This protocol has been adapted from the Montana Fish Wildlife & Parks (MTFWP) plankton tow protocol that is based on the standard United States Bureau of Reclamation (USBR) veliger plankton tow protocol. We integrated the Flathead Lake Biological Station (FLBS) standard eDNA protocol to show additional steps useful for collecting an eDNA sample along with the standard veliger sample. Biologists often take multiple replicate tow samples (N=5) at each site and pool them into one container. This protocol describes the collection of one of these replicates with the addition of a supplemental eDNA sample. This protocol is accompanied by a training video that highlights these supplemental eDNA sample collection steps.