This paper describes the development of a highly sensitive microfluidics flow sensor using MTJ magnetic sensors to detect motion of slow-moving fluids. A motivating application for the proposed device is the development of an implantable flow sensor, capable of monitoring the amount of cerebral spinal fluid drained from the ventricles of the brain. Micro-fabricated ferromagnetic flaps are used to detect motion of the surrounding fluid. The deflection of the flaps is detected by an ultra-sensitive MTJ magnetic field sensor placed outside of the lumen of the catheter. Previous studies have presented a working device with a resolution of up to 1.4 mL/hr. This paper presents the improvements made to the device in terms of sensitivity, thermal noise rejection, and dynamic response. Upon investigation of possible noise sources, a thermally induced sensor drift was found to be the most significant factor affecting the sensors response. A static temperature compensation reduced this drift to less than 120 mL per 12-hr period. Further improvements to the design of the ferromagnetic transducers resulted in a 4.5-fold increase in sensitivity over the previous designs. Results from dynamic testing of the sensor revealed a time constant of 0.4 seconds, which was found adequate for the envisioned application.