Model representations of plankton structure and dynamics have consequences for a broad spectrum of ocean processes. Here we focus on the representation of zooplankton and their grazing dynamics in such models. It remains unclear whether phytoplankton community composition, growth rates, and spatial patterns in plankton ecosystem models are especially sensitive to the specific means of representing zooplankton grazing. We conduct a series of numerical experiments that explicitly address this question. We focus our study on the form of the functional response to changes in prey density, including the formulation of a grazing refuge. We use a contemporary biogeochemical model based on continuum size-structured organization, including phytoplankton diversity, coupled to a physical model of the California Current System. This region is of particular interest because it exhibits strong spatial gradients. We find that small changes in grazing refuge formulation across a range of plausible functional forms drive fundamental differences in spatial patterns of plankton concentrations, species richness, pathways of grazing fluxes, and underlying seasonal cycles. An explicit grazing refuge, with refuge prey concentration dependent on grazers’ body size, using allometric scaling, is likely to provide more coherent plankton ecosystem dynamics compared to classic formulations or size-independent threshold refugia. We recommend that future plankton ecosystem models pay particular attention to the grazing formulation and implement a threshold refuge incorporating size-dependence, and we call for a new suite of experimental grazing studies.