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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. 2 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 3 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 4 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. 6 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 8 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. 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