Size-differential effects of vertical stability on the biomass and production of phytoplankton were investigated in the Lower St. Lawrence Estuary and the Gaspé Current, Canada. In summer, when nitrate concentrations were low and the ratio of critical depth to surface mixed layer depth was high, the biomass (chlorophylla) and production were dominated by phytoplankton <5μm. Phytoplankton >5μm were found only where low vertical stability allowed nitrate replenishment in the euphotic zone. In autumn, the ratio of critical depth to mixed layer depth was relatively low (≈1·0). Nitrate concentrations in the euphotic zone were high throughout the system because of the combined effects of low dynamic stability in the Lower Estuary, which resulted in nutrient enrichment of the surface layer, and horizontal advection. Phytoplankton <5μm exhibited low standing stock and little variability relative to phytoplankton >5μm, and appeared to be related to temperature alone. Phytoplankton >5μm accounted for departures from background levels of production and biomass, which were tightly coupled to hydrodynamics. A positive, size-dependent relationship between phytoplankton biomass and the Brunt-Väisälä frequency was found, suggesting that variability in the large size fractions was explained primarily by their residence time in the euphotic zone. It follows that, in summer and autumn, the production of large phytoplankton was primarily governed by variations in the vertical stability of the water column associated with horizontal advection, through their effects on nutrient replenishment and the residence time of diatoms in the euphotic zone.