Marine spatial planning (MSP) should assist managers in guiding human activities towards sustainable practices and in minimizing user-conflicts in our oceans. A necessary first step is to quantify spatial patterns of marine assemblages in order to understand the ecosystem’s structure, function, and services. However, the large spatial scale, high economic value, and density of human activities in near-shore habitats often makes quantifying this component of marine ecosystems especially daunting. To address this challenge, we developed an assessment method that employs abiotic proxies to rapidly characterize marine assemblages in near-shore benthic environments with relatively high resolution. We evaluated this assessment method along 300 km of the State of Maine’s coastal shelf (< 100m depth)—a zone where high densities of buoyed lobster traps typically preclude extensive surveys by towed sampling gear (i.e., otter trawls). During the summer months of 2010-2013, we implemented a stratified-random survey using a small remotely operated vehicle that allowed us to work around lobster buoys and to quantify all benthic megafauna to species. Stratifying by substrate, depth, and coastal water masses, we found that abiotic variables explained a significant portion of variance (37- 59%) in benthic species composition, diversity, biomass and economic value. Generally, the density, diversity, and biomass of assemblages significantly increased with the substrate complexity (i.e., from sand-mud to ledge). The diversity, biomass and economic value of assemblages also decreased significantly with increasing depth. Lastly demersal fish densities, sessile invertebrate densities, species diversity, and assemblage biomass increased from east to west, while the abundance of mobile invertebrates and economic value decreased, corresponding mainly to the contrasting water-mass characteristics of the Maine Coastal Current system (i.e., summertime current direction, speed, and temperature). Integrating modeled predictions with existing GIS layers for abiotic conditions allowed us to scale up important assemblage attributes to define key foundational ecological principles of MSP and to find priority regions where some bottom-disturbing activities would have minimal impact to benthic assemblages. We conclude that abiotic proxies can be strong forcing functions for the assembly of marine communities and therefore useful tools for spatial extrapolations of marine assemblages in congested (heavily used) near-shore habitats.