Marine ecosystems play an integral role in the functioning of life on earth. To predict how they will respond to global changes, and to effectively manage and maintain services upon which humans rely, we must understand how biological processes at the cellular level generate macroscopic patterns in the oceans. Here, we discuss how physics and biogeochemistry influence and constrain marine ecosystem structure and function, and outline key regularities and patterns of variability that models should aim to reproduce. We identify unanswered questions regarding how size-dependent physiological and ecological processes are linked to turbulent mixing, dealing specifically with how size structure is related to mixing over a range of spatial scales and how it is linked to the fate of primary production in the sea.