Nitrogen use efficiency (NUE) is a critically important concept for evaluating crop production systems and can be greatly impacted by fertilizer management as well as soil- and plant-water relationships. Extreme flooding events that occur outside the climatic normal and its variability can cause direct damage to the standing crops besides reducing nutrient available to crops, thus affecting crop yield or indirect damage such as long-term changes to landscape and soils. Further, over 5.3 billion tons of soil is lost annually through water erosion with a loss of ~8 Mt of NPK. The use efficiency in terms of plant uptake and finally converting to yield is abysmally low and in the range of 32–35% or may be even less in some ecosystems. It has been estimated that in India average use efficiency of N was 22% suggesting that a major amount of applied N is wasted. The low NUE of the crop creates environment-related problems, leaching, emission leads to global warming, and eutrophication which brings many undesirable changes in ecological pyramid. To reduce the hazardous effects and to produce higher yield at low N level, it is essential to identify the genotypes which can absorb more N and efficiently utilize them to give higher and profitable yield under changing climate condition. The various nitrogen use efficiency parameters like agronomic efficiency, physiological efficiency, apparent recovery efficiency, and utilization efficiency were calculated from the field experiment, and the AE vs PE model was used to classify and delineated rice genotypes by using EC 725224 as standard N-efficient rice genotypes. The genetic variation existed in NUE was due to rhizospheric effects of extent and pattern of root architecture. The NUE was further improved by applying neem-coated urea, gypsum-coated urea, and sand-incubated urea in different levels under high N-efficient and responsive genotypes.