Previous analyses of SeaWiFS ocean color and hydrographic data [Ji, R., Davis, C. S., Chen, C. et al. (2007) Influence of ocean freshening on shelf phytoplankton dynamics. Geophys. Res. Lett., 34, L24607. doi: 10.1029/2007GL032010] have suggested that changes in the intensity of low-salinity Scotian Shelf Water (SSW) inflow can significantly influence the winter-spring phytoplankton dynamics in the Scotian Shelf and Gulf of Maine region. In the present study, a 3-D coupled biological–physical model was applied to examine underlying mechanisms through a quantitative comparison of circulation pattern, water column stability, nutrient/phytoplankton concentrations and net primary productivity between low and high freshening scenarios. The model results revealed that observed levels of surface freshening can significantly change water column stability and therefore control the winter-spring phytoplankton bloom dynamics in different regions. Freshening caused earlier blooms both on the Scotian Shelf and in the eastern Gulf of Maine, agreeing with inferences drawn from prior empirical analyses. Earlier phytoplankton blooms in the low surface salinity case were followed by earlier depletion of nutrients at the surface along with earlier decline of blooms compared with the high surface salinity case. The model results also suggested that surface water freshening can impede vertical nutrient exchange between surface and deep waters, thus reducing the overall spring primary productivity throughout the region. The coupled model described in this study provides a unique tool to quantify the response of lower trophic level production to climate-scale environmental disturbances in a complex but ecologically important shelf ecosystem that has a history of such alternations in surface salinity.