Whale bones and wood on the deep-sea floor provide resource pulses that support characteristic faunal assemblages in an otherwise food-poor environment. To isolate the role of bathymetric and geographical drivers of organic-fall diversity and community structure, the study of organic-rich substrates of similar sizes, qualities, and seafloor durations is necessary. We used a comparative experimental approach to examine the roles of depth, location, and substrate type in structuring organic-fall faunal assemblages. Four free-vehicle landers containing replicate wood, whale-bone, and inorganic hard (control) substrates were deployed for 15 mo at depths of ~1600 and ~2800 m, spaced at ~400 km along the Washington-Oregon (USA) margin. The landers collected a total of ~84890 macrofaunal individuals of 144 species. Wood, bone, and control substrates supported assemblages with different community structures on all landers. Community composition was significantly different between depths and between locations at similar depths, indicating variability on regional and bathymetric scales. Wood blocks at ~1600 m were heavily degraded by wood-boring xylophagaid bivalves. Xylophagaid colonisation was lower in deeper wood blocks, which we hypothesise results partly from lower propagule supply as wood falls decrease in abundance with distance from terrestrial sources of wood. Bone-eating Osedax colonised whale bones, but bone degradation was low compared to some NE Pacific whale falls of similar duration; nonetheless, bones exhibited reducing conditions and supported sulphophilic species. Our study demonstrates quantitatively that co-located wood falls and whale bones support highly distinct, species-rich assemblages and thus promote biodiversity on the deep-sea floor.