Increasing interest in offshore development has motivated intensified efforts to map the seafloor for marine spatial planning. However, surficial geologic maps do not accurately represent habitats for various species groups of concern. This study used a bottom-up approach to integrate macrofaunal densities and benthic conditions on the Pacific Northwest shelf to identify macrofaunal assemblages and associated habitat features. Benthic cores and water-column profiles were collected from 137 stations from 50 to 110m depth. Analyses grouping stations based on both similar species abundances and benthic conditions resulted in six broad habitats. Within the sampled depth and latitudinal range, sediment characteristics were the primary structuring variable. A major break in assemblages was detected between sediment that had less than 1% silt/clay and those containing more than 1% silt/clay. Assemblages differed primarily in the bivalve species present and secondarily in polychaete species. Within the greater than and less than 1% silt/clay habitats, further discretization of assemblages was based mostly on differing abundances of characteristic bivalves and polychaetes associated with differing median grain sizes, which did not correspond to traditional definitions of fine or medium sand. These data show that a bottom-up methodology is necessary to discern habitats for macrofauna and that site-specific physical sampling is necessary to predict macrofaunal assemblage composition. However, if detailed sediment characteristics are known, macrofaunal assemblages may be predicted without time-intensive biological sampling and processing. These results also indicate that seemingly small sedimentary changes due to offshore installations may have measureable effects on the relative abundances and even the species composition of macrofauna.