Sequestration of atmospheric carbon dioxide in the world’s oceans is still poorly understood despite its important role in the Earth’s climate system. Understanding the nature of vertical downward flux of organic matter remains a key goal of oceanography. Large sinking aggregates, such as zooplankton fecal pellets and marine snow, transport organic matter to the deep ocean. These aggregates affect nutrient and organic matter distribution in the water column, feed life in the dark ocean, and control carbon dioxide removal from the atmosphere. While much work has been done on marine snow at a bulk level or even on the scale of individual marine snow aggregates, we are only just beginning to understand how the aggregate composition and turnover mechanisms control export and attenuation processes of organic matter through the water column. We have studied how regional and seasonal plankton community structure influence aggregate composition, sinking velocities, microbial activity, and protist and zooplankton grazing on sinking aggregates. In this way it is possible to link small scale structuring and microbial interactions within individual aggregates to their full water column distribution and contribution to biogeochemical cycling from the surface to the deep ocean.