Changes in the spatial distribution of the dinoflagellate Ceratium hirundinella were observed in astratified, medium-sized (16 km2) Argentinean reservoir over several days. A fluorescence profilingtechnique was used to identify persistent patchiness in the distribution of the dinoflagellate.A three-dimensional numerical model was used to reconcile a range of different unsteady processesand prove that the initial source of heterogeneity in the system was the vertical migration ofCeratium. Once migration established vertical heterogeneity, the dominant influence on the patchdynamics alternated between control by migration and control by mixing and transport. This ledto the development of persistent horizontal patchiness. The analysis revealed that the region of thelake inhabited by Ceratium was highly predictable and from this result it was determined thatphysical processes (with some influence from migration) control the habitat of this dinoflagellaterather than biological/chemical gradients. When the spatial habitat of a particular phytoplanktonspecies can be isolated in this manner, the resources available to the species can be more accuratelydetermined by further study. The results are particularly applicable to the study of motile/buoyantplankton in aquatic systems that are periodically subject to moderate or strong wind forcing events.