DescriptionTaxonomic shifts can alter predator feeding preference and modify ecosystem function through top-down biological control. In Barnegat Bay-Little Egg Harbor Estuary, sea nettle (Chrysaora quinquecirrha) abundances have increased in the northern portions of the estuary, where salinity and density of anthropogenically hardened surfaces are favorable. Here I evaluate the geographical variation in top-down influence of C. quinquecirrha on marine plankton communities. I simulated a range of jellyfish- to copepod-dominated ecosystems using a highly size-resolved nutrient-phytoplankton-zooplankton (NPZ) model. Zooplankton feeding is parameterized as a community-averaged value based on predator-prey size ratios and breadth of prey sizes. I compared model output to observational data collected in the estuary during two months of high C. quinquecirrha abundance (July and August 2012). I predicted that observational data from the northern region would be more similar to the jellyfish-dominated model outputs, because C. quinquecirrha abundance is higher in the north. Contrary to expectations, increased C. quinquecirrha abundance in the northern regions of the estuary did not lead to better agreement between observational data from northern sites and C. quinquecirrha feeding based model simulations. All northern sites had observational data more similar to the copepod-dominated model. In fact, the site that was most similar to the jellyfish-dominated model was in the southern region, where C. quinquecirrha are excluded. I suspect that these results indicate complex interactions between C. quinquecirrha and ctenophore Mnemiopsis leidyi. The abundance of M. leidyi, a voracious copepod predator, is greatly reduced in the northern region despite having wide environmental tolerances. Predation by C. quinquecirrha may limit the distribution of M. leidyi and indirectly cause copepod-dominance in the northern region of the estuary. The results of this study suggest that the impact of jellyfish on marine plankton community functioning is site- and taxa-specific. Feeding preferences are shown to be important top-down control on marine phytoplankton communities.