Most ocean acidification (OA) experimental systems rely on pH as an indirect way to control CO2. However, accurate pH measurements are difficult to obtain and shifts in temperature and/or salinity alter the relationship between pH and pCO(2). Here we describe a system in which the target pCO(2) is controlled via direct analysis of pCO(2) in seawater. This direct type of control accommodates potential temperature and salinity shifts, as the target variable is directly measured instead of being estimated. Water in a header tank is permanently re-circulated through an air-water equilibrator. The equilibrated air is then routed to an infrared gas analyzer (IRGA) that measures pCO(2) and conveys this value to a Proportional-Integral-Derivative (PID) controller. The controller commands a solenoid valve that opens and closes the CO2 flush that is bubbled into the header tank. This low-cost control system allows the maintenance of stabilized levels of pCO(2) for extended periods of time ensuring accurate experimental conditions. This system was used to study the long term effect of OA on the coralline red algae Phymatolithon lusitanicum. We found that after 11 months of high CO2 exposure, photosynthesis increased with CO2 as opposed to respiration, which was positively affected by temperature. Results showed that this system is adequate to run long-term OA experiments and can be easily adapted to test other relevant variables simultaneously with CO2, such as temperature, irradiance and nutrients.