We used an environmental DNA (eDNA) autosampler and a backpack manual sampler to collect eDNA samples at Naval Base Ventura County's Point Mugu Sea Range in May and June 2025. Samples were sent to Wilderlab for metabarcoding analysis using their basic panel of five primers to amplify DNA from a variety of taxa, including vertebrates (fish, mammals, reptiles, amphibians, and birds), crustaceans, and freshwater insects. This dataset is the metabarcoding results, which included exact sequent variants (ESVs) and their taxonomic assignments found in each sample using each assay.