Biomass production in arid and semi-arid regions requires a special attention owing to spatiotemporal scarcity of irrigation water wherein improved water use efficiency (WUE) of the crop is targeted. Under field conditions, the crop undergoes dynamic changes in near ground or within-canopy microenvironments. This changed microclimatic condition may have an impact on phenological response of the oilseed crop which in turn would affect biomass productivity, economic seed yield and water use efficiency of the crop. Henceforth, quantification of biomass production and its WUE of oilseed Brassica crop is essentially required owing to have better understanding of the crop water requirement under the era of climate change. Following a 2 years field experiment, it was revealed that the changes in leaf area index were explained by about 68–74%. The best fit polynomial third order regression analysis indicated >93% prediction in biomass production as a function of time factor. Improved biomass partitioning into economic sinks was also observed. Small scale change in near ground microenvironment may reduce the prediction of biomass variability to the extent of 3%. The mean ET variations were observed as 2.4, 1.5 and 3.2 mm day−1 during the critical phenological stages. Mean seed yield, biomass WUE and seed yield WUE ranged between 2.71 and 2.87 Mg ha−1, 11.4 and 13.1 g m−2 mm−1 and 19.3 and 22.9 kg ha−1 mm−1 respectively. Variations in both biomass and seed yield water use efficiencies due to small scale change in near ground microclimates were revealed.