As part of a multidisciplinary program to study the physical-biological interactions regulating carbon flows in the lower St. Lawrence Estuary (LSLE), three cruises were conducted in June–July 1990 during a neap-spring tidal cycle when biological production was expected to be maximal. Nutrient (nitrates and silicates), phytoplankton biomass (chlorophyll), oxygen, temperature, salinity, and current fields were used to elucidate the effect of a freshwater pulse produced by the discharge of the St. Lawrence and Saguenay rivers on the current fields and the biological variability and productivity of the LSLE. A simple Rossby adjustment model is presented to explain the temporal (3–5 days) and spatial (40–50 km) scales of motion in our study region (impact of the freshwater pulse on the circulation). Prior to the passage of the pulse during the neap tide, the circulation was dominated by a downstream outflow and phytoplankton blooms were limited to areas of weak baroclinic currents downstream and along the south shore. The arrival of the pulse during the tidal transition led to the intensification of a transverse current that most likely reduced flushing and allowed phytoplankton biomass to develop further upstream and toward the north shore. During the spring tide, lower salinity waters and the bloom spread along the north shore as the transverse current weakened. Based on these observations, a new conceptual model of mesoscale physical-biological interactions in the LSLE is presented that emphasizes the importance of transverse motions in regulating mesoscale patterns in phytoplankton blooms.