Standard filtration methods have been characterized by poor recoveries when processing large-volume samples of environmental water. A method to pre-remove particulates present in turbid waters would be necessary to enhance recovery of protozoan oocysts. Particulate separation can be achieved by the proposed multiplex particle refining (MPR) system. This system employs multiple counter-flow microfiltration units that are arranged into a cascade-like structure. By use of this design, the target oocysts are pre-concentrated from environmental waters. The performance of the MPR system was investigated using 10-L deionized water and surface water spiked with 100 Cryptosporidium parvum oocysts. A recovery rate of around 85% was obtained for spiked river water. The water samples were processed using high flow rate and a simple filtration protocol. Further experiments were conducted using the MPR as a pre-filter for five commercially available filters. The recovery rates were two- to threefold higher employing the pre-filter than using the filters alone. The merit of the refining system to use different numbers of counter-flow units led to superior oocyst recovery rate for the Filta-Max and Envirochek HV filters, which are approved by the US Environmental Protection Agency. This work demonstrates a feasible tool for improved filtration performance in environmental waters.