Energy fluxes and canopy microclimate of wheat grown on the edaphically stressed shallow basaltic soil at Baramati, India were studied during 2014-15.The crop was grown with optimum irrigation, applied at frequent intervals, resulting in a low seasonal Bowen ratio (H/LE: Sensible heat flux/Latent heat flux) value of 0.23. The diurnal average flux rate for H during various phenophases varied between 2.2 and 16.2 Wm-2 and had a seasonal mean of 11.0 W m-2. LE exchange rates varied between 44.2 and 56.8 W m-2 and the seasonal mean was 49.0 W m-2.Evapo-transpiration (ET) of wheat in the location under standard growing condition was estimated at 312 mm.However, the crop could actually evapotranspire water in the range of 187-248 mm,as measured through an eddy covariance based protocol, even though it received about 410 mm of water through irrigation and rainfall. Canopy condition were interpreted through hyperspectra based indices, viz. NDVI and LSWI which indicated atleast two instances of stress, one around maximum tillering and the other between anthesis and dough stages.Net primary production and yield during the 105 day long growing season were 558 g C m-2 and 3.3 t ha-1, respectively and the productivity gap could be minimized by addressing the major edaphic limitations, i.e. low soil volume and high seepage losses.