This data set contains information on the occurrence and abundance of intertidal marine invertebrates and macro algae collected across five islands with 10 sites in the Boston Harbor in 2023. This data was collected using an intertidal biodiversity monitoring protocol developed specifically for the mixed coarse substrate habitat found on the inner islands of Boston Harbor, including Gallops, Georges, Lovells, Peddocks, and Thompson Island. Species were identified and total counts of mobile invertebrates and percent cover for macro algae and sessile invertebrates in randomly distributed 0.5 square meter quadrats. Data included in this release was used to determine community composition and diversity metrics across high biodiversity and erosional sites for the five islands.