SIGMACO2 and NH4+ in natural waters can be rapidly (approximately 60 samples h-1),precisely (approximately 1% RSD), and simply determined in small samples (20 mul, SIGMACO2; 50 mul, NH4+) with an inexpensive flow injection analysis system (FIA). A gas-permeable membrane is used to remove CO2 or NH3 from acidic (SIGMACO2) or basic (NH4+) reagent streams into a receiving stream and conductivity detector. Linear negative responses occur over a wide range of concentrations (<0.1-20 mM SIGMACO2; 0.1-100 muM NH4+). Adding Zn2+ to sulfidic samples prevents H2S interferences for CO2 and allows determination of H2S at high concentration (>0.1 mM) by difference (with, without Zn). Interferences from fatty acids (SIGMACO2) and methylamines (NH4+) are unlikely at natural levels. These methods correlate well with traditional techniques.