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In this paper, it is presented the counter-flow refinery (CFR) system, which is a novel approach of continuous pathogen enrichment device for large-volume raw water. The device is comprised by two refining levels, in each of which the counter-flow microconcentrator units are arranged in series. The designed CFR module is able to concentrate 100-L water samples by a concentrating factor >500. By spiking Cryptosporidium Parvum oocysts in surface water, the system achieved the recovery efficiency as high as 89.2% without clogging for a processing time of <1.5h.