The Boston Harbor Islands National Recreation Area has an extensive intertidal zone, with 47% of the area composed of mixed-coarse substrate. Given anticipated climate-change impacts such as sea-level rise and ocean warming, and other stressors associated with the urban environment, the critical ecosystem functions (i.e., species habitat, food-web support) provided by this dominant mixed-coarse habitat of Boston Harbor, and elsewhere throughout the Northeast, have been and will likely be further altered. To evaluate the present-day epibenthic invertebrate communities and to determine what environmental factors of the mixed-coarse substrate affect community structure, we used a stratified random design to sample epibenthic macroinvertebrates along with various physical and environmental variables from the intertidal zone. Epibenthic macroinvertebrate species assemblages and diversity differed significantly between wave-exposed and wave-protected sites, with higher diversity present at protected sites. We also found that environmental variables collectively explained up to 67% of the variation in species assemblages, with elevation, organic content, water content, and sediment type individually explaining up to 56%, 30%, 42%, and 33% of the variation, respectively. This study provides a baseline for long-term monitoring aimed at understanding the response of cobble and mixed-coarse intertidal communities to multiple disturbances, and a foundation to support habitat restoration or other management actions.