Download 1 NUMERICAL MODELING FOR SAN JUAN ESTUARY

NUMERICAL MODELING FOR SAN JUAN ESTUARY
CIRCULATION AND WATER QUALITY IMPROVEMENTS
Mitchell A. Granat
U.S. Army Corps of Engineers, Jacksonville District, 400 West Bay Street, Jacksonville, Florida, USA
32232
SUMMARY
A three-dimensional hydrodynamic and water quality numerical modeling system has been
developed to evaluate various scenarios for improving the circulation and water quality characteristics of
the San Juan Bay Estuary System. This modeling effort was initiated for the San Juan Bay Estuary
Program Office, through funding provided by U.S. Environmental Protection Agency, Region II, to U.S.
Army Corps of Engineers, Jacksonville District and the Waterways Experiment Station. This paper
discusses the steps followed in the selection and development of the modeling system and the testing
program. The field data collection effort required for model validation is reviewed. The standard testing
protocol (STP) selected for the evaluation of the various alternatives is discussed. A total of six separate
testing scenarios ranging from structural modifications including canal widening and deepening, tide
gates, and pumping ocean water into an interior lagoon, to various alternative loading reduction
conditions are described. This modeling system is available for testing other plans of improvement or for
assessments of future alterations to the system. The developed modeling system is a valuable tool that
should be used in the successful coastal zone management of the San Juan Estuary System.
KEY WORDS: San Juan Estuary; Numerical Modeling; Hydrodynamic Modeling; Water Quality
Modeling, Coastal Zone Management
BACKGROUND
The San Juan Bay Estuary System (SJBES) consists of an interconnected system of shallow
bays, canals, and lagoons that are connected to the Atlantic Ocean. The system is located on the
eastnorthern coast of Puerto Rico and includes areas of six different municipalities; Catano, Guaynabo,
San Juan, Carolina, Loiza, and Toa Baja. SJBES (Figure 1) consists of seven primary estuarine water
bodies including (a) San Juan Bay and Harbor, the western most part of the system, (b) Condado Lagoon
along the north coast of the bay which also opens to the Atlantic Ocean, (c) Martin Pena Canal at the
southeastern end of the bay connecting San Juan Bay with (d1) San Jose Lagoon and (d2) Los Corozos
Lagoon in central SJBES, (e) Suarez Canal connecting San Jose Lagoon with (f) Torrecillas Lagoon
which opens to the Atlantic Ocean at Boca de Cangrejos and (g) Pinones Lagoon in the eastern most
portion of SJBES. Freshwater mainly enters the system through Puerto Nuevo River, Juan Mendez
Creek, San Anton Creek, Blasina Creek and Malaria Channel, as well as surface water runoff, rainfall,
and other indirect sources. Power plant and industrial discharge may also be introduced into SJBES.
SJBES is surrounded by a growing metropolitan area with a population around one million
people and is host to a large tourist population. The system is significantly degraded and threatened due
to an increase in anthropogenically-generated waste. The area surrounding the estuary can be
characterized by rapid social and economic development, which contributes to the large waste load the
system receives. All but Pinones have been significantly modified via dredging, sand mining,
channelization, and sedimentation. In addition, all but Pinones Lagoon have received inadequately
1
N
(b)
Bayamon
Bahia
de (a)
San Juan
Atlantic Ocean
(d2 )
Laguna Condado
Boca de
Cangrejos
(f)
Laguna
La Torrecilla
(e)
San
Fernando
(d1 )
(c)
Cano Martin Pena
Malaria
(g)
Laguna
San Jose
Canal
Suarez
Laguna
de
Pinones
Margarita
Rio Piedras
Juan Mendez
San Anton
Blasina
Figure 1. General San Juan Bay Estuary location map
treated or raw sewage. All waterbodies have experienced anoxic conditions for sustained periods of time
and some exhibit hyper-eutrophic conditions. The estuary’s health is threatened by many problems.
Among the worst are toxic and pathogenic contamination, loss of habitat, marine debris, changes in
living resources, and solid waste (Abreu 1995).
The U.S. Army Corps of Engineers, Jacksonville District (CESAJ) was requested by the San
Juan Bay Estuary Program Office (SJBEPO) Management Committee (MC) to investigate the potential
development and application of a numerical model for the San Juan Bay National Estuary Program. The
primary purpose of the modeling system is to study potential structural and non-structural alternatives
with the goal of providing improved circulation and water quality characteristics within San Juan Bay and
Estuary. The numerical modeling study will provide decision makers with modeling results that could be
used to evaluate the proposed alternatives and identify priority items for implementation.
The U.S. Army Corps of Engineers Waterways Experiment Station (WES) responded to CESAJ
and the MC’s request and proposed three different levels of numerical modeling, each with associated
increasing complexity and cost, to support the National Estuary Program goals. Table 1 provides a
typical cost summary for each level, based on a generic and limited knowledge of data availability and
study needs and interests. Due to the complexity of the SJBES, a three-dimensional modeling approach
was anticipated for each level.
LEVELS OF APPROACH
A Level I (Low) study involves three-dimensional hydrodynamic modeling of water levels,
velocity, discharge, salinity and density, and a companion, indirectly coupled, three-dimensional water
quality model (hydrodynamic model output data will be used as the driving or boundary forcing conditions
for input into the water quality model) to examine DO, BOD, coliform bacteria, and a conservative tracer
to analyze mixing and residence times. A Level I study is envisioned as taking from 9 to 12 months to
complete and between $275,000 - $375,000.
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TABLE 1. Typical Costs For Generic 3-D Modeling Efforts
LEVEL/DETAIL
MODELING
HYDRO FIELD
DATA
WATER QUALITY
DATA
TOTAL
I (LOW)
3-D Hydro,
Basic WQ
$150 K - $ 200 K
$ 75 K
$ 50 K - $ 100 K
$275 K - $ 375 K
$ 300 K - $ 500 K
$ 100 K - $ 200 K
$ 500 K $ 1 MILLION
$ 900 K $1.7 MILLION
AS HIGH AS
$ 1 MILLION
OR MORE
$ 200 K OR
MORE
$ 500 K SEVERAL
$ MILLIONS
$1.7 MILLION SEVERAL
$ MILLIONS
9 TO 19 MONTHS
II (MEDIUM)
3-D Hydro,
Basic WQ,
Eutrophication
18 TO 24
MONTHS
III (HIGH)
3-D Hydro,
Basic WQ,
Contaminants
ONE TO
SEVERAL YEARS
Field data costs can vary considerably based on available data and modeling needs and requirements
A Level II (Medium) study expands the Level I study to include eutrophication. This would
include the same models as Level I plus nutrients, phytoplankton, and sediment diagenesis (physical and
chemical interchange between the water column and the bed sediments). Up to 22 different constituents
could be analyzed in this approach, depending on the content of available data. This approach is
envisioned as taking from 18 to 24 months to complete and could cost from $900,000 to $1,700,000.
The wide range in cost is a result of unknown details of intended study requirements, i.e., input, data
synthesis, number and types of testing conditions and alternatives to be examined.
A Level III (High) study involves modeling contaminants (organic chemicals and heavy metals)
in addition to the basic water quality modeling. This type modeling could require from one year to several
years to complete and from $1,700,000 to several million dollars, depending on study issues and budget.
The Level III efforts are the most complex and, therefore, the most risky in undertaking with potential
limited success.
Screening level models, for example 1-D or zero dimensional models could also be developed
and used for preliminary reconnaissance level assessments at a reduced cost and level of assurance, or
2-D models, generally at an intermediate cost, could be applied for systems that are either vertically or
laterally well-mixed. The specific types of questions to be answered and the processes to be modeled
are important in the selection of the type of model chosen and the level of sophistication necessary. For
example, if long-term hydrodynamic simulations were required, a finite difference model would be
considered. If detailed complex geometry and short-term simulations were required, a finite element
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model would be considered. The fundamental difference between these two types of models is the
underlying procedure used in solving the governing equations of motion, and is beyond the scope of this
paper.
SCOPES OF WORK
A preliminary scope of work was prepared and presented to the MC describing anticipated study
approaches, field data collection, modeling tasks, and schedules. This was revised according to
discussions and desires of the MC. A limited Level II study approach was chosen keeping costs at the
lower end of such an effort. Based on the desired long-term water quality simulations and the relatively
simple geometry modifications of interest, a finite difference modeling scheme was selected. A similar
set of models and approach was used in the Chesapeake Bay EPA Study.
The developed modeling system is comprised of three indirectly coupled companion numerical
modeling programs. ADCIRC (ADvanced CIRCulation), a large scale finite element numerical model of
the western Atlantic Ocean, Gulf of Mexico, and Caribbean Sea, was revised and used to develop the
open ocean water surface elevation boundary conditions (Westerink, et. al., 1992). These data were
used to drive the three-dimensional finite difference hydrodynamic model CH3D-WES (Curvilinear
Hydrodynamics in 3 Dimensions - Waterways Experiment Station) of San Juan Estuary. The obtained
hydrodynamic data were then used by the multi-dimensional water quality model CE-QUAL-ICM
(integrated compartment method). A sediment diagenesis submodel is included that simulates the decay
and mineralization of bottom organic matter and the resulting nutrient and DO fluxes between the
sediments and the water column.
As the name implies, CH3D-WES makes hydrodynamic computations on a curvilinear or
boundary-fitted grid. Figure 2 illustrates the SJBES planform grid which consists of 2,690 planform cells
with a maximum of 30 vertical layers (ocean). Each layer is 0.91 m thick except for the surface layer
which varies with the tide. Modeled physical processes include tides, winds, density effects, freshwater
inflows, turbulence, evaporation, and the effects of the earth’s rotation. Temperature and salinity are
Figure 2. CH3D-WES planform grid of San Juan Bay Estuary
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simulated and coupled to the momentum equation to provide the effects of density-induced flow.
Vertical turbulence is modeled through a κ−ε model. The boundary fitted coordinates feature provides
enhancement to fit navigation channels and irregular shorelines and permits adoption of an accurate and
economical grid schematization. However, the vertical dimension is Cartesian (z-plane approach) which
allows for modeling stratification on relatively coarse grids (Chapman, et. al., 1996). Shallow areas are
modeled with one layer which effectively treats areas in a vertically-averaged sense. A detailed
discussion of the equations solved and the solution algorithm can be found in Johnson, et. al. (1991).
The water quality model CE-QUAL-ICM was developed during the Chesapeake Bay Study
(Cerco and Cole 1993, and 1994). This model has linkages to the hydrodynamics computed by CH3DWES and uses the finite volume approach for numerical treatment. For the SJBES, temperature,
salinity, dissolved oxygen (DO), one group of phytoplankton, dissolved organic carbon, particulate
organic carbon, particulate organic nitrogen, dissolved organic nitrogen, nitrate+nitrite nitrogen,
ammonium nitrogen, particulate organic phosphorus, dissolved organic phosphorus, total inorganic
phosphorus, chemical oxygen demand, total suspended solids, fecal coliform bacteria, and a
conservative tracer are the 17 water quality state variables to be addressed. The model also includes a
benthic sediment diagenesis submodel that simulates the decay and mineralization of bottom organic
matter and the resulting nutrient and DO fluxes between the sediments and the water column. The
sediment diagenesis submodel dynamically couples sediment-water column interactions.
FIELD DATA COLLECTION
As identified in Table 1, field data collection needs and associated costs could be one of the
largest cost items in the study. During the model validation process, field data are necessary to adjust
modeling coefficients and demonstrate the models ability to reproduce field conditions. The magnitude
and cost of the data collection effort is dependent on the specific requirements of the modeling study and
the availability of previously collected synoptic data (data collected at similar times throughout the area
of interest). Synoptic time-varying information are generally necessary at the model boundaries to
provide the boundary forcing conditions used to drive the model as well as information at interior
locations to demonstrate that the model can confidently reproduce the desired response to the physical
processes of interest and the observed field conditions. To stay within the limited SJBES study budget,
the data collection effort was designed to collect only the essential minimum required data. This data
collection program comprised three inter-related but separate components -- hydrographic,
hydrodynamic, and water quality data collection.
Hydrographic Data Collection. Proper geometric schematization of the modeled area of interest
is one of the most important aspects of a hydrodynamic model. The model is, of course, an
approximation of the system and the required geometric resolution is dependent on the specific issues or
questions of interest. Since the most recent comprehensive survey of the SJBES dates to the late
1970’s and early 1980’s, prior to the surge of development within the system, a new bathymetric survey
was undertaken. For this particular study, over 175 bank to bank transect lines were surveyed
throughout the system with a transect line spacing of approximately 500 ft. This information provided an
updated bathymetry for the development of the computational grid.
Hydrodynamic Field Data Collection. The designed hydrodynamic data collection program
included both long-term, continuous data collection and a short-term, intensive data collection effort.
The long-term data were collected during 22 June - 19 August 1995 and consisted of continuous water
surface elevation recordings and concurrent near surface salinity measurements at twelve locations,
additional salinity measurements at 0.8 depth at five other locations, and fixed depth current speed,
direction and salinity at six other locations (Figure 3). Environmental Devices Corporation (ENDECO)
model 1029 (Stations S1, S3, S4, and S5) and 1152 SSM electronic water level recorders (S1, S2, S6,
5
N
Atlantic Ocean
R1
Boca de
Cangrejos
S3
Bayamon
S10
S1
Bahia
de
San Juan
S4
R2
S9
R3
S6
San
Fernando S2
Laguna
La Torrecilla
Laguna Condado
S5
Cano Martin Pena
R4
S8
Laguna
San Jose
Malaria
S12
R5
S7
S11
Canal
Suarez
Laguna
de
Pinones
R6
Margarita
Rio Piedras
Juan Mendez
San Anton
Blasina
Figure 3. Hydrodynamic field data collection locations
S7, S8, S9, S10, S11, and S12) were used to obtain water elevation data, ENDECO 1152 SSM and
Hydrolab Datasonde 3 (S1, S2, S4, S5, S7, and S10) instrumentation were used to collect salinity data,
and ENDECO model 174 SSM current meters (S1, S3, S5, S8, and S10) were used for the collection of
the velocity data. Biological fouling of the salinity and water level sensors was a typical problem with the
long-term deployments as was vandalism and/or accidental destruction.
In addition to the long-term data, a short-term intensive data collection effort was undertaken
during 17 - 19 August 1995. These data consisted of approximately bi-hourly boat transect profile
measurements of current speed and direction using a boat mounted Acoustic Doppler Current Profiler
(ADCP) and a mid-channel vertical profile of salinity using a Datasonde 3 Hydrolab along six profile lines
in the connecting canals as identified in Figure 3 (R1 - R6). A complete description of the field data
collection procedures followed and summary information can be found in Fagerburg (1997).
Water Quality Field Data Collection. This component of the field effort was designed to estimate
material loadings from selected tributary streams, to estimate sediment/water interactions, and to
characterize water column conditions for selected open-water portions of the SJBES. Data collection
efforts included tributary sampling (temperature, DO, specific conductance and pH) at a representative
location in each of eight tributaries, water column sampling (temperature, pH, specific conductivity, DO
concentration, Secchi Disk transparency, and water depth) at 25 stations located throughout the SJBES,
fecal coliform bacteria enumeration at each water column and tributary sampling location, and
sediment/water material flux measurements at eight representative core locations in SJBES. Chemical
sampling and analyses were conducted at the tributary and open water stations identified in Figure 4.
Daily flow measurements for Rio Piedras were also obtained from the U.S. Geological Survey gage at
Hato Rey.
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AO-1
N
SJB-1
Atlantic Ocean
SA-1
Bayamon
T-8
SJB-3
AO-2
LC-1
TL-1
TL-2
Laguna Condado
SJB-2
SJB-5
MP-1
SJ-1
MP-2
SJB-4
SJ-2
PN-1
Bahia de
Cano Martin Pena
T-6
Malaria
TL-4
PL-1
TL-3
T-7
San Juan
Laguna
La Torrecilla
SJ-4
SC-1
SJ-5
SJ-3
TL-5
Canal
Suarez
PL-2
Laguna
de
Pinones
T-5
Laguna San Jose
Margarita
T-4
Rio Piedras
T-3
Juan Mendez
T-2
San Anton
T-1
Blasina
Figure 4. Open-water and tributary water quality field data collection locations
As a result of low to no discharge at some of the tributary sampling locations, the initial tributary
sampling design for the eight tributary locations was abandoned after the first two sampling events (5
and 17 July 1995) and replaced with concentrated sampling in Juan Mendez and Rio Piedras in an
attempt to better document potential impacts of storm-runoff events. This revised sampling design
involved the collection and storage of multiple samples throughout the storm hydrograph, from which a
subset of samples representing both the rising and falling portions of the hydrograph were saved for
subsequent analyses.
The open-water water-column samplings were taken five times, approximately every two weeks
during the eight week sampling period (26 June - 24 August 1995). Due to logistics, different portions of
the system were sampled on consecutive days, generally over a 3-4 day period. Diel in situ
measurements of DO, temperature, pH, specific conductivity, and turbidity were also recorded at 15minute intervals at two locations in San Jose Lagoon during the period 1200 hr, 23 August 1995 to 1745
hr, 24 August 1995.
Core samples were collected and returned to a field laboratory for incubation and analysis to
estimate sediment-water interactions. Intact sediment water microcosms were collected by SCUBA
divers during the period 10-14 August 1995. Figure 5 illustrates the location of these eight sediment
water flux stations. Sediment-water material fluxes were measured using short term incubations of
intact core samples. Fluxes were estimated based on changes in DO, ammonia, nitrate-nitrite, and
phosphate concentrations of water overlying each core. Core sampling followed a standard static (batch)
protocol with 5 equally spaced in time samples taken over the six-hour incubation period. Flux rates
were determined using a regression approach in which the slope of the change in concentration versus
time estimates the flux rate. A complete description of the water quality field data collection effort
including detailed procedures and methods used and summary results can be found in Kennedy et al
(1996).
7
N
Atlantic Ocean
Boca de
Cangrejos
Bayamon
Bahia
de
San Juan
SJC-3
SJW-5/6
SJS-4
San
Fernando
Laguna
La Torrecilla
Laguna Condado
TL-7
SOC-2
Cano Martin Pena
SOS-1
Malaria
Margarita
Laguna
San Jose
Rio Piedras
Juan Mendez
10
-9/
L
P
SC-8
Canal
Suarez
Laguna
de
Pinones
San Anton
Blasina
Figure 5. Sediment-water flux sampling locations
MODEL VALIDATION & STANDARD TESTING PROTOCOL
The obtained field data are used during model validation to help adjust modeling coefficients and
to demonstrate the model’s ability to reproduce observed field conditions. The validation process for the
SJBES is presently ongoing and will be reported in a future paper. Once verified, the developed
modeling system can be used with confidence to evaluate various scenarios, identify the sensitivity of
the system to specific modifications, and help identify priority items for implementation. The
development of an optimum standard testing protocol (STP) to be followed during the testing and
assessment phase is critical to the success of the study. This STP includes the conceptual approach to
be followed and a standard set of boundary forcing conditions to be used throughout the testing phase.
An effective STP allows valid model-to-model comparisons so that the relative worth of each of
the management options can be evaluated -- differences in results between successive model runs
should only be the result of and related to the specific testing condition of interest and not an artifact of
some other variation in the testing scheme. During initial assessments, combining two or more options
or variations should be avoided to allow true process and response assessments while avoiding potential
interactions between options or scenarios. Later testing can include multiple combined scenarios to
assess potential interactions between promising alternatives.
For the SJBES, both the hydrodynamic model (HM) and the water quality model (WQM) must be
executed for each scenario, since flows from the HM are used to drive the WQM, and in most cases, the
proposed management alternative affects the flows. The developed STP, however, requires that the HM
be run for only one complete 28-lunar day (lunar month) tidal cycle selected from the 22 June - 19
August 1995 field data collection program, and then this 28-lunar day cycle is run in a repetitive fashion
throughout the WQM simulation. To properly compare different management options, the WQM is run
until it reaches an equilibrium condition that is time varying during the 28-day lunar cycle but repeats
itself from lunar month to lunar month. The respective 28-lunar day input flows, loadings, and other
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boundary forcing conditions are similarly cycled until the desired dynamic equilibrium condition is
achieved. The time to reach this dynamic equilibrium depends upon how long it takes the sediments and
water column to reach equilibrium, where periods of several years are anticipated. In this manner,
results from each of the tests can be compared and related back to observed field conditions.
SCENARIO TESTING
A total of six different alternative conditions will be examined and evaluated with the models.
The first set of conditions to be examined includes modifications associated with improvements to Martin
Pena Canal. A new base-line condition, to be considered a “future existing condition,” will be run from
which all other conditions will be compared. This condition includes recent or presently planned and
authorized Federal improvements to the SJBES including the San Juan Harbor Channel deepening
project and the Puerto Nuevo project. Two additional improvements to be evaluated and considered
include a widened to 70 feet and deepened to 3 feet Martin Pena Canal and a widened to 200 feet and
deepened to 10 feet Martin Pena Canal. One of these three conditions will be selected by the SJBEPO
MC to be incorporated as part of the new future base-line condition and will be included in the remaining
scenario testing.
Other alternatives to be evaluated include an assessment of filling previously dredged holes in
San Jose Lagoon, deepening and widening Suarez Canal in conjunction with the installation of a tide
gate, and pumping clean ocean water into San Jose and Los Corozos Lagoons. The primary purpose of
these two later scenarios is to increase the circulation and resulting flushing out of San Jose Lagoon.
The tide gate will allow flood flow into San Jose Lagoon from Boca de Cangrejos, but will be closed
during the ebb cycle to prevent flow from leaving San Jose Lagoon through Suarez Canal. Three
different load reduction scenarios will also be examined. The first load reduction will evaluate a 50
percent reduction (a decrease in concentration rather than flow) of all tributary loadings. The second
load reduction will involve removing all the non-sewered loadings emptying into the SJBES and diverting
them to the treated effluent that is discharged into the ocean. The third load reduction to be evaluated
involves removing all storm water discharges and diverting these to the treated ocean effluent. A final
condition to be run will include a single combination of selected scenarios to examine potential
interaction of promising alternatives. Each of the above six alternatives will be evaluated against the
selected new future base-line condition.
CONCLUSION
A state-of-the-art three-dimensional numerical hydrodynamic and water quality modeling system
has been developed for the San Juan Bay Estuary System. This modeling project included a limited
field data collection program for use in the model validation process. Six separate alternatives will be
examined and evaluated as part of this study. These scenarios range from structural modifications
including canal widening and deepening, tide gate, and pumping ocean water into San Jose Lagoon, to
various alternative load reduction conditions. The modeling system will be available for testing other
plans of improvement or for assessment of future alterations to the system. The models should prove to
be valuable tools in the successful coastal zone management of the San Juan Bay Estuary System.
REFERENCES
Abreu, H. (1995), San Juan Estuary Program, 6 pages.
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Cerco, C.F., and Cole, T.M. (1993), “Three-Dimensional Eutrophication Model of Chesapeake Bay,” J.
Hydraulic Engineering, Am. Soc. Civil Eng., Vol 119, No. 6, pp. 1006-1025.
Cerco, C.F., and Cole, T.M. (1994), “User Manual for the Three-Dimensional Water Quality Model, CEQUAL-ICM,” Draft Instructional Report, U.S. Army Engineer Waterways Experiment Station, Vicksburg,
MS.
Chapman, R.S., Johnson, B.H., and Vemulakonda, S.R. (1996), “User’s Guide for the Sigma-Stretched
Version of CH3D-WES,” Technical Report HL-96-21, U.S. Army Engineer Waterways Experiment
Station, Vicksburg, MS.
Fagerburg, T.L. (1997), “Field Data Collection Report, San Juan Bay Estuary, San Juan, Puerto Rico,
Draft Technical Report, HL-97- , U.S. Army Engineer Waterways Experiment Station, Vicksburg, MS.
Johnson, B.H., Kim, K.W., Heath, R.E., Hsieh, B.B., and Butler, H.L. (1991), “Development and
Verification of A Three-Dimensional Hydrodynamic, Salinity, and Temperature Model of Chesapeake
Bay, Volume 1: Main Text and Appendix D,” Technical Report HL-91-7, U.S. Army Engineer Waterways
Experiment Station, Vicksburg, MS.
Kennedy, R. H., Hains, J. J., Boyd, W. A., Lemons, J., Herrmann, F., Honnell, D., Howell, P., Way, C.,
Fernandez, F., Way, T. M., and Twilley, R. R. (1996), “San Juan Bay and Estuary Study: Water Quality
Data Collection,” Miscellaneous Paper EL-96-9, U.S. Army Engineer Waterways Experiment Station,
Vicksburg, MS.
Westerink, J.J., Luettich, R.A., Baptista, A.M., Scheffner, N.W., and Farrar, P. (1992), “Tide and Storm
Surge Predictions Using A Finite Element Model,” Journal of Hydraulic Engineering, Vol 118, pp 13731390.
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