Nitrogen (N) is a key nutrient for rice (Oryza sativa L.) and its availability in soil profile can influence the plant root morphology and total nutrient uptake. This study evaluated if N from deeper soil layers would increase rice root growth, N uptake and influence plant nutritional status. Flooded rice was grown in undisturbed soil samples from three locations with 15 N-labeled ammonium sulfate application at different depths (0, 10, 20, 30, and 45 cm). At rice heading, chlorophyll content and photosynthesis rate were measured at flag leaves and rice biomass production, root morphology, and total N and 15 N uptake were evaluated. Higher biomass and N uptake were observed with N application at near soil surface layers. The majority of rice N uptake was derived from soil, which was more evident when N fertilizer was injected at 45 cm deep (on average 74%). The highest root growth was observed at the near surface layers with constant decrease in depth, up to 60 cm. Roots from deeper layers exhibited smaller diameter, as they were mainly highly branched roots. The N application at 30 and 45 cm depths provided N later in the season, resulting in plants with lower total biomass but with higher N content in aboveground biomass, with higher chlorophyll content, photosynthesis rate, and carboxylation efficiency by Rubisco. The N available below 20 cm contributes to plant nutrition and root growth, hence soils with available N in depth likely cause plants to function more optimally in photosynthates supply.