Abstract: The effects of water stress (water logging and non-water logging) and nitrogen forms (ammonium, nitrate and mixture of both) on concentrations of substrates in sugar and nitrogen metabolism (including nitrate, soluble sugar, reducing sugar and free amino acid) in roots, sheaths and stems, and leaves of maize at seedling stage were analyzed in a sand culture experiment. The results showed that under non-water logging conditions, ammonium treated maize had the highest concentration of soluble sugar and free amino acid in different parts of the plant. Dry biomass of different parts of nitrate-treated maize plants was significantly lower than that of ammonium-treated plants. Root and leaf dry biomasses were also significantly lower in ammonium-treated plants than plants treated with mixed nitrogen after seven days of water logging. Water logging significantly reduced nitrate concentration in roots and leaves of nitrate-treated maize plants by 62.6% and 30.0%, respectively. Furthermore, water logging significantly increased soluble/reducing sugar and free amino acid concentrations in roots, soluble/reducing sugar concentrations in sheaths and stems, and soluble sugar and free amino acid concentrations in leaves of ammonium-fed plants. It, however, increased reducing sugar concentration in roots, sheaths and stems and leaves, and free amino acid concentration in leaves of nitrate-fed plants. Ammonium rather than nitrate or mixed nitrogen alleviated therefore the negative effects of water logging resulting from more substrates of sugar and nitrogen metabolism when ammonium was the solely form of nitrogen.