We measured dissolved CO2 independently from DO. We equilibrated a closed loop of atmospheric gas in an equilibration chamber submerged to 0.5 m. The equilibrated gas volume was about 234 ml. We recirculated gas for the last 10 minutes of every 30 minute period, with a flow rate of about 9 ml s-1. A pump exchanged lake water every minute during equilibration. Equilibrated gas was diverted to the IRGA, equipped with a 14 cm sample cell for lakes with CO2 concentration under 2000 ppm or a 5 cm sample cell for lakes with CO2 concentration between 2000-20000 ppm. Following analysis of equilibrated gas, solenoids were activated to route atmospheric gas (taken 10 cm above the water) for CO2 analysis.
Additional detail of the methods available in Hanson et al. (2003)
Hanson, P. C., D. L. Bade, S. R. Carpenter, and T. K. Kratz. 2003. Lake metabolism: Relationships with dissolved organic carbon and phosphorus. Limnol. Oceanogr. 48: 1112-1119.