Changes in concentrations of oxidative material, antioxidase activities and chlorophyll fluorescence were investigated in Potamogeton polygonifolius exposed to different concentrations of ammonium nitrogen. The results show that 10mg/L of ammonium nitrogen had a little effect on photosynthetic capacity of P. polygonifolius. However, the 5 mg/L to 10 mg/L concentration of ammonium nitrogen could increase oxygen radicals and enhance the defensive capacity by stimulating the antioxidant enzymes activity and increasing content of secondary metabolites. 10 mg/L concentration of ammonium nitrogen had significant effect on the activity of antioxidant enzymes and content of secondary metabolites. The increased antioxidant capacity may alleviate ammonium induced oxidative stress, and thus enhance the endurance of plants to cope with ammonium stress. Overall, higher concentration of ammonium nitrogen had some effect on P. polygonifolius and consequently, the concentration and impact of ammonium nitrogen should be considered when using P. polygonifolius was chosen as candidate plants for the to remediate water ecosystem.