On the Florida Bay Modeling Workshop
April 17-18, 1996

Submitted to the
Program Management Committee
Florida Bay Research Program


Neal E. Armstrong, Chair
Department of Civil Engineering
The University of Texas at Austin
Austin, TX

Dominic Did Too
HydroQual, Inc.
Mahwah, NJ

Donald Hansen
University of Miami
Miami FL

Harry Jenter
U.S. Geological Survey
Reston, VA

Ian P. King
University of California - Davis
Davis, CA

Steven C. McCutcheon
U.S. Environmental Protection Agency
Athens, GA

Donald C. Raney
University of Alabama
Tuscaloosa, AL

Richard Signell
U.S. Geological Survey
Woods Hole, MA

Florida Bay Model Review Panel

Draft #2

May 28, 1996


The Florida Bay Research Program consists of studies supported by participating federal (National Park Service, National Oceanic and Atmospheric Administration, U.S. Fish and Wildlife Service, National Biological Service, U.S. Geological Survey, U.S. Environmental Protection Agency, and the U.S. Army Corps of Engineers) and state (Department of Environmental Protection and South Florida Water Management District) agencies (Florida Bay Research Program, 1995). This program resulted from a science plan prepared in 1994 (Armentano et al. 1994) which itself was based in part on recommendations of a panel of independent scientists from outside the Florida region (Boesch, et al. 1993). This panel was asked to review evidence concerning the deterioration in the Florida Bay ecosystem and the relationship between this deterioration and freshwater inputs to the Bay. While the time available to conduct this review was very brief, the panel did come to a series of conclusions and recommendations based on its assessment of the causes of deterioration of the Florida Bay ecosystem and the requirements for its restoration. One of those recommendations was to expand the knowledge of water flow, both within the watershed, within the Bay, and between the watershed and Bay and to "develop and verify a two-dimensional hydrodynamic/water quality model of the Bay into which boundary currents, tides, surface and groundwater flows, precipitation, evaporation, and winds are incorporated to create a tool capable of predicting circulation, residence time, salinity and water quality under different flow and climatic conditions."

The Florida Bay Science Plan (Armentano et al. 1994) embodied this recommendation for a circulation model by including as one of its tasks the development of "a circulation dynamics model for Florida Bay". The model was to "incorporate existing model structure from other water bodies as much as possible" as well as "be capable of simulating circulation and transport across the Bay as a whole, both within the major sub-environments and within local basins". It was expected that ecological modeling efforts would proceed in parallel and cooperatively with the circulation model. Further, it was believed that a two-dimensional circulation model would suffice unless it was shown later that a three-dimensional model would be needed. Finally, integration of the circulation model of Florida Bay with larger-scale physical oceanographic, hydrological, and meteorological models that would provide boundary conditions and forcing functions was desired as was inclusion of erosion and sea level rise as two continuing processes.

During the October 17-18, 1995, Florida Bay Science Conference, several mathematical models of circulation in Florida Bay were presented and discussed. Finite-segment, two-dimensional, and three-dimensional models had been developed and/or applied to the Bay as part of a strategy to examine several modeling approaches. Based on the work presented at that conference, the Panel believed that a three-dimensional modeling approach should be selected and further developed. One of the models presented at that conference was a two dimensional model developed by the U.S. Army Corps of Engineers and being applied to Florida Bay by Lisa Roig and others at the Waterways Experiment Station (WES).

It is the Corps model which has become the primary circulation model effort for Florida Bay, and it, along with associated models, was the subject of review at this Florida Bay Modeling Workshop held in Marathon, FL on April 17-18, 1995. Along with the circulation model, there were discussed: ecological processes and models for sediment transport, nutrient cycling, seagrasses, ecological modeling, water quality modeling; physical boundary conditions relating to Bay-ocean connections, Bay-atmosphere interactions, and Bay-land connections (freshwater and groundwater inputs). The Program Management Committee goals for the workshop were "to bring investigators together to discuss and critically evaluate each others work, to obtain individual and collective evaluation by impartial observers, to begin coordination, and then to modify our research programs and models as appropriate for achieving our collective goals." The objective was to evaluate current activities to ensure the best possible outcome in circulation model development for Florida Bay with emphasis on compatibility, linkages, and suitability for related activities including additional modeling, research, and restoration. As the "impartial observers", this Panel was given the charge to evaluate circulation models for their appropriateness for Florida Bay; to look for missing opportunities and holes in activities with the program; to identify future needs; and to focus on timeliness, technical transferability, date requirements, and relevance to current issues.

Following the presentations, the Panel came to several conclusions regarding the technical aspects of the modeling program which are given below.


The Panel concludes that the two-dimensional RMA2 finite element model may be an appropriate choice by WES to simulate Florida Bay circulation given the Jacksonville District's narrow initial emphasis of using the model to determine the impact on Florida Bay salinity of modifications to the C-111 canal. However, the Panel does have concerns regarding linkage of RMA2 with a sediment transport model and ultimately with a water quality model.

Florida Bay is a complex combination of shallow bays, keys, bars, cuts, and narrow, shallow passages that covers a large geographical area and is forced hydrodynamically by tides, winds, density currents, and others. As a finite element, single layer (and hence vertically averaged) hydrodynamic model utilizing an unstructured grid (with "wetting" and "drying") to represent the natural system and incorporating salinity, RMA2 appears to be an appropriate choice to model circulation and salinity in Florida Bay as affected by modifications to the C-111 canal. It has been used, according to the Corps, in a number of applications including shallow water systems similar to Florida Bay. Revisions to RMA2 either have been made or are being made to increase the model's appropriateness for the Bay through the addition of salinity for density currents and evaporation as it will affect water balance and hence salinity. While the former enhancement is complete, the latter is not, and there are reportedly no examples available at this time of salinity prediction performance. The ability of the modified RMA2 to model salinity is critical to its successful application to Florida Bay, and the Management Committee should be kept appraised of progress in achieving this capability and the hydrodynamic review group (see below) should evaluate this capability at some appropriate point in the near future.

While RMA2 is a two-dimensional, vertically averaged model and hence is not able to represent vertical gradients, the Panel finds its use in preference to a three-dimensional model is probably appropriate, for present evidence suggests that nearly all of Florida Bay is well mixed vertically due to wind action. A possible exception is in the more western section that opens out into the Gulf of Mexico, particularly the area that would be encompassed by a new western boundary for the model (see below). Data presented at the workshop indicated slight vertical stratification off the western edge of Florida south of the Shark River Slough entry point following a high runoff event, but this slight stratification would not preclude the use RMA2 in this area. If stratification becomes an issue, the Management Committee and especially the Jacksonville District must revisit the selection of RMA2. Upgrading to the three-dimensional model RMA10 might be a logical step for WES, but, based on comments at the Workshop, the Corps does not appear ready to use RMA10 in Florida Bay. Again, the hydrodynamic review group could provide a review of these issues at the appropriate time and make a recommendation to the Management Committee.

Of great concern to the Panel is the linkage of RMA2 to other models to address sediment transport and water quality. The hydrodynamicówater quality model linkage is discussed below, but there is a very definite need to examine in the immediate future how RMA2 can be interfaced with the U.S. Geological Survey's work on sediment transport and whether the suggested linkage of RMA2 with the Corps' SED2D model will provide the sediment transport capability needed. The Panel recommends that the Management Committee address this issue very soon in conjunction with linkage with a water quality model. If it becomes apparent that adequate linkages cannot be made between RMA2 and sediment transport and water quality models, then the RMA2 model should be used to provide preliminary circulation information, and the Management Committee should evaluate and select a state-of-the-art two or three dimensional water quality model to ensure such a model is available for support for the broad range of decisions that must be made for Florida Bay management.


The Panel concludes that, while an unstructured finite element network may be an appropriate choice to represent the narrow cuts and highly variable resistance to flow within the Bay, the number of elements currently in the RMA2 model probably can be reduced lowering the model's run time while retaining the desired resolution. Also, the bathymetry used with this grid must be the most recent available. The Panel further concludes that the network needs to be extended westward and northward along the west coast of Florida to accommodate expanded boundary conditions.

The number of finite elements initially selected (>10,000) for use in RMA2 may be prolonging excessively long computer run times and precluding use of the model in production runs by the SFWMD and others. Fewer elements are probably adequate, and it is recommended that a coarser network be developed that lump some of the detail but still provide the same overall response. It was noted during the workshop that this finite element network for RMA2 currently uses circa 1890 bathymetry but that this bathymetry was being updated. The Panel strongly recommends that this update take place before coarsening of the grid is attempted and further modeling is performed.

Experiences in Chesapeake Bay and other estuaries indicates that the current western boundary for the RMA2 model is inappropriate and should be moved westward onto the shelf and northward to include the effects of Shark River Slough on salinity and circulation along the west coast of Florida as well as Florida Bay. This new boundary should coincide with current measurement programs so that these vital forcing processes can be taken into account and the effects validated with the present boundary measurements. Extension of the finite element network to add the westward and northward extension will add more elements to this already large network and slow computer execution time more; thus, the need for a coarser network is even greater.


The Panel concludes that the boundary conditions are inadequately addressed at this time, that freshwater inflow from surface water and groundwater emanating from the Everglades into the Bay must be characterized, that the western boundary be extended over the shelf and northward of the Shark River inflow point, and that boundary conditions offshore of the Keys must be determined.

The boundary conditions for this system are a critical component of the model application. Three major issues must be addressed before there is a successful simulation. First, the representation of the northern land boundary must be adequately resolved. The quantity and distribution of freshwater inflow from the Everglades must be correctly represented or the salinity gradients in these areas cannot be predicted properly. It is not clear that the detailed study of the Buttonwood Ridge by the U.S. Geological Survey is going to provide a clear answer to how much flow is entering the system in that area. The proposed methodology presented to the Panel did not clearly show that water flow and materials fluxes could be accounted for. Nor is it clear that using FEMWATER will provide that information over and above what the SFWMD will be able to achieve. The proposed revision of FEMWATER to simulate surface water/groundwater interactions in canals, like the fresh water at the land-sea boundary, will require specification or extensive measurement to calibrate. These measurements seem to be available already for the C- 111 Canal or easily obtained making expensive and time consuming expansion of FEMWATER unnecessary. The Panel recommends that a rigorous and detailed water balance of Florida Bay be attempted to quantify or validate the fresh water flux and other boundary fluxes.

Second, as noted above and in recognition of the complicated salinity and velocity structure at the western edge of Florida Bay, the original boundary of RMA2 needs to be moved offshore onto the shelf and to the north allowing representation of the Shark River Slough plume. Extension of the network westward will not make the modeling problem any simpler. The only apparent solution for long term simulation is to drive the model with boundary conditions from a larger scale model. The Corps' ADCIRC model initially appears adequate although it was reported to lack the wind driven components that are necessary to properly predict circulation in this area. The NOAA effort in this same area appears to be well developed at this point and should be considered as a source for ocean boundary conditions. It is recommended that quality and usability of results from each of these models be critically evaluated as soon as possible with a view to selecting which large scale model to apply.

Third, the interaction of the western boundary and the southeastern boundary must be consistently described or the net flow in either the southeast direction through the Keys or vice versa will not be correctly generated. Construction of the model using elevation boundary conditions is relatively difficult because of the sensitivity of currents to very small head losses, particularly in deeper waters. This is aggravated in this case because most of the head loss appears to occur in the constrictions that control flows through the Keys. If the large scale model does not simulate the head difference accurately then the results will be of limited usefulness.


The Panel concludes that water quality modeling, including seagrasses and benthic exchange, is an essential tool in the development of the restoration plan for Florida Bay and that such modeling be initiated as soon as practicable.

A specific recommendation of the Boesch et al. (1993) panel was the development and application of a two-dimensional hydrodynamic/water quality model for Florida Bay which could be used to simulate circulation, salinity, and water quality under different flow and climatic conditions. While the Florida Bay Science Plan (Armentano, et al. 1994)is essentially silent concerning water quality modeling and the studies in progress presented at the Florida Bay Science Conference in October 1995 did not include any work on water quality modeling, the need for water quality models was noted again in the Boesch et al. (1995) panel report.

The Panel strongly reaffirms the recommendations of the Boesch et al. (1993,1995) panel reports, it concludes that water quality modeling (including seagrasses and benthic exchange) is needed, and it recommends that a water quality model be developed for Florida Bay as soon as practicable. It is unfortunate that development of a water quality model is not now underway and that the need to link the Corps' circulation model with a water quality model was not anticipated earlier. The difficulties of linking the Corps' finite element model with a finite difference water quality model are substantial as evidenced by the discussions at the workshop, and the Panel encourages the Management Committee to address the question of whether it will be possible for the Corps to successfully link their finite element model with a finite difference water quality model for use in Florida Bay or whether a separate water quality model should be developed.

The question of what water quality variables are to be modeled, what time and space scales are to be used, and so forth are a matter of balancing the requirements of the problems to be solved, the time and resources available, and the applicable state of the art.. A method to arrive at a consensus design is to hold a workshop at which those who know Florida Bay and who know modeling are invited with the purpose of reaching a consensus on the model design. This should be done in the near future.


The Panel concludes the following are needed: a central repository and vigorous coordination of field measurement programs; additional hydrodynamic field measurements on the western boundary of the Bay; and additional water quality data to support a water quality modeling effort.

The lack of an adequate central repository (even of a simple map) of field measurement programs has led to duplication of effort and locations of instruments. Again, the Boesch et al. (1993, 1995) panels pointed out the need for coordination and exchange of such information to avoid these inefficiencies. The Program Management Committee may wish to consider a coordination subcommittee for data collection programs and to empower the subcommittee to oppose uncoordinated data collection or data collection of limited quality.

Besides duplicative field measurements, there may be gaps in critical circulation and water quality data. While the April workshop was not designed to review existing data collection efforts, there may be gaps in defining boundary conditions and calibration data. The western boundary was particularly troublesome, for uncertainties with currents in the western waters makes it essential that the long term measurements be judiciously located to maximize data flow to the overall study of Florida Bay. Though the moorings may be difficult to maintain, the effects of Shark River Slough seems dominant well into Florida Bay. To define the salinity and velocity structure on the recommended western boundary, it is recommended that two or three moorings be moved to help determine conditions along the northern boundary. Further, the Panel recommends that the Corps' groundwater modeling effort be shifted to western boundary measurements done in concert with NOAA and University of Miami investigators who have already foreseen the data needs for the Bay.

The data collection efforts in the inlets of the Keys should provide valuable calibration data if WES properly defines the boundaries. However, the WES data collection efforts are not well defined for all critical flow conditions through the inlets.

The present modeling effort by the Corps has been developed without direct consideration of any future water quality modeling. As a consequence the Corps' field measuring program has not been designed to gather data other than those required for their immediate needs. Consequently, these synoptic sampling efforts are probably too brief and are inconsistent with current and future synoptic sampling by NOAA and the University of Miami. Water quality and hydrodynamic data collection should be coordinated to be sure that measurements defining the water balance and constituent balances are simultaneously defined for the Bay. Synoptic sampling and long term monitoring must be coordinated to cover all boundary conditions and internal calibration points simultaneously and with continuity in time to connect synoptic snapshots of the Bay. The coordination is best accomplished using preliminary simulations of the Bay to define effective sampling locations and frequencies (largest gradients in space and time). Thus, the Panel recommends that WES develop definitive data needs for model calibration, and NOAA tailor existing and expanded circulation and salinity monitoring efforts using expert crews already available to provide these data. Otherwise, the current NOAA data collection program is disconnected from programs to analyze and understand the Bay making those data collection programs less effective. The studies of Florida Bay can only be effective if a team approach is employed. At the present there is no team approach in operation.

The limited sediment process research by the USGS should also be coordinated. These limited studies are duplicative, as both WES and the USGS are defining roughness coefficients in their separate studies. Interactions of these two groups that would lead to a combined effort to address the roughness coefficient estimation would be desirable. The USGS wave model studies and field data collection activities are not linked to hydrodynamic modeling that normally includes wave modeling with circulation modeling. Whether the sediment data collection efforts and wave modeling are adequate for management decisions evolving around sediment is unknown at this point, but no other agency has had the foresight to address what may be an important issue. Nevertheless, the USGS should carefully consider advances in the Great Lakes and other estuarine systems rather than assuming a priori that Florida Bay sediments are unique. All sediments have unique characteristics, but one can still simulate the general behavior of resuspension, deposition, flocculation, and desegregation from site-specific characteristics.


The Panel concludes that field data collection coordination, hydrodynamic model evaluation, and water quality model selection groups should be formed to support the data collection and modeling efforts in and around Florida Bay.

Since unexpected problems are likely to occur with the circulation modeling, a model evaluation group could prove very valuable to the modeling process by helping to insure that the best approaches are taken. This group should consist of experts with local knowledge of Florida Bay circulation issues as well as modelers, and, like the membership of this Panel, these individuals should come from outside the agencies performing the particular work (i.e., hydrodynamic modeling). Such groups could also be formed for water quality modeling efforts as well as data collection coordination as noted above.


Armentano, T.V., M. Robblee, P. Ortner, N. Thompson, D. Rudnick, and J. Hunt. 1994. Science Plan for Florida Bay. A Science Planning Document Provided to the Interagency Working Group on Florida Bay.

Boesch, D.F., N.E. Armstrong, C.F. D'Elia, N.G. Maynard, H.W. Paerl, and S. Williams. 1993. Deterioration of the Florida Bay Ecosystem: An Evaluation of the Scientific Evidence. Report to the Interagency Working Group on Florida Bay. National Fish and Wildlife Foundation, Washington, D.C.

Boesch, D.F., N.E. Armstrong, J.C. Cloern, L.A. Deegan, R.D. Perkins, and S.L. Williams. 1995. Report of the Florida Bay Science Review Panel on Florida Bay Science Conference: A Report by Principal Investigators, October 17 & 18, 1995. Report to the Program Management Committee, Florida Bay Research Program.