In vitro techniques for the processing of flowing blood and its components have recently emerged from microfluidics. The blood flow rate and hematocrit are two keys parameters to monitor for guaranteeing the reliability of these techniques. But, there is a lack of monitoring methods adapted to low flow rates and small tubing. In this study, we exploit minimization approaches of continuous Doppler measurements to survey the blood flow rate. Combined with a packing factor model, we also estimate hematocrit from the Doppler spectrum. The presented method is implemented with a continuous-wave (CW) Doppler probe mounted on a 3D-printed support. The accuracy of the flow rate was measured in the range from 0.5 to 1.5 mL/min. For each of four different blood bags, hematocrit in the range under 8% was estimated from the Doppler spectrum using a packing factor model derived from the other three bags. Flow rate estimation shows a mean measurement error under 3% for a measurement time of 2 s. The mean error is still under 5% for a measurement time of 0.5 s. Hematocrit estimation for the four blood bags shows errors of 1.4%, 1.1%, 0.67%, and 0.70% Hct for a measurement time of 5 s. The versatility and simplicity of the method make it highly valuable for in vitro blood processing, in particular for low hematocrit blood fractionation techniques derived from microfluidics, as it can be performed through sterile tubing.