In this paper we have used a three-dimensional coupled physical and biological model to examine the marine ecosystem of Jiaozhou Bay. Physical processes included (1) the M2 tide, (2) river discharges, and (3) winds. The biological model described a simple, phosphorous-based, lower trophic food web system. The model results showed that tidal mixing had a direct impact on temporal and spatial distributions of nutrients and phytoplankton as well as on shellfish aquaculture. Nutrients and phytoplankton were well mixed vertically by tidal motion. Their concentrations were highest around northwestern and northern regions of the bay near river sources and decreased with water depth from the inner bay to the outer bay. A phytoplankton bloom can occur around the northwestern coast due to the accumulation of nutrients under southeasterly wind conditions. The flux analysis suggests that in summer the nutrients in Jiaozhou Bay was directly supplied and maintained by physical processes, but the temporal variation of phytoplankton was controlled dominantly by biological processes associated with nutrient uptake, grazing by zooplankton, and consumption by shellfish. Shellfish aquaculture can modify the bay-scale balance of the ecosystem in Jiaozhou Bay. The loss of phytoplankton in shellfish aquaculture sites tended to be compensated by advection and diffusion from the surrounding waters. A large consumption of phytoplankton by shellfish can cause a net flux of phytoplankton from the Yellow Sea to Jiaozhou Bay, although there was a net nutrient flux flowing out of the bay. The physical mechanism for the water exchange between Jiaozhou Bay and the Yellow Sea was controlled mainly by a chaotic process associated with nonlinear interactions between oscillating tidal currents and double residual eddies. ¿ 1999 American Geophysical Union