We have developed a rapid, sensitive, and automated analytical system to simultaneously determine the concentrations and stable isotopic compositions (δ15N, δ18O, and δ13C) of nanomolar quantities of nitrous oxide (N2O) and methane (CH4) in water, by combining continuous-flow isotope-ratio mass spectrometry and a helium-sparging system to extract and purify the dissolved gases. Our system, which is composed of cold traps and a capillary gas chromatograph that use ultra-pure helium as the carrier gas, achieves complete extraction of N2O and CH4 in a water sample and separation among N2O, CH4, and the other component gases. The flow path following exit from the gas chromatograph was periodically changed to pass the gases through the combustion furnace to convert CH4 and the other hydrocarbons into CO2, or to bypass the combustion furnace for the direct introduction of eluted N2O into the mass spectrometer, for determining the stable isotopic compositions through monitoring the ions of m/z 44, 45, and 46 of CO and N2O+. The analytical system can be operated automatically with sequential software programmed on a personal computer. Analytical precisions better than 0.2‰ and 0.3‰ and better than 1.4‰ and 2.6‰ were obtained for the δ15N and δ18O of N2O, respectively, when more than 6.7 nmol and 0.2 nmol of N2O, respectively, were injected. Simultaneously, analytical precisions better than 0.07‰ and 2.1‰ were obtained for the δ13C of CH4 when more than 5.5 nmol and 0.02 nmol of CH4, respectively, were injected. In this manner, we can simultaneously determine stable isotopic compositions of a 120 mL water sample with concentrations as low as 1.7 nmol/kg for N2O and 0.2 nmol/kg for CH4. Copyright © 2010 John Wiley & Sons, Ltd.