This research aims to introduce the easy, inexpensive and fast analytical method for spectrophotometric measurement of boron in water samples. Here, the BF4—Methylene blue (MB) formation was selected and accomplished faster using ultrasonic and, then the dispersive liquid microextraction (DLLME) condition was optimized for the flow-based determination of the boron. Some influential factors such as reaction time (10 min), the concentration of NaF (0.3 M), H2SO4 solution (0.2 M) and Methylene blue (0.5 M), type and volume of organic solvent (300 µL of chloroform), type, and volume of disperser solvent (1 mL Acetone), were studied. Under the optimum conditions, this work showed a limit of detection of 0.01 µg/L and a linearity range of 0.1–1.2 mg/L. Also, the relative standard deviation and the enrichment factor were 4% (N = 7) and 25, respectively. Finally, the boron contents in the samples of reverse osmosis desalination process were measured. The results showed that the optimal BF4—MB formation time could be two times shorter using an ultrasonic bath and flow base analysis could make the determination of the collected sediments of DLLME, easier and faster.