The patterns and drivers of marine biodiversity and ecosystem functioning and how biological communities influence ecological processes remain poorly understood, especially for deep-sea and other remote environments. Such constraints impair effective protection of important organisms and ecosystem functions from human impacts and global change through conservation strategies such as Marine Protected Areas (MPAs). This thesis explores different aspects of biodiversity and ecosystem functioning in deep-sea sedimentary habitats, focusing on macrofaunal biodiversity and organic matter remineralization, which can be quantified through the measurement of inorganic nutrient flux rates at the sediment-water interface. I examine the roles of biogenic (e.g., sea pen fields) and geophysical (e.g., submarine canyons) habitats along the Northwest Atlantic continental margin in regulating biodiversity and functioning. Through literature review and experimentation, I explore how biological traits of organisms influence the ecology and functioning of biological communities and can potentially inform MPA design and improve conservation outcomes. My findings demonstrate the important role of biogenic and geophysical habitats in shaping macrofaunal communities, mostly by altering food availability and creating habitat heterogeneity, and the central role of food availability in driving macrofaunal diversity at regional scales. The interacting effects of several abiotic and biotic factors that act over different spatial and temporal scales complicated efforts to discern patterns of organic matter remineralization. Some macrofaunal taxa and measures of biodiversity clearly influenced variation in benthic flux rates, reiterating the importance of biological communities in driving ecosystem processes. Biological trait expression analysis helped in understanding patterns and underlying drivers of community structure, despite poor correlations between traits and benthic flux rates, highlighting the need for further studies. The findings of this study highlight the importance of protecting multiple ecologically important and sensitive marine habitats in order to maintain biodiversity and functions but also punctuate the need for further studies to characterize biological traits of under-studied organisms and effectively apply trait-based approaches to improve conservation outcomes.