Shallow water habitat is recognised as central to the ecological health of estuarine systems. However, data on the structure of flows, mixing, light variability and benthic grazing in shallow waters are extremely limited. A series of field and numerical studies were undertaken to investigate the role of both wind-waves and currents in determining vertical mixing in shallow water and examine the resulting implications for phytoplankton dynamics.; Measurements of the vertical distribution of the dissipation of turbulent kinetic energy were made in the shallow embayment of Grizzly Bay, San Francisco Bay. Under conditions of whitecapping waves, dissipation of turbulent kinetic energy in the upper portion of the water column was greatly enhanced, relative to the predictions of wind stress wall-layer theory. The ability of one dimensional hydrodynamic models to reproduce the dissipation and velocity profiles was tested. The k-omega turbulence model was found to best replicate the field measurements. A one dimensional phytoplankton model was used to investigate the influence of whitecapping waves on phytoplankton dynamics in a shallow water column. In a very turbid water column the critical benthic grazing rate for bloom initiation is low and does not vary with the additional source of turbulent kinetic energy due to wave breaking. For a less turbid water column the critical benthic grazing rate for bloom initiation is significantly lower with wave breaking compared with the bed stress source of mixing alone. Finally, field experiments were undertaken to measure the influence of hydrodynamics on the removal of phytoplankton by benthic grazers in Suisun Slough, North San Francisco Bay. The benthic grazing rate was determined to be positively correlated to the bed shear stress.
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