Abstract: This study is an environmental baseline survey using lipidomic techniques and various lipid compounds as biomarkers for living and dead microbial cells that lived in or were transported to Scotian Slope shallow marine sediments. Distinct stratigraphic patterns were observed for individual lipid classes in the upper 9 metres of sediment below sea floor. Archaeal lipids were found to be originating from the both the water column and ocean floor sediments and increase by bathymetric depth, while distribution of bacterial and eukaryal lipids reflected a high contribution of heterotrophic bacterial communities, decrease by bathymetric depth. The distribution of various compound classes varies systematically with sediment depth, resulting in four stratigraphically overlapping archaeal lipidomes, seven for bacterial lipidomes, as well as distinct MK lipidomes, reflecting ~26,000 Kyr of changing water column loading and in situ sedimentary production from benthic communities.