Excess boron (B) is toxic to aquatic organisms and humans. Boron is often present in water with high salinity. To evaluate the potential of duckweed (Lemna minor L.) for removing B from water under salt stress, we cultured duckweed in water with 2 mg/L of B and sodium chloride (NaCl) concentrations ranging from 0 to 200 mM for 4 days. The results show that with increasing salinity, the capacity of L. minor to accumulate B initially decreased and then increased. L. minor used different mechanisms to accumulate boron at lower and higher levels of salt stress. The growth and chlorophyll synthesis of L. minor were significantly inhibited when the concentration of NaCl reached 100 mM. Our results suggest that L. minor is suitable for the accumulation of B when NaCl salinity is below 100 mM.