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. Thus the field experiment was conducted to explore the role of boron and zinc on the phenology and yield of fine rice in different rice cultures during rice growing seasons 2008 and 2009 at Agronomic Research Farm, University of Agriculture, Faisalabad (31⁰-25’N,73⁰-09’E). Basal application of boron & zinc alone or in combination was done in Aerobic rice (T₁), Flooded rice (T₂) and Flooding for two weeks after transplanting and with supplement irrigation up to panicle initiation and again flooded starting from panicle initiation to physiological maturity (T₃).  Study revealed that change in soil water contents, nutrients (B & Zn) dynamics in the soil were changed which had significant effect on growth, yield and quality of fine rice. The rice crop significantly reduced yield and impair quality when it was subjected to grow in aerobic condition. However, crop was not affected significantly when it was grown in modified rice culture (T₃) and performed as good as the normal flooded rice (T₂). Application of zinc alone or in combination with boron enhanced chlorophyll contents in T₂ similar to T₃ while the crop grown in aerobic condition (T₁) significantly reduced chlorophyll contents. Maximum paddy yield was recorded in flooded rice (T₂) with the combined application of boron and zinc which was statistically similar with T₃. Yield increment in T₂ and T₃ rice cultures may be attributed due to the improved productive tillers. These results demonstrate that introduction of aerobic rice cultivation for fine rice can increase the deficiency problem of micronutrients (B & Zn) in calcareous soil.