This study investigates the potential impact of ammonia, intended for use in green energy, on tropical marine species. The effects of ammonia exposure were assessed on juvenile Orange Mud Crab (Scylla olivacea) and juvenile Barramundi (Lates calcarifer) over 96 h. For S. olivacea, the median lethal concentration (LC50) of ammonia was identified as 6.995 mg/L, with significant impacts on growth observed through changes in carapace length, width, and wet weight. Fifty crabs were exposed to five ammonia concentrations (0 mg/L, 2.5 mg/L, 5 mg/L, 7.5 mg/L, 10 mg/L). For L. calcarifer, gill histology and behavior were examined. Forty-nine fish were exposed to six concentrations (0 mg/L, 2 mg/L, 4 mg/L, 6 mg/L, 8 mg/L, 10 mg/L, 12 mg/L). Behavioral responses included initial ammonia avoidance, with increasing mortality (10% at 8 mg/L and 70% at 12 mg/L) by Day 4. Histological analysis revealed severe gill damage, especially at higher concentrations. Both species showed high tolerance to ammonia, but significant morphological and behavioral changes were noted at higher concentrations. These findings highlight the need for stringent safety measures and a mitigation plan in ammonia’s application within the green energy sector to prevent environmental harm.