We present the first results of the assimilation of ocean colour datasets into coastal ocean biogeochemical models for the
tropical Fitzroy Estuary and Keppel Bay system (FEKB) contingent to the Great Barrier Reef lagoon. As part of the
Great Barrier Reef Monitoring Program, a regional algorithm for operational delivery of valid coastal ocean colour
products was recently developed for FEKB. A new generation of regional specific algorithm for the FEKB system had to
be developed for large satellite datasets of the MODIS sensors as the global algorithms failed. Concurrently, a
biogeochemical model was developed for the system, built upon a three-dimensional hydrodynamic and sediment
dynamic model, and simulating nitrogen and phosphorus dynamics including the dynamics of dissolved organic material
as well as pelagic and benthic primary production. One of the aims was to provide estimates of material fluxes from
Keppel Bay to the Great Barrier Reef Lagoon. The biogeochemical model was run first with fixed boundary conditions
based on the limited in situ measurements, then with boundary conditions derived from satellite datasets using the
region-specific algorithm. Several methodologies for linking of remote sensing observations to model variables were
evaluated over a period of one year (2004). When remote sensing information was used to inform the boundaries,
estimates of material fluxes in the model changed substantially in magnitude and direction.
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