Water level management is one factor in producing a higher rice yield. The objective of this study was to compare the effects of different water levels on the yield and biomass of three Japonica rice cultivars, i.e., Nikomaru (NM), Himenorin (HR), and Hinohikari (HH). Rice was transplanted in totally nine plastic boxes with dimensions of 96.0 x 45.8 x 35.8 cm, and with a soil particle density of 1.46 g cm−3. Each box contained 10 hills of rice with 3 seedlings per hill. Water levels were controlled as 2, 5, and 10 cm for each cultivar from 70 days after transplanting. We measured yield and biomass from 3 selected plants on each box. The highest yield was obtained with 5 cm for NM, with 10 cm for HR, and with 10 cm for HH as 7.68, 7.73, and 6.90 t ha−1, respectively. For NM, yield with 10 cm was 4.4% lower than with 5 cm, however, the harvest index (HI) with 10 cm was higher compared with 5 cm due to the lower biomass, but not significantly. Both for HR and HH, HI with 10 cm was the highest. We suggested that keeping the water level at 10 cm could produce a higher grain yield compared with shallower water level ponding for all cultivars.