Two wheat genotypes were grown in hydroponic culture, containing 4 mM KNO3, NH4Cl and NH4NO3. Activities of N metabolizing enzymes, aminotransferases, carbohydrate and TCA cycle enzymes were analyzed along with protein, amino acid, N, sugar content and growth parameters in shoot and root. After 12 days, the size of shoot and root system decreased significantly when plants were supplied with NH4Cl as exclusive N source. Under NH4NO3 growth parameters, N and carbon metabolism were elevated as compared to NH4Cl but less than KNO3 source indicating inhibition of NH4+ toxicity by NO3− uptake. Our results suggested that GDH, aminotransferases and PEPC play an important role in ammonium detoxification by its incorporation into amino acids. Thus, the morphologic differences among plants growing in NH4+ or NO3− nutrition confirm the hypothesis that N source determines the growth habit of plant in wheat by modulating the endogenous levels of protein and sugar content.