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Size-based microfluidic filtration systems can be affected by clogging, which prevents their use in high-throughput and continuous applications. To address these concerns, we have developed two microfluidic lobe filters bioinspired by the filtration mechanism of two species of manta ray. These chips enable filtration of particles around 10–30 μm with precise control and high throughput by using two arrays of equally spaced filter lobes. For each filter design, we investigated multiple inlet flow rates and particle sizes to identify successful operational parameters. Filtration efficiency increases with fluid flow rate, suggesting that particle inertial effects play a key role in lobe filter separation. Microparticle filtration efficiencies up to 99% were obtainable with inlet flow rates of 20 mL min −1 . Each filter design successfully increased microparticle concentrations by a factor of two or greater at different inlet flow rates ranging from 6–16 mL min −1 . At higher inlet flow rates, ANSYS Fluent simulations of each device revealed a complex velocity profile that contains three local maxima and two inflection points. Ultimately, we show that distances from the lobe array to the closest local maxima and inflection point of the velocity profile can be used to successfully estimate lobe filtration efficiency at each operational flow rate.