River water collected from 27 sites in 21 rivers, groundwater from 66 sites in 34 cities, and 2 sewage plants in the Niigata Prefecture, Japan (total 301 samples) were analyzed for methyl tert-butyl ether (MTBE) using an improved purge-and-trap-GC–MS method. The amount of MTBE found in water samples from the 27 river sites ranged from 0.003 to 5.3μgl −1 . MTBE was found in all 27 sites during winter but it was found at only 9 sites and 14 sites, respectively, during the summer. MTBE was found most frequently (in 21 sites) at levels ranging from 0.003 to 0.009μgl −1 during February. The highest levels of MTBE were always found in the samples collected from the same site. The amount of MTBE found in sewage water samples ranged from <0.003 to 0.025μgl −1 . No significant differences were observed between the amounts of MTBE recovered from inflow and outflow waters. Relatively high levels (0.02–0.034μgl −1 ) of MTBE were found in January at two sites, which were located on the upper course of the Shinano River. MTBE levels ranged from 0.004 to 0.035μgl −1 and from 0.005 to 0.041μgl −1 at the mouths of the Shinano River and Agano River, respectively. The levels of MTBE in groundwater collected from 66 sites in 34 cities in Niigata Prefecture ranged from <0.003 to 5.9μgl −1 .