Three-month-old mulberry (Morus alba L.) cultivars, i.e. S13 (drought: tolerant) and S54 (drought sensitive), were subjected to different regimes of water stress conditions for a duration of 10 days. The activities of nitrate reductase (NR: EC 1.6.6.1), nitrite reductase (NiR: EC 1.6.6.4.), protease, glutamine synthetase (GS: EC 6.3.1.2), glutamate synthase (GOGAT: EC 1.4.1.13), glutamate dehydrogenase (NADH-GDH: EC 1.4.1.2 and NADPH-GDH: EC 1.4.1.4), aspartate aminotransferase (AAT: EC 2.6.1.1) and alanine aminotransferase (AlAT: EC 2.6.1.2.), along with total protein content, free amino acid level, ammonia and glutamine contents were measured in both genotypes under water stress conditions. The tolerant genotype (S13) registered a higher metabolic activity leading to a greater accumulation of amino acids coupled with lesser amounts of ammonia accumulation in the tissue. Further, it is realised that no process of endogenously generated ammonia was responsible for the differential accumulation of ammonia between the genotypes under stressful conditions. However, this difference in ammonia levels among the varieties can be attributed to the difference exhibited in the reassimilation of ammonia, whereby the tolerant genotype (S13) recorded a relatively better reassimilation capacity of ammonia. From these findings, the drought tolerance of S13 seems to be associated at least in part with its ability to maintain greater levels of amino acid pool coupled with more pronounced reassimilation of ammonia.