| The effects of hydrodynamics on phytoplankton dynamics in shallow estuaries has been studied with three numerical models. We used a 1D phytoplankton model to study the effects of density stratification, tide-induced vertical turbulent mixing, and sinking on phytoplankton bloom initiation under light limitation and benthic grazing. Strain-induced periodic stratification does not appear to increase the likelihood of a bloom beyond that of an unstratified water column, whereas persistent stratification does. The details of the stratification (e.g. surface layer depth, pycnocline thickness, vertical density difference, tidal current speed) are also important in promoting bloom onset. Surface and bottom layers in a stratified water column are not truly decoupled; turbulent and advective leakage can cause the loss of a significant percentage of the biomass produced in the surface layer.; A Pseudo-2D model allowed us to hypothesize as to the relative importance of various processes in a coupled channel/shoal system. Processes identified as "First Order" (capable of controlling the occurrence of a systemwide bloom) are lateral exchange, benthic grazing in the shoal, and light attenuation in the shoal. Processes identified as "Second Order" (capable of controlling only systemwide bloom magnitude or the occurrence of a local bloom) are channel stratification, benthic grazing in the channel, and light attenuation in the channel.; TRIM-BIO, a depth-averaged hydrodynamic model (TRIM2D) with incorporated phytoplankton dynamics, allowed us to explore the effects of realistic horizontal transport and bathymetry. Under grazing-limited conditions, deeper regions may be the most productive; whereas, under light-limited conditions, shallower regions may be the most productive. Very shallow regions experience great M{dollar}sb2{dollar} and spring/neap variability in effective growth rates, due to the temporal shallowing/deepening of the water column and benthic grazing. The following "global" mechanisms may control the occurrence and location of a bloom: (1) import to a region; (2) export from a region; (3) "buffer zones" which receive phytoplankton from the shallowest areas on ebb, allowing the phytoplankton to avoid extremely low or negative effective growth rates nearshore under high grazing; and (4) "lateral sloshing" of phytoplankton during ebb from the shoals into the channel, where effective growth rates are commonly negative. |
