The Boston Harbor Islands is the only coastal drumlin archipelago in the USA, featuring a distinctive and uncommon geological intertidal habitat known as mixed coarse substrate, which supports a range of coastal species and ecological processes. Recently designated as one of America’s 11 most endangered historic places due to climate change impacts, coastal adaptation and restoration efforts are crucial to their preservation. Such efforts can benefit from historic and current knowledge of endemic and emergent biodiversity. To investigate broad trends in coastal biodiversity, we compiled an inventory of marine coastal macroalgae, macroinvertebrates, fish, mammals, and shorebirds observed in the harbor since 1861. Records span 159 years, consisting of 451 unique taxa from 19 phyla. Analysis of average taxonomic distinctness (AvTD) revealed increases in diversity towards the end of the twentieth and early twenty-first century, likely associated with improved water quality (dissolved oxygen; AvTD > 85, p = 0.01) due to harbor restoration in the 1980s. Macroinvertebrates comprised 50% of the records, making this the most diverse taxonomic group in the time series. A significant increase of non-indigenous species, primarily macroinvertebrates and macroalgae, was observed over the last 20 years near human infrastructure and across multiple islands, a consequence of global change and characteristic of most urban harbors. The mixed coarse intertidal habitat, which makes up > 70% of Boston Harbor’s inner islands and supports high macroinvertebrate and macroalgal diversity (47% of species records), is not routinely monitored; our findings serve as a foundational resource for climate adaptation projects and decision-making.