Environmental DNA (eDNA) metabarcoding may have utility in biodiversity surveys of marine environments, particularly for small, rare, or cryptic taxa that are more difficult to study using traditional methods (e.g., trawling and visual surveys). For this study, we used an eDNA metabarcoding approach to characterize biodiversity in the above-seafloor water column across three West Coast-based research cruises, focusing on understudied deep sea habitats (~800-3200 m). Approximately 100 eDNA seawater samples were collected during three research expeditions using Niskin bottles that were either mounted on remotely operated vehicles (ROVs, most samples) or using a conductivity/temperature/depth (CTD) rosette with niskin bottles. The research expeditions targeted deep seafloor habitats in the California Current Large Marine Ecosystem (CCLME) of potential biological/geological interest from three regions: Northern California, plus Northern and Southern Cascadia. Samples then underwent DNA extraction, amplification, and sequencing, as described in the methods. Taxonomy was assigned using the bioinformatic procedures described in the methods.