An apparatus and method for determining a continuous CSF flow rate in an implanted CSF shunt in real-time. The system/method utilize a Peltier sensor formed on a flexible pad that is placed against the patients skin. The Peltier sensor includes a Peltier device coupled to a thermal resistor that is contact with the patients skin over the CSF shunt location. The Peltier device is operated continuously, controlled by the Peltier temperature sensor to a predetermined temperature that is below the patients core temperature to form a temperature differential that causes any heat generated by the skin/CSF flow to be detected by a skin temperature sensor and the Peltier temperature sensor. Upstream and downstream temperature sensors, as well as control temperature sensors, are utilized to form a zero flow rate baseline that is used to calibrate a Peltier signal that corresponds to a real-time CSF flow rate. A sensor processing device processes all sensor data for generating the zero flow rate baseline and the Peltier signal.