A novel Multiplexed Particle Refining (MPR) pre-filter was developed to be combined with biomedical membrane filters for recovering protozoa in raw water. The performance of the device is based on pre-separation of micro-sized water particulates. Characteristic tests were conducted with 10-L surface water seeded with 100 Cryptosporidium parvum oocysts. Results showed a significant increasing of the protozoan recovery by employing the MPR prior to membrane filtration. US EPA recommended Envirochek HV and Filta-Max filters recover 52.6% and 71.2% oocysts with the MPR pre-filtration, in contrast to 22.4% and 42.5% recovered by the filters alone.