The seasonal variations of water quality parameters as nitrite plus nitrate (NO⁻;_x), total phosphate (PO³⁻₄), chlorophyll a (chl a), and dissolved oxygen (DO) are analyzed across the Croatan-Roanoke-Albemarle-Pamlico-Core Sounds estuarine system (CAPES). Overall, several patterns are observed: The Chowan-Roanoke-Albemarle system is generally phosphorous limiting for phytoplankton growth, whereas both the Tar-Pamlico and the Neuse Rivers are generally nitrogen limiting. The largest PO³⁻₄ gradients exist in the upstream portion of the Albemarle Sound, and the largest NO⁻_x gradients exist in the lower Neuse and the Tar-Pamlico Rivers. Dissolved oxygen appears to have the strongest seasonal signal among the water quality variables, with highest DO values observed during winter (within the CAPES and in the nearshore area) or spring (in the continental shelf and deeper ocean) and lowest during summer. Chlorophyll a concentrations are highest during spring (within the CAPES) or winter (offshore). In contrast, the NO_x⁻ and PO³⁻₄ concentrations in both the Tar-Pamlico and Neuse River estuaries are usually higher during the second half of the year. The time differences of the peak nutrient and chl a concentrations suggest that highest algal growth rate (and hence nutrient uptake rate) occurs during spring, and the consumed nutrients are released to the water column through a nutrient recycling method later in the year.

A coupled three-dimensional hydrodynamic water quality model is then applied to the entire system. The general model setup and parameter derivation of the model is presented here. The basic observed water quality characteristics such as the nutrient limiting pattern and the spatial gradients across the system are reproduced in the model. The model results also suggest that nutrient fluxes, generated from the diagenesis of deposited organic matter and released from the sediment bed, could be an important mechanism for nutrient recycling in the region.