In this study, heterogeneous ion exchange membranes were tested for separation and recovery of boron and lithium from aqueous solutions with bipolar membrane electrodialysis (EDBM). The results indicated that separation efficiencies and recoveries of both boron and lithium were strongly influenced by the acid and base solutions employed in acid and base cells, flow rate of sample solution and electrical potential applied. It was concluded that separation efficiencies and recoveries of boron and lithium were improved with an increase in the flow rate of sample solution. The highest separation efficiencies were 93% and 69% for lithium and boron, respectively at 50 L/h of sample solution flow rate. The highest recoveries of lithium and boron were achieved as 57% and 41%, respectively at this condition. When electrical potential increased from 15 V to 25 V, boron and lithium separation efficiencies and recoveries obtained were higher. At 30 V of electrical potential, pH of sample solution decreased because of the proton leakage into the sample cell. Since anionic borate ions in sample solution cell were considered to be converted to neutral boric acid, this situation resulted in lower separation efficiencies and recovery of boron from sample solution. By applying optimal process conditions (25 V and 50 L/h of sample solution flow rate), 59% of boron recovery and 73% of lithium recovery were obtained in acid and base cells, respectively.