Climate change-induced freshening of the ocean can enhance vertical stratification and alter circulation patterns in ways that influence phytoplankton dynamics. We examined the timing of spring phytoplankton blooms and the magnitude of net primary productivity in the Nova Scotian Shelf (NSS) - Gulf of Maine (GoM) region with respect to seasonal and interannual changes in surface water freshening from 1998 to 2006. The general pattern of temporal westward progression of the phytoplankton bloom corresponds with the gradient of increasing sea surface salinity from the NSS in the east to the western GoM. Increased freshening enhances the spatial gradients in bloom timing by stimulating earlier blooms upstream (NSS), but it has less impact downstream (the western GoM). Strong spatial gradients (increasing westward) of mean chlorophyll concentration and net primary productivity during post-bloom months (May–June) indicate that lower sea surface salinity upstream can likely impede nutrient fluxes from deep water and therefore affect overall productivity.