The dual isotope approach using the stable isotope ratios of nitrate nitrogen (δ15NNO3) and oxygen (δ18ONO3) is a strong tool for identifying the history of nitrate in various environments. Basically, a rapid procedure for determining δ15NNO3 and δ18ONO3 values is required to analyze many more samples quickly and thus save on the operational costs of isotope-ratio mass spectrometry (IRMS). We developed a new rapid procedure to save time by pre-treating consecutive samples of nitrous oxide microbially converted from nitrate before IRMS determination. By controlling two six-port valves of the pre-treatment system separately, IRMS determination of the current sample and backflush during the next sample pre-treatment period could be conducted simultaneously. A set of 89 samples was analyzed precisely during a 25-h continuous run (17 min per sample), giving the fastest reported processing time, and simultaneously reducing liquid nitrogen and carrier helium gas consumption by 35%. Application of the procedure to an irrigated rice paddy watershed suggested that nitrate concentrations in river waters decreased in a downstream direction, mainly because of the mixing of nitrate from different sources, without distinct evidence of denitrification. Our procedure should help with more detailed studies of nitrate formation processes in watersheds.