abstract Zooplankton in the Hudson River estuary include both freshwater and estuarine species and range in body lengths from microns to millimeters. Measurements of abundance and biomass as well as community rate processes indicate that zooplankton do not generally exert significant grazing pressure on phytoplankton. In addition, recycling of nutrients by zooplankton is not significant to primary producers because concentrations of dissolved nutrients are quite high in the Hudson and controlled by other processes. Zooplankton do provide an important linkage in the food web as they are key prey items for many young-of-year fish as well as fish that are primarily planktivorous throughout life. Long-term observations indicate many zooplankton populations undergo regular seasonal cycles in abundance, typically with increases during warm, low-flow periods of the year. The invasion of the zebra mussel into the Hudson had strong impacts on zooplankton in the freshwater section of the estuary. Microzooplankton such as rotifers declined dramatically. Cladocerans also declined in annual average abundance between pre- and post-zebra mussel periods when the effects of wet and dry years are taken into account. Zebra mussels, however, had little effect on larger zooplankton. Regulation of zooplankton appears to be a function of physical forces that affect population residence times as well as food and predators. Evidence for food limitation is mixed. Some species benefit from food supplements in experimental trials, but the reduction of phytoplankton biomass in association with the zebra mussel invasion had no effect on cladoceran egg production. There are a variety of potential predators, and calculations indicate fish exert high rates of mortality on zooplankton.