Duckweed plays a major role in the removal of nitrogen (N) and phosphorus (P) from water. To determine the effect of salt stress on the removal of N and P by duckweed, we cultured Lemna minor, a common species of duckweed, in N and P-rich water with NaCl concentrations ranging from 0 to 100 mM for 24 h and 72 h, respectively. The results show that the removal capacity of duckweed for N and P was reduced by salt stress. Higher salt stress with longer cultivation period exerts more injury to duckweed and greater inhibition of N and P removal. Severe salt stress (100 mM NaCl) induced duckweed to release N and P and even resulted in negative removal efficiencies. The results indicate that L. minor should be used to remove N and P from water with salinities below 75 mM NaCl, or equivalent salt stress.