Invasive New Zealand mudsnails (Potamopyrgus antipodarum, NZMS) have infested freshwater aquaculture facilities in the western United States and disrupted stocking or fish transportation activities because of the risk of transporting NZMS to naive locations. We tested the efficacy of a gravity-fed, hydrocyclonicseparation system to remove NZMS from an aquaculture water source at two design flows: 367 L/min and 257 L/min. The hydrocyclone effectively filtered all sizes of snails (including newly emerged neonates) from inflows. We modeled cumulative recovery of three sizes of snails, and determined that both juvenile and adult sized snails were transported similarly through the filtration system, but the transit of neonates was faster and similar to the transport of water particles. We found that transit times through the filtration system were different between the two flows regardless of snail size, and the hydrocyclone filter operated more as a plug flow system with dispersion, especially when transporting and removing the larger sized adult and juvenile sized snails. Our study supports hydrocyclonic filtration as an important tool to provide snail free water for aquaculture operations that require uninfested water sources.