The effects of colored dissolved organic matter (CDOM) from freshwater runoff and seasonal cycle of temperature on the dynamic of phytoplankton and zooplankton biomass and production in the Gulf of St. Lawrence (GSL) are studied using a 3-D coupled physical-plankton ecosystem model. Three simulations are conducted: (1) the reference simulation based on Le Fouest et al. (2005), in which light attenuation by CDOM is not considered and maximum growth rate (μmaxμmax) of phytoplankton and zooplankton are not temperature-dependent (REF simulation); (2) light attenuation by CDOM is added to REF simulation (CDOM simulation); and (3) in addition to CDOM, the μmaxμmax of phytoplankton and zooplankton are regulated by temperature (CDOM+TEMP simulation). CDOM simulation shows that CDOM substantially reduces phytoplankton biomass and production in the Lower St. Lawrence Estuary (LSLE), but slightly reduces overall primary production in the GSL. In the LSLE, the spring phytoplankton bloom is delayed from mid-March to mid-April, resulted from light attenuation by CDOM. The CDOM+TEMP simulation shows that the spring phytoplankton bloom in the LSLE is further delayed to July, which is more consistent with observations. Annual primary production is reduced by 33% in CDOM+TEMP simulation from REF and CDOM simulations. Zooplankton production is the same in all three simulations, and export of organic matter to depth is reduced in CDOM+TEMP simulation, suggesting that temperature controlled growth of phytoplankton and zooplankton enhances the coupling between primary production and zooplankton production under the seasonal temperature cycle of the GSL.