Aquatic invasive species have drastically changed how the San Francisco Estuary functions. During the past 2 decades, the effects of invasive species in the estuary may have increased in response to frequent and severe drought conditions. The invasive overbite clam (Potamocorbula amurensis), and the Asian Clam (Corbicula fluminea) have well documented consequences on the estuarine food web, but their responses to drought are not well understood. Another invasive species, the jellyfish Maeotias marginata, can further affect the food web, but these effects have not been studied. We investigated the population responses of these invasive species to dry years and their potential effects on the pelagic food web using data from the Interagency Ecological Program’s monitoring surveys. We found M. marginata rapidly moves upstream with changing salinities during dry years, though it sees its highest abundance during high-outflow years in Suisun Bay and Suisun Marsh. Grazing rates of M. marginata in the estuary have not been quantified but are potentially high during localized blooms. The two invasive clams overlap in distribution, but have opposite population responses to drought conditions, with increases in P. amurensis densities and decreases in C. fluminea densities in dry years. With increasing P. amurensis densities, the clams’ combined annual filtration rates increase during drier years in the confluence and Suisun Marsh. Like M. marginata, P. amurensis also shifts upstream during droughts, but because adults cannot move immediately with a change in salinity, the population center of distribution shifts upstream the year after a dry year as a result of juvenile recruitment. If multiple dry years occur in a row, and both P. amurensis and M. marginata move upstream together, their effects on the food web could be compounded, and phytoplankton and zooplankton biomass could steeply decline in the confluence, affecting higher trophic levels in the estuary.