Due to their role as primary producers, phytoplankton are essential to the productivity of estuarine ecosystems. However, it is important to understand how these nearly passive organisms are able to persist within estuaries, when river inflow results in a net outflow to the ocean. Estuaries are also representing challenging habitats due to a strong salinity gradient. So far, little is known about how phytoplankton are able to be retained within estuaries. We present a new individual-based Lagrangian model of the Elbe estuary which examines possible retention mechanisms for phytoplankton. Specifically, we investigated how reproduction, sinking and rising, as well as diel vertical migration may allow for populations to persist within the estuary. We find that vertical migration especially rising favors the retention, fast sinking does not. We further provide first estimates on outwashing losses. Our simulations illustrate that riverbanks and tidal flats are essential for the long-term survival of phytoplankton populations, providing refuges from strong downstream currents. These results contribute to the understanding needed to advance ecosystem-based management of estuaries.
