narragansett bay hydrodynamics, water quality, sediment flux and water clarity by mohamed a....

Narragansett Bay Hydrodynamics, Water Quality, Sediment Flux and

Water ClarityBy Mohamed A. Abdelrhman, PhD, PE

USEPA-AEDCHRP-EPA Workshop

July 7, 2015

Topics Covered

I. Hydrodynamics II. Water QualityIII. Benthic Sediment Quality & FluxIV. Light Attenuation& Water Clarity

I. Hydrodynamic

Environmental Fluid Dynamics Code ( EFDC)Hamrick (1992, 1996), 3-D hydrodynamic and water quality model, curvilinear-orthogonal horizontal grid

and a sigma terrain-following vertical grid8 Vertical Layers

Objective: Resolve the following for WASP and EFDC1. Hydrodynamics

• Water surface Elevation• Currents

2. Temperature3. Salinity4. Stratification 5. Local Flushing Behavior

GIS Map withRivers, Data Stations & WWTPs

Bathymetric DataNational Geophysical Data Center(GEODAS)

50% Riparianto 4 Rivers

50% Riparian to East Br, west Br, Sakonnet Riv

Freshwater Inflow WWTPsRivers

Forcing Functions for 20091. Freshwater inflow: 8 rivers + 11 WWTPs + Precipitation + 5% Ground Water2. Freshwater Temperature3. Wind Speed & Direction4. Shortwave Solar Radiation and Cloud Cover5. Relative Humidity6. Atmospheric Pressure

7. Water Temperature (NP)8. Water Salinity (GD + 2ppt)9. Water Surface elevation (NP)

Boundary Conditions

Initial Conditions1. Dye Distribution with Freshwater

Tidal Elevation Example

Calibration of Hydrodynamics

Water Temperature Examples

Salinity Examples

Current Speed Examples

Skill Parameters9) Maximum Value

10) Receiver Operator Characteristic, ROC

1) Correlation coefficient,

2) Root mean square error,

3) Reliability index,

4) Average error (bias),

5) Average absolute error,

6) Modeling efficiency,

7) Absolute relative error,

8) Index of agreement,

ParameterCorrelation Coefficient (non-dim)

Root mean square error (dim)

Reliability indexb

(non-dim)

Average error (dim)

Average absolute error (dim)

Modeling efficiency (non-dim)

Absolute relative error

(non-dim)

Index of agreement (non-dim)

Observed maximum

(dim)

Predicted maximum (dim)

Number of observationsdescription

Parameterar

[1.0]RMSE[zero]

%RI

[1.0]AE

[zero]%

AAE[zero]

%MEF[1.0]

ARE[zero]

d[1.0]

O P % n

Salinity

PDs 0.81 3.61 14 1.37 -0.40 -2 2.78 11 0.65 0.30 0.89 25.34 24.39 4 4815

PDb 0.80 7.36 25 1.41 -5.80 -20 6.32 22 0.07 0.34 0.77 29.36 25.30 14 4669

BRs 0.72 2.84 10 1.06 -0.46 -2 2.33 8 0.46 0.10 0.75 29.76 27.60 7 4054

BRb 0.65 4.37 14 1.07 -4.21 -13 4.21 13 -22.87 0.14 0.29 32.07 29.27 9 4054

CPs 0.69 2.13 7 1.04 -0.49 -2 1.71 6 0.44 0.07 0.80 30.29 29.23 3 2989

CPb 0.40 1.69 5 1.03 -1.31 -4 1.42 4 -4.95 0.05 0.42 31.93 31.72 1 3658

GBs 0.62 3.44 12 1.06 -3.17 -11 3.20 11 -6.21 0.12 0.45 29.29 28.60 2 8475

GBb 0.42 3.60 12 1.06 -3.32 -11 3.33 11 -11.54 0.12 0.35 30.66 28.60 7 8027

SRs 0.73 1.90 6 1.03 -1.64 -6 1.67 6 -1.26 0.06 0.63 29.56 28.70 3 3713

SRb 0.69 2.71 9 1.04 -2.55 -8 2.55 8 -7.37 0.09 0.45 30.37 28.69 6 3533

NPIs 0.70 1.18 4 1.02 -0.54 -2 0.97 3 0.34 0.03 0.78 30.14 29.73 1 3402

NPIb 0.51 1.53 5 1.02 -1.35 -4 1.35 4 -6.79 0.05 0.43 31.20 30.06 4 3215

MVs 0.72 0.98 3 1.02 -0.15 -1 0.77 3 0.42 0.03 0.84 30.60 31.03 -1 3593

MVb 0.47 1.18 4 1.02 -0.77 -2 0.96 3 -1.76 0.03 0.57 31.28 31.23 0 3221

QP1s 0.73 1.05 3 1.02 0.69 2 0.80 3 0.08 0.03 0.78 31.24 31.83 -2 3553

QP1b 0.55 0.54 2 1.01 0.06 0 0.44 1 -0.38 0.01 0.71 31.71 32.16 -1 3219

TWs 0.59 1.35 4 1.02 0.71 2 1.05 3 0.08 0.04 0.69 32.40 32.62 -1 8163

TWb 0.38 1.43 4 1.02 1.02 3 1.18 4 -0.89 0.04 0.53 32.90 33.46 -2 8709

PPs 0.75 1.47 5 1.02 -0.72 -2 1.23 4 0.22 0.04 0.83 30.86 31.25 -1 3487

PPb 0.53 0.73 2 1.01 -0.37 -1 0.57 2 -1.31 0.02 0.64 31.89 32.53 -2 3647

MHs 0.71 1.56 5 1.03 -0.71 -2 1.32 4 0.35 0.05 0.80 29.35 28.94 1 3214

MHb 0.47 2.20 7 1.04 -1.85 -6 1.93 6 -7.03 0.07 0.42 31.04 30.20 3 3214

AVERAGE 0.62 2.22 7.38 1.06 -1.24 -4.12 1.91 6.35 -3.15 0.08 0.63 30.60 29.87 2.46

Salinity Prediction Skill Green > 80%, Red > 90%8760 h


Root mean square error

(dim)

Reliability index

Average error (dim)

Average absolute

error (dim)


Absolute relative error Index of

agreement (non-dim)

Observed maximum

(dim)

Predicted maximum

(dim)

Number of

observationsdescription (non-dim) (non-dim)

Parameterar RMSE

%RI

AE [zero] %AAE

% MEF [1.0]ARE d

O P % n[1.0] [zero] [1.0] [zero] [zero] [1.0]

Salinity PDs 0.81 3.61 14 1.37 -0.40 -2 2.78 11 0.65 0.30 0.89 25.34 24.39 4 4815PDb 0.80 7.36 25 1.41 -5.80 -20 6.32 22 0.07 0.34 0.77 29.36 25.30 14 4669BRs 0.72 2.84 10 1.06 -0.46 -2 2.33 8 0.46 0.10 0.75 29.76 27.60 7 4054BRb 0.65 4.37 14 1.07 -4.21 -13 4.21 13 -22.87 0.14 0.29 32.07 29.27 9 4054CPs 0.69 2.13 7 1.04 -0.49 -2 1.71 6 0.44 0.07 0.80 30.29 29.23 3 2989CPb 0.40 1.69 5 1.03 -1.31 -4 1.42 4 -4.95 0.05 0.42 31.93 31.72 1 3658GBs 0.62 3.44 12 1.06 -3.17 -11 3.20 11 -6.21 0.12 0.45 29.29 28.60 2 8475GBb 0.42 3.60 12 1.06 -3.32 -11 3.33 11 -11.54 0.12 0.35 30.66 28.60 7 8027SRs 0.73 1.90 6 1.03 -1.64 -6 1.67 6 -1.26 0.06 0.63 29.56 28.70 3 3713SRb 0.69 2.71 9 1.04 -2.55 -8 2.55 8 -7.37 0.09 0.45 30.37 28.69 6 3533NPIs 0.70 1.18 4 1.02 -0.54 -2 0.97 3 0.34 0.03 0.78 30.14 29.73 1 3402NPIb 0.51 1.53 5 1.02 -1.35 -4 1.35 4 -6.79 0.05 0.43 31.20 30.06 4 3215MVs 0.72 0.98 3 1.02 -0.15 -1 0.77 3 0.42 0.03 0.84 30.60 31.03 -1 3593MVb 0.47 1.18 4 1.02 -0.77 -2 0.96 3 -1.76 0.03 0.57 31.28 31.23 0 3221QP1s 0.73 1.05 3 1.02 0.69 2 0.80 3 0.08 0.03 0.78 31.24 31.83 -2 3553QP1b 0.55 0.54 2 1.01 0.06 0 0.44 1 -0.38 0.01 0.71 31.71 32.16 -1 3219TWs 0.59 1.35 4 1.02 0.71 2 1.05 3 0.08 0.04 0.69 32.40 32.62 -1 8163TWb 0.38 1.43 4 1.02 1.02 3 1.18 4 -0.89 0.04 0.53 32.90 33.46 -2 8709PPs 0.75 1.47 5 1.02 -0.72 -2 1.23 4 0.22 0.04 0.83 30.86 31.25 -1 3487PPb 0.53 0.73 2 1.01 -0.37 -1 0.57 2 -1.31 0.02 0.64 31.89 32.53 -2 3647MHs 0.71 1.56 5 1.03 -0.71 -2 1.32 4 0.35 0.05 0.80 29.35 28.94 1 3214MHb 0.47 2.20 7 1.04 -1.85 -6 1.93 6 -7.03 0.07 0.42 31.04 30.20 3 3214

AVERAGE 0.62 2.22 7.38 1.06 -1.24 -4.12 1.91 6.35 -3.15 0.08 0.63 30.60 29.87 2.46

Salinity Prediction Skill Red > 90%


Root mean square error (dim)

Reliability indexb

(non-dim)

Average error (dim)

Average absolute error (dim)


Absolute relative error

(non-dim)

Index of agreement (non-dim)

Observed maximum

(dim)

Predicted maximum (dim)

Number of observationsdescription

Parameterar

[1.0]RMSE[zero]

%RI

[1.0]AE

[zero]%

AAE[zero]

%MEF [1.0]

ARE[zero]

d[1.0]

O P % n

Temperature

PDs 0.98 1.95 7 N/A -1.55 -5 1.69 6 0.88 0.10 0.97 28.22 25.51 10 4816

PDb 0.96 1.87 7 1.06 -1.44 -5 1.57 6 0.81 0.09 0.95 27.89 24.28 13 4669

BRs 0.91 1.98 7 1.05 -1.31 -5 1.59 6 0.70 0.08 0.92 27.79 24.87 11 4054

BRb 0.96 1.02 4 1.03 0.43 2 0.84 3 0.89 0.05 0.97 25.31 24.63 3 4054

CPs 0.87 1.58 6 1.03 -0.84 -3 1.22 4 0.65 0.06 0.90 27.17 25.26 7 2989

CPb 0.96 1.24 5 1.03 0.83 3 0.96 4 0.83 0.06 0.96 24.56 25.00 -2 3658

GBs 0.991.73 6

N/A-1.42 -5 1.47 5 0.95 0.12 0.99 28.65 26.69 7 8474

GBb 0.992.33 8

N/A-1.92 -7 1.98 7 0.91 0.16 0.98 28.29 25.78 9 8027

SRs 0.99 1.48 5 1.04 -1.37 -5 1.37 5 0.89 0.07 0.97 27.59 26.25 5 3551

SRb 0.97 1.17 4 1.04 -0.60 -2 0.97 4 0.91 0.05 0.98 26.86 26.23 2 3533

NPIs 0.97 0.80 3 1.02 -0.08 0 0.60 2 0.94 0.03 0.98 27.18 25.57 6 3402

NPIb 0.98 0.92 4 1.02 0.59 2 0.70 3 0.90 0.04 0.98 24.84 25.36 -2 3215

MVs 0.98 0.72 3 1.02 0.03 0 0.56 2 0.95 0.03 0.99 26.34 26.05 1 3482

MVb 0.97 1.26 5 1.03 0.93 4 1.00 4 0.83 0.05 0.96 24.97 25.87 -4 3390

QP1s 0.98 0.70 3 1.02 0.22 1 0.57 2 0.95 0.03 0.99 25.35 25.93 -2 3553

QP1b 0.96 1.48 7 1.04 1.24 6 1.25 6 0.68 0.07 0.93 22.47 24.92 -11 3219

TWs 0.99 0.87 3 1.12 -0.14 -1 0.68 3 0.98 0.06 1.00 25.30 24.82 2 8163

TWb 0.99 1.13 5 1.09 0.28 1 0.88 4 0.97 0.08 0.99 23.90 23.26 3 8709

PPs 0.98 0.72 3 1.02 0.16 1 0.55 2 0.95 0.03 0.99 26.78 26.35 2 3487

PPb 0.96 1.59 7 1.04 1.30 6 1.31 6 0.59 0.08 0.92 22.40 25.07 -12 3647

MHs 0.95 1.25 4 1.03 -0.86 -3 0.97 3 0.81 0.05 0.95 28.06 26.19 7 3214

MHb 0.94 1.19 5 1.03 0.80 3 0.96 4 0.76 0.05 0.94 24.87 25.56 -3 3214

Prsc

0.99 1.93 7 1 -1.50 -6 1.63 6 0.92 0.13 0.98 26.9 25.01 7 8623

FR1sc

0.99 1.76 7 1 -1 -5 1.46 5 0.95 0.11 0.99 27 26.45 1 8263

Npsc

0.99 1.13 5 1 0.21 1 0.89 4 0.97 0.08 0.99 24.1 25.82 -7 8760

AVERAGE 0.97 1.35 5.17 1.08 -0.29 -0.90 1.11 4.22 0.86 0.07 0.97 26.10 25.47 2.05

Water Temperature Prediction Skill Green > 80%, Red > 90%



(dim)

Reliability index

Average error (dim)

Average absolute

error (dim)


Absolute relative error Index of

agreement (non-dim)

Observed maximum

(dim)

Predicted maximum

(dim)

Number of

observationsdescription (non-dim) (non-dim)

Parameterar RMSE

%RI

AE [zero] %AAE

% MEF [1.0]ARE d


Temperature PDs 0.98 1.95 7 N/A -1.55 -5 1.69 6 0.88 0.10 0.97 28.22 25.51 10 4816PDb 0.96 1.87 7 1.06 -1.44 -5 1.57 6 0.81 0.09 0.95 27.89 24.28 13 4669BRs 0.91 1.98 7 1.05 -1.31 -5 1.59 6 0.70 0.08 0.92 27.79 24.87 11 4054BRb 0.96 1.02 4 1.03 0.43 2 0.84 3 0.89 0.05 0.97 25.31 24.63 3 4054CPs 0.87 1.58 6 1.03 -0.84 -3 1.22 4 0.65 0.06 0.90 27.17 25.26 7 2989CPb 0.96 1.24 5 1.03 0.83 3 0.96 4 0.83 0.06 0.96 24.56 25.00 -2 3658

GBs 0.99 1.73 6 N/A -1.42 -5 1.47 5 0.95 0.12 0.99 28.65 26.69 7 8474

GBb 0.99 2.33 8 N/A -1.92 -7 1.98 7 0.91 0.16 0.98 28.29 25.78 9 8027

SRs 0.99 1.48 5 1.04 -1.37 -5 1.37 5 0.89 0.07 0.97 27.59 26.25 5 3551SRb 0.97 1.17 4 1.04 -0.60 -2 0.97 4 0.91 0.05 0.98 26.86 26.23 2 3533NPIs 0.97 0.80 3 1.02 -0.08 0 0.60 2 0.94 0.03 0.98 27.18 25.57 6 3402NPIb 0.98 0.92 4 1.02 0.59 2 0.70 3 0.90 0.04 0.98 24.84 25.36 -2 3215MVs 0.98 0.72 3 1.02 0.03 0 0.56 2 0.95 0.03 0.99 26.34 26.05 1 3482MVb 0.97 1.26 5 1.03 0.93 4 1.00 4 0.83 0.05 0.96 24.97 25.87 -4 3390QP1s 0.98 0.70 3 1.02 0.22 1 0.57 2 0.95 0.03 0.99 25.35 25.93 -2 3553QP1b 0.96 1.48 7 1.04 1.24 6 1.25 6 0.68 0.07 0.93 22.47 24.92 -11 3219TWs 0.99 0.87 3 1.12 -0.14 -1 0.68 3 0.98 0.06 1.00 25.30 24.82 2 8163TWb 0.99 1.13 5 1.09 0.28 1 0.88 4 0.97 0.08 0.99 23.90 23.26 3 8709PPs 0.98 0.72 3 1.02 0.16 1 0.55 2 0.95 0.03 0.99 26.78 26.35 2 3487PPb 0.96 1.59 7 1.04 1.30 6 1.31 6 0.59 0.08 0.92 22.40 25.07 -12 3647MHs 0.95 1.25 4 1.03 -0.86 -3 0.97 3 0.81 0.05 0.95 28.06 26.19 7 3214MHb 0.94 1.19 5 1.03 0.80 3 0.96 4 0.76 0.05 0.94 24.87 25.56 -3 3214Prsa 0.99 1.93 7 1 -1.50 -6 1.63 6 0.92 0.13 0.98 26.9 25.01 7 8623FR1sa 0.99 1.76 7 1 -1 -5 1.46 5 0.95 0.11 0.99 27 26.45 1 8263Npsa 0.99 1.13 5 1 0.21 1 0.89 4 0.97 0.08 0.99 24.1 25.82 -7 8760

AVERAGE 0.97 1.35 5.17 1.08 -0.29 -0.90 1.11 4.22 0.86 0.07 0.97 26.10 25.47 2.05

Water Temperature Skill Red > 90%



(dim)

Reliability

indexb

Average error (dim)

Average absolute

error (dim)


Absolute relative

errorIndex of

agreement (non-dim)

Observed maximum

(dim)

Predicted maximum

(dim)

Number of

observations

description (non-dim) (non-dim)

Parameterar RMSE

%RI

AE [zero] %AAE

% MEF [1.0]ARE d


Elevationc

PR 0.93 0.19 12 N/A 0.03 2 0.17 11 0.84 0.42 0.96 1.60 1.69 -6 8751

FR1 0.94 0.17 10 N/A 0.03 2 0.15 9 0.87 0.37 0.97 1.65 1.67 -1 8757

Sub-tidal Elevationc

PR 0.99 0.04 7 N/A 0.03 6 0.03 6 0.92 0.26 0.98 0.53 0.58 -9 8747

FR1 0.99 0.03 6 N/A 0.03 5 0.03 6 0.93 0.24 0.98 0.55 0.55 -1 8745



(dim)

Reliability index

Average error (dim)

Average absolute

error (dim)


Absolute relative

error Index of agreement (non-dim)

Observed maximum

(dim)

Predicted maximum

(dim)

Number of observation

sdescription (non-dim) (non-dim)

Parameterar RMSE

%RI

AE [zero] %AAE

% MEF [1.0]ARE d


Elevation PR 0.93 0.19 12 N/A 0.03 2 0.17 11 0.84 0.42 0.96 1.60 1.69 -6 8751FR1 0.94 0.17 10 N/A 0.03 2 0.15 9 0.87 0.37 0.97 1.65 1.67 -1 8757

Sub-tidal Elevation

PR 0.99 0.04 7 N/A 0.03 6 0.03 6 0.92 0.26 0.98 0.53 0.58 -11 8747FR1 0.99 0.03 6 N/A 0.03 5 0.03 6 0.93 0.24 0.98 0.55 0.55 -1 8745 Salinity GD 0.05 1.90 6 1 1.47 4 1.57 5 -1.27 0.05 0.16 32.70 33.96 -4 8761

Water Surface Elevation Prediction Skill Green > 80%, Red > 90%

Sample of Hydrodynamic Results

Example of Stratification

Sample of Hydrodynamic Results

1. Introduction 1.1. Background 1.2. Objectives 1.3. Approach 1.4. Water Quality Setting 1.5. Data

1.5.1. River point source loads 1.5.2. WWTP point source load 1.5.3. Non-point source loads 1.5.4. Historic observations

2. The Water Quality Model 2.1. Algae

2.1.1. Production 2.1.1.1. Effect of nutrients 2.1.1.2. Effect of light 2.1.1.3. Effect of temperature 2.1.1.4. Effect of salinity on cyanobacteria

2.1.2. Basal metabolism 2.1.3. Predation 2.1.4. Settling

2.2. Organic Carbon 2.2.1. Particulate Organic Carbon 2.2.2. Dissolved organic Carbon

2.3. Phosphorus 2.3.1. Particulate Organic Phosphorus 2.3.2. Dissolved Organic Phosphorus 2.3.3. Total Phosphate

2.4. Nitrogen 2.4.1. Particulate Organic Nitrogen 2.4.2. Dissolved Organic Nitrogen 2.4.3. Ammonium Nitrogen 2.4.4. Nitrate Nitrogen

2.5. Silica 2.5.1. Particulate Biogenic Silica 2.5.2. Available Silica

2.6. Chemical Oxygen Demand 2.7. Dissolved Oxygen 2.8. Total Active Metal 2.9. Fecal Coliform Bacteria

II. Water Quality

Three-dimensional Modeling of Water Quality and Ecology in Narragansett Bay

By: Mohamed A. Abdelrhman 3. Model Configuration

3.1. Numerical grid 3.2. Initial and boundary conditions 3.3. Point-source loadings 3.4. Time step and run duration 3.5. Input files

4. Model Calibration, Validation, and Skill 4.1. Validation of dissolved oxygen 4.2. Validation of Chl-a 4.3. Skill Analysis

5. Sample of model predictions 5.1. Contemporary DO and hypoxia 5.2. DO and hypoxia without direct loads from WWTPs 5.3. Chl-a with and without WWTPs 5.4. Contemporary monthly vertical profiles of DO 5.5. Contemporary vertical profiles of Chl-a 5.6. Contemporary hourly vertical profiles of DO at CP on day 240 5.7. Contemporary hourly vertical profiles of Chl-a at CP on day 240

6. Summary and Conclusion 6.1. Future work

REFERENCES Appendix A: Point-source loading from WWTPs Appendix B: Dissolved oxygen concentration in riverine inflow Appendix C: ROC graphs Appendix D: Sample of model result Appendix E: Values of water quality parameters used for Narragansett Bay

Now

State Variables for Narragansett BayWater Column

1) cyanobacteria (Bc)2) diatom algae (Bd)3) green algae (Bg)4) refractory particulate organic

carbon (RPOC)5) labile particulate organic carbon (LPOC)6) dissolved carbon (DOC)7) refractory particulate organic phosphorus (RPOP)8) labile particulate organic phosphorus (LPOP)9) dissolved organic phosphorus (DOP)10) total phosphate (PO4t)

11) refractory particulate organic nitrogen (RPON)12) labile particulate organic nitrogen (LPON)13) dissolved organic nitrogen (DON)14) ammonia nitrogen (NH4)15) nitrate nitrogen (NO3)16) particulate biogenic silica (SU)17) dissolved available silica (SA)18) chemical oxygen demand (COD)19) dissolved oxygen (DO)20) total active metal (TAM) 21) fecal coliform bacteria (FCB)22) macro algae (Malg)

Objective: Provide DO and Chl-a concentrations in space & time

Water Quality Model Chart

WQ Forcing Functions for 20091. Riverine Loading: PO4t, DON, NH4, NO3+NO2, SA, DO2. WWTPs Loading: PO4t, DON, NH4, NO3+NO2, DOP, COD, FCB

WQ Boundary ConditionsConcentrations: PO4t, DON, NH4, NO3+NO2, SA, Bc, Bd, Bg

WQ Initial ConditionsConcentrations of all state variable after 5 yearly runs for 2009

WQ Benthic FluxCalibrated Flux : SOD, PO4d, NH4, Sid

Sample of DO Results Before Final Calibration

Initial Periods of Hypoxia at All Stations

StationPred Chronic

(h)Obs Chronic

(h)Pred Acute

(h)Obs Acute

(h)PD 276 1803.5 0 580.25CP 2113 1737.75 729 256.75GB 1017 1813.75 123 770.25SR 299 1607.25 2 731.75BR 1495 1177.5 345 199.25NPI 1155 1419.5 102 423.25PP 2176 1253.75 149 57.5MV 365 1115 0 290QP1 1175 539.25 0 3.25TW 4588 333.75 413 0MH 664 1066.75 89 131

TOTAL (h) 15323 13867.75 1952 3443.25Total (d) 638 578 81 143

Stations and associated areas to calculatearea-weighted Chl-a concentrations

Sample of Chl-a Results Before Final Calibration

Sample Chl-a Results Before Final Calibration

Sample of Monthly Vertical Profiles (early results)

Sample of Hourly Vertical Profiles on Day 240

III. Benthic Sediment Quality & Flux

Modeling Benthic Sediment Processes to Predict Water Quality and Ecology in Narragansett Bay

By Mohamed A. Abdelrhman

From Park et al. (1995), Based on the model of DiToro and Fitzpatrick (1993)

Coupled with CE-QUAL-ICM (Cerco and Cole, 1993)

Objective: Provide benthic fluxes in space and time

1. Introduction ............................................................................................................................. 1

2. Mass balance of ammonium, nitrate, phosphate, and sulfide/methane in sediment layers .... 3

3. Mass balance of silica in sediment layers ............................................................................... 5

4. Temperature of benthic sediment ............................................................................................ 6

5. Modeled sediment processes................................................................................................... 6

5.1. Depositional Flux ......................................................................................................... 6

5.2. Diagenesis Flux ............................................................................................................ 7

5.2.1. Ammonium Nitrogen ............................................................................................ 8

5.2.2. Nitrate Nitrogen..................................................................................................... 8

5.2.3. Phosphate Phosphorus ........................................................................................... 9

5.2.4. Carbon (Sulfide/methane and oxygen demand) .................................................... 9

5.2.4.1. Sulfide ........................................................................................................... 10

5.2.4.2. Sediment oxygen demand ............................................................................. 10

5.2.4.3. Methane ......................................................................................................... 10

5.3. Chemical Flux............................................................................................................. 11

6. Boundary conditions ............................................................................................................. 11

7. Initial conditions ................................................................................................................... 11

8. Model coefficients and parameters ....................................................................................... 12

9. Calibration and Validation .................................................................................................... 12

10. Summary and Conclusion ................................................................................................. 22

References ..................................................................................................................................... 23

Appendix A: Values of sediment water quality parameters used for Narragansett Bay ............. 25

Appendix B: Time series graphs of sediment water quality parameters and fluxes for Narragansett Bay ........................................................................................................................... 33

Flow chartFully Coupled Sediment& Water Quality Model

Layer 1 cmOxic, Anoxic

Layer 2 = 80 cmAnoxicG1 Labile HL 20d

G2 Refractory HL 1yrG3 Inert

State VariablesState variable number and description Name

(1) particulate organic carbon G1 class in layer 2 POC1



(4) particulate organic nitrogen G1 class in layer 2 PON1



(7) particulate organic phosphorus G1 class in layer 2 POP1



(10) particulate biogenic silica in layer 2 PSi

(11) sulfide/methane in layer 1 H2S1

(12) sulfide/methane in layer 2 H2S2

(13) ammonium nitrogen in layer 1a NH41

(14) ammonium nitrogen in layer 2 NH42

(15) nitrate nitrogen in layer 1 NO31

(16) nitrate nitrogen in layer 2 NO32

(17) phosphate phosphorus in layer 1 PO41

(18) phosphate phosphorus in layer 2 PO42

(19) available silica in layer 1 SI1

(20) available silica in layer 2 SI2

(21) ammonium nitrogen flux FNH4

(22) nitrate nitrogen flux FNO3

(23) phosphate phosphorus flux FPO4D

(24) silica flux FSAD

(25) sediment oxygen demand (flux) BFO2

(26) release of chemical oxygen demand (flux) BFCOD

(27) sediment temperature SMT

CalibrationFlux temperature relationships for Narragansett Bay

(Kremer and Nixon, 1978)

(Fulweiler and Nixon, 2010)

Calibrated Benthic Fluxes

IV. Light & Water ClarityLight Modeling light attenuation and backscattering to promote the recovery of submerged

aquatic vegetation (SAV) in estuaries and coastal embayments: Application to

Narragansett Bay, Rhode Island

By Mohamed A. Abdelrhman

six major contributors to the loss of light intensity through the water column: (1) attenuation by pure fresh water(2) attenuation by phytoplankton (algae) pigment(3) attenuation by nonchlorophyllous particles (non-algae particles, NAPs, also called

total suspended solids, TSS)(4) attenuation by dissolved organic matter (also called yellow substances, or colored

dissolved organic matter, CDOM)(5) backscattering by phytoplankton particles(6) backscattering by NAPs/TSS

Objective: Provide irradiance levels in space and time

𝐵𝑒𝑒𝑟 𝐿𝑎𝑚𝑏𝑒𝑟𝑡 𝐿𝑎𝑤 : 𝐸𝓁=𝐸𝑜𝑒− (𝑎+𝑏 ) 𝓁

Equations Eo

Eℓ

ℓ

Calibration

Keith et al. 2002: Narragansett Bay coefficients 0.06 and 0.65

Ongoing Bio-Optical modeling at AED by (Thursby & Keith)

PredictedChl-a

Concentration

PredictedChl-a Concentration

Irradiance Profiles

The Photic DepthMaximum depth with Irradiance > Threshold

(550 μmole m-2 s-1for SAV)

Photic Period Profiles

Total period with Irradiance > Threshold (550 μmole m-2 s-1for SAV)

SummaryI. Hydrodynamics

1. Acceptable Skill for Predictions of Temperature, Salinity, and Surface Elevation2. Ability to predict vertical stratification for Temperature, Salinity, Density, and

Brunt Vaisala Frequency3. Can calculate Circulation and Flushing behavior

II. Water Quality1. Predicts Chl-a concentration from three Agal groups2. Predicted DO concentration and Hypoxia in space and time

III. Benthic Sediment Quality & Flux1. Provides Calibrated Benthic Fluxes in space and time2. Fully coupled with the water quality model

IV. Light Attenuation& Water Clarity1. Provides Irradiance levels in space and time2. Provides adequate depth for healthy SAV 3. Provides periods with adequate irradiance for healthy SAV4. Can guide SAV recovery and sustainability efforts

narragansett bay hydrodynamics, water quality, sediment flux and water clarity by mohamed a....

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