Systems and methods have been developed for treating the waste water contaminated with methanol and boron in addition to other contaminants. The systems and methods allow specifically for the removal of the methanol and boron without the addition of significant chemicals to raise the pH. The water is treated by removing the methanol via biological digestion in a bioreactor, separating a majority of the contaminants from the water by reverse osmosis and removing the boron that passes through the reverse osmosis system with a boron-removing ion exchange resin.