This data set contains environmental DNA (eDNA) data enumerating the presence of intertidal marine vertebrates, invertebrates, and macro algae collected across 5 islands with 10 sites in the Boston Harbor in 2023. This data was collected using water samples collected in association with other intertidal biodiversity monitoring protocols developed specifically for the mixed coarse substrate habitat found on the inner islands of Boston Harbor, including Gallops, Georges, Lovell (alternatively known as Lovells Island), Peddocks, and Thompson Island. Species were identified using an eDNA metabarcoding approach targeting the 12s (vertebrate) and 18s (invertebrate and macro algae) gene regions. Total read count scores for species detected are reported, with scores greater than 1 signaling a positive detection, and scores of 0 signaling no detection. Data included in this release was used to determine community composition and diversity metrics across high biodiversity and erosional sites for the 5 islands.