Due to a reduction of world water resources, rice cultivation has shifted from flooded to aerobic condition. This shift may alter soil physico-chemical conditions and cause reduced availability and uptake of nutrients, especially boron and zinc in calcareous soils, and may ultimately reduce yield. Thus a field experiment in a calcareous soil was conducted in which basal application of boron & zinc alone, or in combination, was undertaken in rice grown aerobically (T1), flooded for the entire growth period (T2) or flooded for two weeks after transplanting, given supplemental irrigation up to panicle initiation and then flooded from panicle initiation to physiological maturity (T3).  The study showed that rice crop was significantly reduced growth in term of Leaf Area Index (LAI), Leaf Area Duration (LAD), Crop Growth Rate (CGR), Total Dry Matter accumulation (TDM) and Net Assimilation Rate (NAR) when it was grown in aerobic condition. However, the crop was not affected significantly different from normal flooded rice (T2) when it was grown in modified rice culture (T3). 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) had significantly lower chlorophyll content.