In Chesapeake Bay substantial quantities of organic matter are produced during the spring bloom, which contributes to severe chronic bottom oxygen depletion during the summertime. However, the details of this transport in the estuarine system under realistic forcing is still unclear. In this Research, a three-dimensional model was used to investigate the production, transport, and fate of organic matter in Chesapeake Bay. Analysis of a control volume in the deep channel revealed that the sinking flux of fast-sinking particulate organic nitrogen (PON) into the deep channel is comparable to the horizontal advective transport. The model analysis also revealed a pronounced east to west transport of PON during the springtime and a tendency to export mass from the eastern shore to the deep channel and from the deep channel to the western shore of the Chesapeake Bay, and also a convergence of mass transport on the western shore. This transport is consistent with the lateral estuarine circulation in Chesapeake Bay that arises due to the asymmetry of the flood-neap tidal cycle. In addition, the model revealed that seasonal variations in wind alter the magnitude and distribution of organic matter flux in the along channel and cross channel direction, with northerly winds during the springtime favoring more northward organic matter transport and more organic matter accumulation in the deep channel, however, the lateral net flux direction remains the same.

In Chesapeake Bay, phytoplankton biomass typically peaks in spring whereas primary production peaks in summer. For this to happen, phytoplankton growth rates must be low in spring and high in summer and very likely there must be low grazing losses in spring and high grazing losses in summer as well. In this research, a three dimensional coupled physical-biological model is used to explore how these seasonal patterns in phytoplankton and primary production arise during the year from 2000 to 2005. It is shown that with the seasonal variation of maximum carbon to chlorophyll ratio, temperature control on phytoplankton growth, and temperature-dependent zooplankton grazing effects, my model can capture the spring peak in phytoplankton biomass and the summer peak in the primary production, agreeing well with the observations. The model simulates high phytoplankton growth rates in the summer, with the maximum growth rates occurring in late summer. The model also reveals that nutrient supply shifts from river-derived nitrate in the springtime to organic matter- derived ammonium during summer. The simulation results also reveal that a substantial fraction of the ammonium that supports the high summer production is derived from allochthonous transport rather than autochthonous ammonium production. The transport process provides as large as 50% ammonium needed for uptake during summertime in the mesohaline Chesapeake Bay. My research also confirms the importance of nutrient recycling in supporting high summer production in Chesapeake Bay.

Denitrification is an essential process in the marine nitrogen cycle because it removes bioavailable nitrogen from the aquatic system. Current understanding of denitrification variability in Chesapeake Bay is severely constrained by the sparse observations that provide insufficient coverage in both space and time. In this research, denitrification variability is examined in the Chesapeake Bay using a three dimensional coupled physical-biogeochemical model based on the Regional Ocean Modelling System (ROMS). Model simulations indicate that denitrification occurs not only in the sediment but also in the water column at significant, though somewhat lower rates. Model results indicated that the water column accounts for around 7.5% of the total denitrification amount that occurred in the system during the 2001 and 2002 period of this study. This conflicts with the historical assumption that water column denitrification in Chesapeake Bay is negligible. The model also reveals the spatial patterns in denitrification with more denitrification occurring in the upper to middle bay due to higher availability of organic matter in these areas compared to the lower bay. In terms of temporal variability, denitrification peaks in the sediment in spring while in the water column it peaks in the summer. The reason for this difference in the timing is related to the availability of oxygen: In the spring oxygen levels in the water column are too high to allow denitrification so it happens only in the sediment where low oxygen levels persist all year around. In summer low oxygen and depletion of nitrate below the pycnocline completely shuts down denitrification in the sediment in the mesohaline and polyhaline region of the by. However, water column denitrification continues at the interface between oxygenated waters near the surface and oxygen-depleted waters below where coupled nitrification-denitrification happens. The model also reveals that denitrification removes significant quantities of biologically available nitrogen, meaning that without this process, more summertime primary production would occur in the form of more surface chlorophyll, increasing as much as 10ug/L in the middle bay region, which would, in turn, lead to more oxygen depletion.