A method and system for multi-zone control of temperature for a substrate is described. The temperature control system comprises a heat exchanger coupled to two or more fluid channels in a substrate holder configured to support the substrate. The heat exchanger is configured to adjust the temperature of a heat transfer fluid flowing through the two or more fluid channels. The temperature control system further comprises a heat transfer unit having an inlet that is configured to receive heat transfer fluid from the heat exchanger at a bulk fluid temperature. Additionally, the heat transfer unit comprises a first outlet configured to couple a portion of the heat transfer fluid at a first temperature less than the bulk temperature to a first fluid channel of the two or more fluid channels, and a second outlet configured to couple a remaining portion of the heat transfer fluid at a second temperature greater than the bulk fluid temperature to a second fluid channel of the two or more fluid channels.