Phytoplankton are key in estuaries, as they form the ecosystem's base. Despite being washed out by river flow and facing a large range of different salinities, they persist. Our Lagrangian simulation of the Elbe estuary shows that buoyancy helps them to be retained. Riverbanks and tidal flats offer refuges from strong currents. Our findings emphasize the need for careful ecosystem management in estuaries.