Global oceans are an important sink of atmospheric carbon dioxide (CO2). Therefore, understanding the air–sea flux of CO2 is a vital part in describing the global carbon balance. Eddy covariance (EC) measurements are often used to study CO2 fluxes from both land and ocean. Values of CO2 are usually measured with infrared absorption sensors, which at the same time measure water vapor. Studies have shown that the presence of water vapor fluctuations in the sampling air potentially results in erroneous CO2 flux measurements resulting from the cross sensitivity of the sensor. Here measured CO2 fluxes from both enclosed-path Li-Cor 7200 sensors and open-path Li-Cor 7500 instruments from an inland measurement site are compared with a marine site. Also, new quality control criteria based on a relative signal strength indicator (RSSI) are introduced. The sampling gas in one of the Li-Cor 7200 instruments was dried by means of a multitube diffusion dryer so that the water vapor fluxes were close to zero. With this setup the effect that cross sensitivity of the CO2 signal to water vapor can have on the CO2 fluxes was investigated. The dryer had no significant effect on the CO2 fluxes. The study tested the hypothesis that the cross-sensitivity effect is caused by hygroscopic particles such as sea salt by spraying a saline solution on the windows of the Li-Cor 7200 instruments during the inland field test. The results confirm earlier findings that sea salt contamination can affect CO2 fluxes significantly and that drying the sampling air for the gas analyzer is an effective method for reducing this signal contamination.