A new microscale filtration technique was developed to perform high-throughput (HT) studies of filtration performance by integrating a multi-channel microfluidic flow control (MMFC) system that can operate in either constant flux or constant transmembrane pressure (TMP) mode with a "stirred well filtration" module. With this approach, up to eight parallel microscale filtration experiments can be performed with direct real-time measurement of the resulting flux or required TMP. A series of proof-of-concept experiments were conducted to demonstrate the usefulness of this approach to study the filtration behavior of single protein solutions and separation of two binary mixture solutions: polymer-polymer and protein-polymer.