We investigated the effects of short-term root-zone hypoxic stress and exogenous calcium application or deficiency in an anoxic nutrient solution on nitrogen metabolism in the roots of the muskmelon cultivar Xiyu No. 1. Seedlings grown in the nutrient solution under hypoxic stress for 6 d displayed significantly reduced plant growth and soluble protein concentrations. However, NO 3 − uptake rate and activities of nitrate reductase and glutamate synthase were significantly increased. We also found higher amounts of nitrate, ammonium, amino acids, heat-stable proteins, polyamines, H 2O 2, as well as higher polyamine oxidase activity in the roots. In comparison to the reactions seen under hypoxic stress, exogenous calcium application led to a marked increase in plant weights, photosynthesis parameters, NO 3 − uptake rate and contents of nitrate, ammonium, amino acids (e.g., glutamic acid, proline, glycine, cystine, γ-aminobutyric acid), soluble and heat-stable proteins, free spermine, and insoluble bound polyamines. Meanwhile, exogenous calcium application resulted in significantly increased activities for nitrate reductase, glutamine synthetase, and glutamate synthase but decreased activities for diamine and polyamine oxidase, as well as lower H 2O 2 content in roots during exposure to hypoxia. However, calcium deficiency in the nutrient solution decreased plant weight, photosynthesis parameters, NO 3 − reduction, amino acids (e.g., alanine, aspartic acid, glutamic acid, γ-aminobutyric acid), protein, all polyamines except for free putrescine, and the activities of glutamate synthase and glutamine synthetase. Additionally, there was an increase in the NO 3 − uptake rate, polyamine oxidase activity and H 2O 2 contents under hypoxia–Ca. Simultaneously, exogenous calcium had little effect on nitrate absorption and transformation, photosynthetic parameters, and plant growth under normoxic conditions. These results suggest that calcium confers short-term hypoxia tolerance in muskmelon, most likely by promoting nitrate uptake and accelerating its transformation into amino acids, heat-stable proteins or polyamines, as well as by decreasing polyamine degradation in muskmelon seedlings.