The equatorial Pacific Ocean is the largest natural source of CO2 to the atmosphere, and it significantly impacts the global carbon cycle. Much of the large flux of upwelled CO2 to the atmosphere is due to incomplete use of the available nitrate (NO3) and low net productivity. This high-nutrient low-chlorophyll (HNLC) condition of the equatorial upwelling zone (EUZ) has been interpreted from modeling efforts to be due to low levels of silicate (Si(OH)4) that limit the new production of diatoms. These ideas were incorporated into an ecosystem model, CoSINE. This model predicted production by the larger phytoplankton and the picoplankton and effects on air-sea CO2 fluxes in the Pacific Ocean. However, there were no size-fractionated rates available for verification. Here we report the first size-fractionated new and regenerated production rates (obtained with 15N−NO3 and 15N−NH4 incubations) for the EUZ with the objective of validating the conceptual basis and functioning of the CoSINE model. Specifically, the larger phytoplankton (with cell diameters > 5 μm) had greater rates of new production and higher f-ratios (i.e., the proportion of NO3 to the sum of NO3 and NH4 uptake) than the picoplankton that had high rates of NH4 uptake and low f-ratios. The way that the larger primary producers are regulated in the EUZ is discussed using a continuous chemostat approach. This combines control of Si(OH)4 production by supply rate (bottom-up) and control of growth rate (or dilution) by grazing (top-down control).