Drip-irrigated rice (
Oryza sativa
L.) in calcareous soil exhibits signs of iron (Fe) deficiency. This study aimed to explore whether NH
4
+
alleviates Fe deficiency in rice seedlings grown under calcareous conditions. Two rice varieties (cv. ‘T43’ Fe deficiency-tolerant variety and cv. ‘T04’ Fe deficiency-sensitive variety) were used to carry out two independent experiments with exposure to different nitrogen (N) forms (nitrate (NO
3
−
) or NH
4
+
) under calcareous conditions. In experiment 1, plants were precultured in a nutrient solution with excess Fe (40 µM Fe(II)-EDTA) for 14 d and then supplied NO
3
−
-N (AN) or NH
4
−
-N (NN) without Fe for 3, 6, or 12 d. In experiment 2, plants were fed AN or NN with 10 µM Fe(II)-EDTA for 18 d. Compared to plants exposed to AN, leaves of plants exposed to NN showed severe chlorosis and significantly decreased chlorophyll content during Fe starvation. The xylem sap pH and cell wall Fe fraction in both shoots and roots of rice fed NN were significantly higher than those fed AN. However, the Fe concentration in xylem sap, soluble and organelle Fe fractions in both shoots and roots, and the shoot/root Fe content ratio in rice exposed to AN were significantly higher than those in plants exposed to NN. AN reduced the root aerenchyma fraction and root porosity compared to NN, which induced greater water uptake and hydraulic conductance by roots, hence the stronger xylem sap flow rate with AN. The results indicated that NH
4
+
-N alleviated Fe deficiency in rice under calcareous conditions by promoting Fe re-allocation in rice tissues and Fe transportation from roots to shoots.