In this study, the residues of three pesticides with different water solubilities (clothianidin, orysastrobin, and fipronil) in the paddy water, soil, and plants in a paddy field were investigated, after an application of the pesticide granules to a nursery-box. The concentration levels of all pesticides in the paddy water fell below the lower quantification limit (0.1 µg/L clothianidin and fipronil; 0.2 µg/L for orysastrobin) by the time the water had drained in October. In contrast, all pesticides were found in the soil even after 340 days had passed since transplantation. The concentration levels of residual pesticides were higher in the soil around the plants’ roots than in the areas between the plants. At harvest, the pesticides were found in the rice straws, chaff, and plant feet as well. This study revealed that pesticides with a high soil-adsorption coefficient, low water solubility, and high octanol–water partition coefficient tend to be retained in certain parts of the paddy field.