There is growing demand for water across different sectors of production. Yet the extent of water wastage to furnish inefficient irrigation systems especially in flood irrigated rice systems, is not known. In developing countries and in Uganda particularly, most irrigation scheduling in the irrigation schemes is based on rotational system rather than crop water needs. In Doho Rice Irrigation Scheme (DRIS) in eastern Uganda for example, farmers’ plots receive up to 50mm ponding of irrigation water for three days in a week for four months which translates to about 2,400mm of water applied way above average rice water requirements of 700 mm in a season. Too much water not only compromises nutrient use efficiency but has also been associated with a wide spread of water snail, a pest that eats up the young rice seedlings. There is urgent need to establish the minimum water ponding depth needed for a paddy rice crop in a flood irrigated system without compromising the grain yields. The overall objective of this study was to optimize water and nitrogen use efficiencies under the system of rice intensification (SRI) in flood irrigated systems in Uganda. The specific objectives were (i) establish the minimum flooding depth for optimal nutrient use efficiencies and grain yields and (ii) determine the effect of spacing and plant population on water and nitrogen use efficiencies. Field experiments were established for two seasons (December 2021– March 2022 and May - September 2022) in DRIS in eastern Uganda. The treatments included four flooding depths (0 / Field Capacity, 10 mm, 20mm and 40mm) and within each flooding depths were the number of seedlings per hill (1 or 3) and two plant spacings (20 cm x 20cm or 25 cm x 25 cm) as split plots. Crop parameters measured included plant height, number of leaves, number of tillers, number of panicles, above ground biomass, root biomass and grain yield. Our preliminary analysis of results indicates no significant differences in biomass and grain yields among the four flooding depths. Planting one seedling per hill 25 cm x 25 cm led to a higher number of tillers, panicles and consequently biomass and grain yields. We conclude that ponding of up to 10 mm of water every three days and planting of 1 seedling per hole at a spacing 25 cm x 25 cm leads to optimum water and nutrient use efficiencies and increased rice grain yields.