A submersible pCO2 measurement system with a membrane tube equilibrator and a nondispersive infrared gas analyzer was developed. The system was designed to measure the partial pressure of CO2 in seawater and the atmosphere, and physical parameters related to CO2 changes, including light intensity, temperature, salinity, dissolved oxygen, and pH. A CPU controls the operation and logs the data. The analyzer and CPU are contained in a titanium cylinder. The power consumption is 15 W, which is supplied by 1419 dry alkaline manganese dioxide battery cells contained in three PVC cylinders. We tested the system on a barrier reef flat in the Palau Islands, and monitored pCO2 and physical parameters from November 1999 to December 2000. The system worked for 50 hours a week, and we changed the battery unit every 4 months. The accuracy of pCO2 measurement was ±5 μatm and the response time was 3 minutes. The results showed diurnal changes in the pCO2 in reef water on a coral reef flat, which corresponded to daytime photosynthesis and nighttime respiration.