Invasive dreissenid mussels have altered plankton abundance and nutrient cycling in the Great Lakes. In this study, a 1-D hydrodynamic-biogeochemical coupled model is developed to investigate their effects at a mid-depth offshore site in Lake Michigan. Model simulation shows that water surface temperature and vertical thermal structure can be well reproduced. Driven by the simulated vertical mixing, the biological model solves the transport and transformation of nutrients, plankton and detritus in the water column. Mussel grazing and excretion are added at the bottom boundary. The biological model predicts a notable decline of phytoplankton biomass and considerable increase of dissolved phosphorus (DP) in the entire water column at the end of spring. However, the reduction of phytoplankton and the increase of DP are limited to the bottom 20 m in summer as a result of the strong stratification. Model results also show that mussels can maximize particle delivery to the benthos, as the modeled benthic diffusive flux of particulate phosphorus exceeds the passive settling rate by 4.2× on average. Model simulation over a 10-month period indicates that profundal mussels have the potential to significantly change the distribution of energy and nutrients in the water column, even in a deep and stratified environment.