The first long pathlength fiber optic-based sensor system to measure pCO(2) in natural waters and the atmosphere is described. The sensor is based on a liquid-core (an indicator-HCO(3)(-)/CO(3)(2-) buffer solution) waveguide made of a low refractive index amorphous fluoropolymer tubing, the wall of which serves as a gas-permeable membrane to sense pCO(2) changes. The system detects the indicator absorbance changes when the liquid-core reaches CO(2) equilibrium with the surrounding sample. Theoretical calculations demonstrate that due to indicator buffer effects, increasing the optical pathlength is a more efficient way to obtain higher sensitivity than increasing the indicator concentration. Using an 18-cm cell with low indicator concentrations (10 muM), this system achieves a precision and an accuracy of +/-2-3 muatm in the pCO(2) range of 200-500 muatm. The sensor also features a response time (99%) of only 2 min for low-level (<1000 muatm) pCO(2) measurements as a result of high CO(2) permeability of the amorphous fluoropolymer membrane. Field tests indicate that this new sensor is capable of handling both atmospheric and aquatic pCO(2) monitoring.