A comprehensive coastal ecosystem model coupled with 3D hydrodynamic model with non-hydrostatic flow was developedto understand the processes of accumulation of anoxic water masses (and hydrogen sulfide) in borrow pits andtheir upwelling to shallow region. This model was applied to the borrow pit in Mikawa Bay and compared to the observeddata. To examine the effectiveness of the model, the numerical results were compared with those of a hydrostaticpressure model. The comparison proved the non-hydrostatic model to be much more adequate atsimulating the stratification structure and the vertical mixing in the pit. Moreover, it turned out that the non-hydrostaticmodel also reproduces reasonably the upwelling process under strong wind conditions.
