The methods and ideas presented in this working paper are derived primarily from Garrison Bay which is a north temperate homologue to the Bay of Nicoya. Both bays are shallow, subjected to seasonal input of fresh water and extremely muddy. Whereas many of the shallow parts of the Bay of Nicoea are bordered by mangrove or mangal, large parts of Garrison Bay's more shallow areas are covered by eel grass. Since it is well-known that many of the energy flow pathways in tropical and temperate water estuaries are highly dependent upon the structure and function of mangals and eel grass environments, respectively, we are able to take advantage of the Garrision Bay homologue.