A water treatment system and method including a membrane-based boron removal unit includes a boron analyzer for detecting the concentration of boron in a treatment stream. The boron removal unit can be a reverse osmosis (RO) or electrodeionization (EDI) treatment unit. A controller responds to the detected boron concentration to control an operation of the RO or EDI units. In an EDI system, the controller may adjust current or voltage supplied to match current to changes in ionic load and maintain a portion of the dilute cell in a substantially regenerated state. In an RO system, the controller may control the high pressure side flow rate, the brine blowdown rate, the product water permeation rate, pH, or feed rate of chemicals in response to the detected boron concentration value.