in a shallow wetland pond in which changes in both CO2(aq) and CO2(atm) were large. The data obtained showed that large errors may result from extrapolating flux calculations made from short‐term data (e.g. daily) to longer time periods.