A processing system and methods for extracting phytochemicals from plant materials with subcritical water. The processing system includes a water supply interconnected with a high-pressure pump, diverter valve, a temperature-controllable extraction vessel, a cooler, a pressure-relief valve and a collection apparatus for collecting eluant fractions from the extraction vessel. The processing system controllably varies the temperature of subcritical water within the extraction vessel, and may optionally be configured to controllably vary the pH of subcritical water flowing into the extraction vessel. A plant material is placed into the extraction vessel after which a flow of subcritical water is provided through the extraction vessel for extraction of phytochemicals. The temperature of subcritical water is controllably varied during its flow through the extraction vessel water thereby producing a plurality of eluant subfractions corresponding to the temperature changes, thereby separating the different classes of phytochemicals extracted from the plant material.