Invasive species represent a substantial threat to aquatic systems, and aquaculture operations provide a vector for their transportation between waters. Moving large volumes of water during fish spawning or trap‐and‐transfer operations increases the risk of transporting invasive bivalve larvae, particularly from sources experiencing nondetection error. This study evaluated the effectiveness of two portable filter systems at reducing or eliminating zebra mussel Dreissena polymorpha and Asian clam Corbicula fluminea veligers from an infested water source. A small setup was assessed at intervals to 1,420 L using combinations of 20‐ and 5‐μm filters arranged in tandem, whereas a large setup was tested at intervals to 7,041 L with combinations of 30‐ and 5‐μm tandem filters operating at two pressure ranges. Zero veligers were observed in 36 small‐setup filtered water samples. Four zebra mussel veligers and zero Asian clam veligers were observed in 60 large‐setup samples. Total zebra mussel and Asian clam counts from 31 unfiltered control samples were 27,846 and 1,095, respectively. Overall, both filter systems were highly effective at removing zebra mussel and Asian clam veligers and represent simple, cost‐effective safeguards against nondetection error of aquatic invasive species in waters used for aquaculture practices.