Background: Since alkaloids are nitrogenous compounds, the availability of nitrogen (N) is expected to play an important role in the biosynthesis and accumulation of alkaloids in plants. Objective: This study intended to investigate the nitrogen (N) fertilization and water deficit stress (WDS) effects on seed tropane alkaloids elicitation including hyoscyamine (HYO) and scopolamine (SCO), and also antioxidant enzymes activities variations including superoxide dismutase (SOD), peroxidase (POX) and catalase (CAT) in black henbane. Methods: Plants were treated with different nitrogen (0, 0.14, 0.28 and 0.56 g N pot-1 as ammonium nitrate, N0-N3, respectively) and WDS treatments (30, 60 and 90% depletion of water from field capacity, W1-W3). Alkaloids extracted were identified by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS) analysis. Results: Results showed that the highest alkaloid content values in seeds (HYO: 0.145% dw; and SCO: 0.271% dw) achieved in plants grown under sever (W3) and moderate (W2) WDS accompanied with nitrogen supply of 0.28 g N pot-1 (N2), respectively. The maximum and minimum (2.112 and 0.114 g.plant-1) total alkaloids yield were obtained in N3W1 and N3W3 treatments, respectively. Furthermore, SOD activity increased with increasing N fertilization in all WDS treatments. CAT activity increased with WDS up to 60% FC, and then decreased with WDS increase. The POX activity was the opposite to that of CAT activity with N application under WDS levels. Conclusion: Our results suggest that N in appropriate level may act as a modifier for seed physiological responses and as an elicitor for tropane alkaloids biosynthesis pathway in black henbane (hyoscyamus niger) plants.