Fertilizer and moisture availability affect various physiological and growth processes and are key factors in controlling productivity and yield of cotton crop. Two-year experiment (kharif 2012 and 2013) was conducted to evaluate the effects of different fertilizer levels on growth, yield, water and partial factor productivity of fertilizers of furrow irrigated raised bed (FIRB) planted transgenic cotton in semi-arid region of north-west India. The fertilization treatment was based on different ratios of N, P2O5 and K2O. Four fertilizer treatments were designed including 75%, 100%, 125% and 150% of recommended rates with N 175, P2O5 60 and K2O 60 kg/ha. Yield components were measured. Partial factor productivity of fertilizer (PFP), water productivity and economics were calculated. Compared to conventional method of sowing, FIRB planted cotton produced significantly higher yield components, viz. sympods and bolls/plant and boll weight. The seed cotton yield of FIRB planted crop increased by 10.3% in 2012 and 11.2% in 2013. This method of sowing also resulted in higher PFP for individual nutrients, i.e. N, P and K as well as for the total nutrients, i.e. N, P and K. It also provided higher water productivity, net benefit and B:C. Non-Bt genotypes did not show any marked diffence in terms of yield, WP and PFP of nutrients applied over Bt, however, was better in terms of net benefit and B:C. The PFP decreased with the increase of fertilization rates. With 75% RDF, the PFPN during the respective two crop seasons was 14.02 and 12.98 kg seed cotton/kg applied N and decreased to 7.05 and 6.98 with 150% RDF. The corresponding values of PFPP or K were 40.90 and 37.88 which decreased to 21.89 and 20.31 kg seed cotton/kg applied P or K. Similarly, the PFP N,P and K was 8.33 and 7.72 and the corresponding vlaues with 150% RDF were 4.45 and 4.41 kg seed cotton per kg applied N, P and K. Under semi-arid conditions, to achieve higher productivity hybrid cotton (Gossypium hirsutum L.) be planted under FIRB system fertilized with N -175, P2O5-60 and K2O-60 kg/ha.