Diel vertical migration patterns of the dinoflagellates Gonyaulax tamarensis and Heterocapsa triquetra were monitored in an estuarine embayment subject to localized blooms of both species. A concurrent study of tidal flushing using a dye tracer demonstrated an efficient, densitydriven mixing process that exchanged water within the embayment at a rate of approximately 0.5 d-'. Loss rates of the whole pond populations of G. tamarensis and H. trjquetra cells were smaller, ranging between 0.02 and 0.13 d-'. The cells were thus able to maintain a non-mixed distribution even under weakly stratified conditions. This selective retention of the 2 species relative to water exchange was due to the differential advection of surface and bottom waters through the inlet channel and the general avoidance of high irradiance surface layers by the dinoflagellates. Both species migrated to irradiances equivalent to 30% of summer sunlight when nutrients were presumably non-limiting, resulting in subsurface aggregations 1 to 2 m deep. Under nutrient-limited conditions, G. tamarensjsmigration was restricted to irradiance at or below 10 to 15% summer sunlight. Planozygotes (a life-cycle stage preceding cyst formation) migrated in a manner indistinguishable from the remainder of the nutrientlimited G. tamarensis population. The results help to explain the dominance of dinoflagellates in such embayments, the localization of their blooms, and the distribution of their resting cysts in the region.