Production of vigorous seedlings and transplanting at proper age is a primary feature to get good paddy yield. Due to the shrinkage of world water resources rice cultivation is in shift from flooded to aerobic condition. This shift may alter the soil condition that can cause the problem of boron and zinc uptake, which leads toward reduction in final yield. Two field experiments were conducted during 2008 and 2009 growing seasons at Agronomic Research Farm, University of Agriculture, Faisalabad (310-25’N,730-09’E), Pakistan. The first one studied the seeding densities, nitrogen fertilization rate and seedling age in the rice nursery that is used for transplanting. Such treatments were evaluated in term of seedling vigor, plant growth, yield and yield attributes. The study revealed that fertilized seedlings older than 10 days and grown with low seeding density at nursery-bed, significantly improved seedling vigor. Maximum paddy yield (3.7 t/ha) was observed with transplanting youngest seedlings (10-days older) but transplanting of 20-days older fertilized seedlings grown at low seeding densities resulted in almost similar yield (3.6 t/ha) with younger. Older seedlings leads to reduced yield and the lowest yield (2 t/ha) was observed after transplanting unfertilized 40- days older seedlings grown at high seeding density. The best benefit cost ratio (BCR) was observed with S1 (1.59) followed by S2 (1.40) while in nursery management, fertilized seedlings grown with low seeding density found the highest BCR (1.53) in year 2008. The second experiment investigated the nutrition effect of boron and zinc in different rice cultures. Boron and zinc are supplementary nutrients were used as basal fertilizers in the rice fields that had different water management. Results showed that the rice crop significantly reduced yield (42 %) and impair quality when it was subjected to grow in aerobic condition without nutrients application. However, nutrients application in crop grown with periodic flooding and drying improved yield (4.81 t/ha) and quality as compared with aerobic culture (2.89 t/ha) and performed as good as the normal flooded rice. Maximum paddy yield (5.02 t/ha) was recorded in flooded rice with the combined application of boron and zinc which was statistically similar with treatment of periodic flooding and drying. In addition to this the best BCR was achieved with field under periodic flooding and drying (1.89) followed by flooded rice (1.75) and the minimum BCR (1.39) was found in aerobic rice culture . Fertilizer application revealed that maximum BCR (2.05) was recorded with micronutrients application as compared to control during 2008. These findings sustenance the young seedling components of System of Rice Intensification and illustrate that making a minor additional investment in raising a healthy and vigorous seedling in nursery seed-bed, farmers can harvest a reasonable yield benefits. Results also demonstrated that introduction of aerobic rice cultivation for fine rice can increase the deficiency problem of micronutrients (B & Zn) in calcareous soils.