The question of ecosystem stability is central to ecology and paleoecology and is of particular importance for estuaries, which are environmentally highly variable, considered as geologically short lived, and among the most degraded modern ecosystems of our planet. Understanding their ecological dynamics over geological time scales requires paleontological data in a sequence stratigraphic framework, which allows evaluation of paleocommunity dynamics in an environmental context. A 445-m-thick estuarine succession in a satellite basin of the Vienna Basin (Austria) shows continuous sedimentation over 700 k.y. and can be divided into two transgressive systems tracts and a highstand systems tract. In contrast to expectations, no major physical disturbances of the ecosystem involving abrupt changes in diversity and biofacies composition occurred at fl surfaces and at the sequence boundary. Accommodation space remained remarkably constant over the depositional history of the basin, and all changes between depositional environments were therefore more or less gradational. Biotic change along the studied succession can be described as a gradual faunal replacement in response to habitat tracking, a process also reported for some normal marine shelf environments. Benthic assemblages in the estuarine succession were strongly dominated by a few taxa and developed along two indirect gradients, water depth and hydrodynamic energy. These gradients show subtle long-term trends, corresponding to the sequence stratigraphic architecture. Tectonics affected the sequence architecture in this particular marginal marine setting: it controlled accommodation space and sedimentary input, and provided stable boundary conditions over hundreds of thousands of years. Our study demonstrates for the fi rst time that estuaries, which are under great environmental pressure today, are resilient to natural environmental perturbations and can persist over geological time scales.