The “biological pump” is a key component in the global biogeochemistry of carbon dioxide that is sensitive, through a multitude of ecological interactions of euphotic zone plankton, to climatic fluctuations. In this dissertation I address the biological control of vertical carbon flux out of the surface ocean in two regions of the Pacific Ocean. I begin by addressing the hypothesis that most export production in the equatorial Pacific is derived from the primary production of picophytoplankton. Using inverse ecosystem modeling techniques to synthesize detailed rate measurements I show that eukaryotic phytoplankton are the dominant producers of eventually exported material and that export comes after processing by mesozooplankton, but that the results of inverse modeling studies are dependent upon subjective decisions about model structure, input data, and solution schemes. I then move on to studies in the California Current Ecosystem (CCE), where a combination of my own in situ measurements of vertical carbon export and collaborators' measurements of key planktonic rates allow me to address the question of what constitutes sinking flux in this coastal upwelling biome. I begin with simple trophic cycling relationships that use phytoplankton growth, micro- and mesozooplankton grazing, and simple assumptions about organismal efficiency, and show that fecal pellet production could account for the magnitude and variability in carbon export measured by ²³⁴Th disequilibrium during a cruise in May 2006. I then utilize inverse modeling techniques to show that on two spring cruises the contribution of grazing products to export was substantially greater than that of gravitational sinking of phytoplankton, and also that Markov Chain Monte Carlo methods do an accurate job of solving inverse ecosystem models. Finally, I use sediment trap samples to directly assess the contribution of fecal pellets to vertical flux, finding that mesozooplankton pellets were the dominant component of flux during the spring, but that during a fall cruise their contribution was variable, with flux becoming increasingly dominated by non-pigmented small material and marine snow as productivity decreased.