Coastal eutrophication is harming seagrass beds due to high ammonium levels. Zostera marina leaves suffer more from ammonium stress than roots. Roots can handle up to 100 mg/L of ammonium without harm. Leaves show higher ammonium and amino acid levels under stress. Nitrogen storage decreases in leaves with high ammonium. Roots have higher enzyme activity for ammonium assimilation than leaves. Leaves become toxic at ammonium levels above 100 mg/L. This study suggests that Z. marina leaves are more vulnerable to damage from high ammonium levels compared to roots.