A monitoring study was carried out in an alluvial fan area in Tsukui, Central Japan during the study period of 1999-2003, in order to explain selenium (Se) behaviors in ecosystem combined with air, soil and groundwater. Monthly Se concentrations in open bulk precipitation (rainfall+aerosol, gaseous deposition and etc.), soil solution (collected by porous ceramic-cup) and groundwater ranged from 0.1 to 1.4 μg L −1 (volume-weighted average: 0.34 μg L −1 ), 0.21 to 1.0 μg L −1 (0.48 μg L −1 ) and 1.6 to 2.4 μg L −1 (2.2 μg L −1 ), respectively. Se concentration in open bulk precipitation was negatively correlated with the rainfall amount. Se concentration in soil solution significantly increased with DOC concentration in soil solution. Besides, despite atmospheric Se input and rainfall to the grassland study area, Se concentration in soil solution and groundwater received no significant effect from the rainfall amount, pH, Se, DOC, SO 2− 4 , NO − 3 and EC in rainfall. Even though Se concentrations in groundwater were significantly correlated with soil solution volume, Se, DOC and NO − 3 and groundwater level, the result of multiple regression analyses (MRA) indicated that the groundwater Se was negatively influenced by groundwater level, which depended on groundwater recharge. Se was transported into the groundwater through the groundwater recharge that largely increased in this alluvial fan study area after heavy rain.