The impact of a reflective, recurrent coastal resuspension plume on the lower trophic food web system in Lake Michigan was examined using a 3‐D coupled physical and biological model. Numerical experiments were conducted for the March 1998 and 1999 plume events. The comparison between modeling results of these 2 years shows that the spatial distributions of the biological fields (i.e., phosphorus, phytoplankton, detritus, etc.) were closely coupled to the physical environment associated with wind‐induced three‐dimensional circulation and mixing. The influence of suspended sediment plumes on the lake ecosystem was reflected in heterotrophic (secondary) production rather than in the autotrophic (primary) production. Nutrients were maintained through nutrient release from suspended sediments within the plume, while it was supplied by current advection and diffusion in the interior. The cross‐shore flux of nutrients was driven by episodic wind events with a period of about 5–7 days. The flux was offshore during northerly winds and onshore during southerly winds. Comparisons between energy fluxes among biological variables suggest that the microbial loop (detritus‐heterotrophic bacteria and microzooplankton) played an important role in the ecosystem dynamics during plume events. Bacteria were good competitors with phytoplankton for inorganic phosphorus and were also a key supporter for growth of microzooplankton inside and outside the plume. As a result, the lower food web system could be divided into two decoupled loops: (1) detritus‐bacteria‐microzooplankton‐large zooplankton and (2) nutrient‐phytoplankton‐detritus.