The functions of the ecosystem follow its linear structure. The coastal prairies of a watershed contribute dissolved organic matter and both large and small particles of detritus derived from the decomposition of plant and animal remains. Partially decomposed leaves from the water-tolerant trees and shrubs of the fluvial woodlands along riverbanks are flushed into the waterway with each flooding event. Streamside marshes manufacture more organic material for the detritus-based food chain.
Detritus, colonized and conditioned by bacteria and fungi, forms the nutrient and energy source for organisms living in and on the mud bottoms of Mud Lake and Clear Lake. At this point, juvenile marine, organisms find a rich feeding ground within Clear Lake. As they grow larger they gradually forsake this tertiary bay and reverse their initial migration, slowly traversing the secondary and primary bays of the estuary before returning to the sea to mature and reproduce (Pickett and Roger 1997)