This study delves into the intricate environmental ramifications of desalination brine on mangrove seedlings (Avicennia marina Forssk. Vierh), encompassing an extensive examination of plant growth, biomass allocation, soil salinity, leaf elemental composition, and plant biochemical reactions. Seedling propagules were collected from robust grey mangrove trees in Tiabe, Minab port, South of Iran, and planted in plastic pots in September 2020. Following irrigation twice daily, treatments with desalination brine concentrations (0%, 1%, 2%, 3%, 5%, 10%, and 20%) were applied for 6 months. The results reveal that seedling height and diameter remain stable up to 3% brine but exhibit declines at higher concentrations. Leaf area remains unaffected at 1–3% brine but experiences a significant decrease beyond 5%. Seedling vitality sharply declines at 1%, intensifying up to 10%, with the most profound reduction at 20% brine concentration. Biomass allocation in roots, shoots and leaves demonstrates nuanced responses, with soil salinity increasing significantly, particularly at the highest brine concentration of 20%. Sodium and chloride concentrations exhibit tissue-specific variations, and a positive correlation is observed between cadmium concentrations and brine intensity. The study underscores a pollution-induced stress on photosynthetic pigments. Enzyme activities (CAT, POD, SOD) show an escalating trend with brine, peaking at 20%, emphasizing the intricate environmental implications of desalination brine on coastal ecosystems. The findings advocate for sustainable management practices in coastal ecosystems facing anthropogenic stressors.