DYNHYD5 HYDRODYNAMIC MODEL

(VERSION 2.0) AND 

CHLORIDE WATER QUALITY MODEL 

FOR THE DELAWARE ESTUARY

DELAWARE RIVER BASIN COMMISSION

WEST TRENTON, NEW JERSEY

December 2003 
This report was prepared by the Delaware River Basin Commission staff: Carol R. Collier, Executive

Director. Dr. Namsoo S. Suk was the principal author of the report. Dr. Suk is a Water Resources

Engineer/Modeler in the Modeling and Monitoring Branch of the Commission. Significant technical

recommendations and support were provided by Scott C. Hinz and Dr. Victor J. Bierman, Jr. of LimnoTech,

Inc., and Dr. Thomas J. Fikslin, head of the Modeling and Monitoring Branch of the Commission. 

Overall technical guidance and comments were provided by the PCB Model Expert Panel established by the

Commission. The current and former members of the PCB Model Expert Panel during the model

development process are (in alphabetical order):

Robert B. Ambrose, USEPA; Dr. Joel Baker, University of Maryland; Dr. Steven C. Chapra, Tufts

University; Dr. Steven Eisenreich, Rutgers University; Dr. Kevin Farley, Manhattan College; Dr. Rolland

Hemmett, USEPA Region II; Dr. James L. Martin, Mississippi State University; Dale Rushneck, Interface

Inc.; and Dr. Lisa Totten, Rutgers University.

The efforts of the following persons and organizations are gratefully acknowledged (in alphabetical order):

Steve Bearer, intern of the Commission provided editorial effort. 

Gail R. Blum of the Commission compiled and provided water temperature and specific conductance data.

Gregory J. Cavallo and John R. Yagecic of the Commission compiled and provided flow data.

Richard W. Greene of DNREC provided chloride data for the C &D Canal.

Dr. Shih-Long Liao of the Commission provided technical support.

Patricia McSparran of the Commission retrieved and compiled the PCS flow data.

Karen Reavy of the Commission provided all the GIS works in this document.

Edward D. Santoro of the Commission provided chloride monitoring data.

Robert D. Schopp of USGS provided tidal heights data of Burlington, NJ station.

Dr. Christopher K. Sommerfield of University of Delaware provided current velocity data.

Dr. David Velinsky of the Academy of Natural Sciences provided chloride data in Schuylkill River. 

Dr. Kuo-Chuin Wong of University of Delaware and Dr. William C. Boicourt of the University of Maryland

shared their knowledge on C & D Canal hydrodynamics through personal communications. 
EXECUTIVE SUMMARY 

A new hydrodynamic model was needed as a part of the development of Stage 1 TMDLs for polychlorinated 

biphenyls (PCBs) for the Delaware River Estuary. The downstream boundary of the existing 

DYNHYD5 hydrodynamic model (Version 1.0) was updated to establish a hydrodynamic and mass transport 

link to the ocean boundary. High resolution of Zone 6 would require a more comprehensive data collection 

effort and result in unacceptable increases in simulation time. Alternatively, introducing nine junctions to 

represent Zone 6 allowed for improved simulations, resulting from this linkage to the ocean boundary, while 

minimizing impacts to simulation time and model stability. Furthermore, since PCBs TMDLs to be derived 

using this hydrodynamic model applies only to Zones 2 through 5, a more coarse representation in Zone 6 

was acceptable. The newer version of the hydrodynamic model (Version 2.0) extends the downstream 

boundary to the mouth of the Delaware Bay (Zone 6), and consists of 105 junctions and 111 channels. 

The concept of a rolling calibration was used. In rolling calibration, as more data becomes available, the 

simulation period of the model is sequentially extended, and the model is re-calibrated to the expanded data 

set for each extension. The final calibration covers the period from September 1, 2001 to March 31, 2003, 

which is19 months or 577 days. 

The tidal datum for the C&D Canal, Chesapeake City, MD, was modified to correctly simulate the magnitude 

and the amount of net flow through the C&D Canal. Version 2.0 DYNHYD5 hydrodynamic model was 

calibrated against tidal heights to ensure that the model correctly simulated the advective water mass 

movements within the Estuary. The simulated tidal heights were compared with the hourly observed tidal 

heights at six locations along the Estuary. Linear regression yielded slopes ranging from 0.945 to 1.027, and 

intercepts ranging from -0.087 to 0.035 with R-squared values of 0.930 to 0.994, respectively. The 

cumulative frequency distribution comparisons showed good agreement between the simulated and the 

observed tidal heights throughout the ranges of the tidal heights. Lastly, temporal comparisons confirmed 

that the model reasonably simulated both the amplitudes and the phases of the tidal heights throughout the 

calibration period. The predicted current velocities were also compared with the limited observed data to 

further confirm the Model. Based upon these results, the DYNHYD5 hydrodynamic model for the Delaware 

River Estuary (Version 2.0) correctly generates the advective movement of the water mass throughout the 

Delaware Estuary for the entire calibration period. 

A TOXI5 (water quality) model consisting of 87 water column segments was then linked with the outputs 

from the calibrated DYNHYD5 hydrodynamic model and calibrated against the chloride concentrations. The 

main objective in this calibration process was the determination of an advection factor and a set of dispersion 

coefficients for the water quality model to correctly simulate the dispersive mixing within the Estuary. 

Review of comparison plots and the results of regression analyses indicated that the model was able to 

reproduce the temporal and spatial trends, and the magnitude of the chloride concentrations, within a 

reasonable range throughout the tidal portion of the Delaware River. It was therefore concluded that the 

calibrated model properly simulates the advective and dispersive movement of the chloride for the entire 

Estuary. 

Even though Version 2.0 of the DYNHYD5 hydrodynamic model for the Delaware River Estuary could be 

further enhanced with additional data collection and refinements, the calibrated model demonstrates the 

capability to accurately simulate the advective and dispersive movement of a conservative substance in the 

Delaware River Estuary over a wide range of hydrologic conditions. 
TABLE OF CONTENTS 

1. INTRODUCTION ................................................................. 1

1.1 Background ............................................................... 1

1.2 Study Objectives ........................................................... 2

2. CONCEPTUAL APPROACH FOR THE MODEL CALIBRATION ......................... 2

2.1 Constraints for the Extension of the Model Segments .............................. 3

2.2 Concept of the Rolling Calibration and the Calibration Period ....................... 3

3. OVERVIEW OF THE MODELS ..................................................... 3

3.1 Overview of DYNHYD5 Hydrodynamic Model .................................. 3

3.1.1 Governing Equations ............................................... 3

3.1.2 Model Network .................................................... 5

3.2 Overview of TOXIWASP5 ................................................... 5

4. CALIBRATION OF THE HYDRODYNAMIC MODEL .................................. 6

4.1 Model Bathymetry and Geometry .............................................. 6

4.1.1 Bathymetry ....................................................... 6

4.1.2 Model Geometry and the Segmentation ................................. 6

4.2 Data Compilation ......................................................... 17

4.2.1 Tidal Height ..................................................... 17

4.2.2 Inflows ......................................................... 18

4.2.3 Current Velocity .................................................. 19

4.3 Calibration of the DYNHYD5 Hydrodynamic Model ............................. 20

4.3.1 Code Modification ................................................ 20

4.3.2 Assignment of Open Boundaries With Forcing Tides and the Computational Time Step

............................................................. 20

4.3.3 Determination of Manning’s Coefficients .............................. 20

4.3.4 Influence of the C&D Canal ......................................... 22

4.4 Calibration Results ........................................................ 26

4.4.1 Comparisons with Current Velocity ................................... 26

4.4.2 Calibration Results of the Tidal Heights ................................ 27

5 CALIBRATION OF WATER QUALITY (CHLORIDE) MODEL ........................... 30

5.1 Water Quality Model Segmentation ........................................... 30

5.2 Data Compilation and Processes .............................................. 32

5.2.1 DRBC (BoatRun) Monitoring Data ................................... 32

5.2.2 USGS Continuous Monitoring Stations ................................ 32

5.2.3 Other Sources of Data .............................................. 32

5.2.4 Data Process ..................................................... 33

5.3 Calibration of the Chloride Water Quality Model ................................ 36

5.3.1 Assignment of the Boundary Conditions ............................... 36

5.3.2 Determination of the Advection Factor (ADF) and Dispersion Coefficients

............................................................. 36

5.4 Calibration Results of Chloride Concentrations .................................. 38

5.4.1 Comparison with the DRBC Data ..................................... 38

5.4.2 Comparison with USGS Data ........................................ 40

6. FUTURE REFINEMENTS ......................................................... 45
7 REFERENCES ................................................................... 46 

APPENDIX ....................................................................... 48 

A. Input File of the Calibrated DYNHYD5 Hydrodynamic Model (Version 2.0) .......... A1 

B. Input File of the Calibrated Water Quality (chloride) Model ......................... B1 

C. Calibration Results of the DYNHYD5 Hydrodynamic Model for the Delaware River Estuary 

.................................................................... C1 

D. Calibration Results of the Water Quality (chloride) Model for the Delaware River Estuary 

.................................................................... D1 
LIST OF TABLES

Table 4-1: Summary of the junction data. ........................................... 13

Table 4-2: Summary of the channel geometry. ....................................... 15

Table 4-3: Summary of available water surface elevation data from NOAA and USGS for the Delaware

River Estuary. ........................................................ 18

Table 4-4: The direction and magnitude of the simulated, long-term net flow in C&D Canal with

various amount of datum shift. ........................................... 25

Table 4-5: The summary of the regression results between the observed data and the simulated tidal

heights. .............................................................. 27
LIST OF FIGURES

Figure 1-1: Water Quality Zones of the Delaware River Estuary. ........................... 1

Figure 4-1(a): Schematic diagram of the segmentation for the DYNHYD5 hydrodynamic model (Version

2.0): Zone 2 ........................................................... 7

Figure 4-1(b): Schematic diagram of the segmentation for the DYNHYD5 hydrodynamic model (Version

2.0): Zone 3 ........................................................... 8

Figure 4-1(c): Schematic diagram of the segmentation for the DYNHYD5 hydrodynamic model (Version

2.0): Zone 4 ........................................................... 9

Figure 4-1(d): Schematic diagram of the segmentation for the DYNHYD5 hydrodynamic model (Version

2.0): Zone 5 .......................................................... 10

Figure 4-1(e): Schematic diagram of the segmentation for the DYNHYD5 hydrodynamic model (Version

2.0): Zone 6 .......................................................... 11

Figure 4-1(f) : Schematic diagram of the segmentation for the DYNHYD5 hydrodynamic model (Version

2.0) for all Zones: Boundaries are marked in red colored letters and drinking water intakes

are marked in green colored letters. ........................................ 12

Figure 4-2: Map of locations of the tide gage stations in the Delaware River Estuary. ......... 17

Figure 4-3: Daily average flow for the Delaware River at Trenton during the model calibration period.

.................................................................... 19

Figure 4-4: Assigned Manning’s coefficients for the main channel of the model segments. Only the

main stem of the Delaware Estuary is shown. ................................ 21

Figure 4-5: Temporal variations of the simulated chloride at RM 54 related to the inflows at Trenton.

.................................................................... 23

Figure 4-6: Temporal variations of the simulated and the observed chloride concentration at RM 54.

.................................................................... 23

Figure 4-7: Sensitivity simulation results: Impact on chloride concentrations by the datum shift at the

Chesapeake City. ...................................................... 24

Figure 4-8: Comparison between the observed and the simulated current velocity: (a) Spatial plot; (b)

Linear regression results. ................................................ 26

Figure 4-9: The observed and the simulated tidal heights at Reedy Point (River Mile 58.6): (a) for the

entire calibration period; (b) from the period March 10, 2003 to March 31, 2003. .... 28

Figure 4-9: The observed and the simulated tidal heights at Reedy Point (River Mile 58.6): (c) Linear

regression results (n=13,777); (d) cumulative frequency distribution curve. ........ 29
Figure 5-1: Schematic diagram of the segmentation for the water quality model. .............. 31

Figure 5-2: Temporal comparison of chloride concentrations derived from the USGS monitored specific

conductance data and the monitored chloride data at the Reedy Island station. ...... 34

Figure 5-3: Temporal comparison of chloride concentrations derived from the USGS monitored specific

conductance data and the monitored chloride data at the Chester station. ........... 34

Figure 5-4: Temporal comparison of chloride concentrations derived from the USGS monitored specific

conductance data and the monitored chloride data at the Fort Mifflin station. ....... 35

Figure 5-5: Temporal comparison of chloride concentrations derived from the USGS monitored specific

conductance data and the monitored chloride data at the Ben Franklin station. ...... 35

Figure 5-6: Assigned dispersion coefficients for the water quality model. The main stem of Delaware

Estuary is only shown in the schematic. .................................... 37

Figure 5-7: Cumulative frequency distributions of the observed and the simulated chloride

concentrations: Data from three segments (Node 2, 12 and 17) were combined. ..... 38

Figure 5-8: Spatial comparison between the observed data (DRBC_BoatRun) and the simulated chloride

concentrations throughout the Estuary. ..................................... 39

Figure 5-9: Temporal comparison between the observed data (derived from specific conductance from

USGS Fort Mifflin Station) and the simulated chloride concentrations for (a) entire

simulation period; (b) first week of September 2002. .......................... 41

Figure 5-10: Temporal comparison between the observed data (derived from specific conductance from

USGS Chester Station) and the simulated chloride concentrations for (a) entire simulation

period; (b) first week of September 2002. ................................... 42

Figure 5-11: Temporal comparison between the observed data (derived from specific conductance from

USGS Reedy Is. Station) and the simulated chloride concentrations for the calibration period

.................................................................... 43

Figure 5-12: Temporal comparison between the observed data (derived from specific conductance from

USGS Reedy Is. Station) and the simulated chloride concentrations for the first week of

September, 2002. ...................................................... 43

Figure 5-13: Linear regression results between derived and simulated chloride concentrations at Reedy

Is. USGS station (n=13,660). Both data sets were hourly time interval throughout the

calibration period. ..................................................... 44

Figure 5-14: Cumulative frequency distributions of the observed and the simulated chloride

concentrations for the Reedy Island station. ................................. 44
1. INTRODUCTION 

1.1 Background 

A new hydrodynamic model was needed as a part of the development of Stage 1 TMDLs for the 

polychlorinated biphenyls (PCBs) for the Delaware River Estuary. Even though the development of the 

TMDLs for PCBs only covers Zones from 2 to 5 of the tidal portion of the Delaware River, the need to set 

the downstream boundary at the mouth of the Delaware Bay was inevitable (Figure 1-1). The purpose of 

inclusion of the Bay area or the setting the downstream boundary at the mouth of the bay is to generate 

realistic boundary conditions between Zones 5 and 6. Delaware River Basin Commission (DRBC) currently 

maintains two hydrodynamic models. One is DYNHYD5 (DRBC, 1995) and the other is ECOM 

(HydroQual, Inc., 1998). The downstream boundary for both of the models were set at the head of the 

Delaware Bay (Liston Point, DE at River Mile 49). The biggest difference between two models are the model 

dimensions. The DYNHYD5 model is basically a one dimensional model with available branching to 

simulate around the islands, and the ECOM is a z-level, three-dimensional model. The DYNHYD5 

hydrodynamic model was linked with the water quality model (TOXI5) to develop the Total Maximum Daily 

Loads (TMDLs) for the volatile organic compounds in 1998 (DRBC, 1998a; 1998b). The DYNHYD5 model 

was chosen to be updated and used as a hydrodynamic model for the Stage 1 TMDLs for PCBs because of 

the limited data availability and the well known characteristics of the relatively well mixed Delaware Estuary 

system (Wong and Garvine, 1984). 

The existing DYNHYD5 model was renamed for Version 1.0 and the newly developed DYNHYD5 is named 

Version 2.0 of the DYNHYD5 hydrodynamic model for the Delaware River Estuary. 

Figure 1-1: Water Quality Zones of the Delaware River Estuary. 

1
The segmentation of the existing DYNHYD5 hydrodynamic model has been extended to include the 

Delaware Bay (Zone 6) in this version of the DYNHYD5 hydrodynamic model (Version 2.0). In addition 

to the extension to the mouth of the Bay, one of the major differences in this newly developed hydrodynamic 

model is the length of the calibration period. Version 1.0 was calibrated over nine days and validated over 

six day period while Version 2.0 was calibrated over 19 months (577 days) covering wide range of flow 

conditions. 

1.2 Study Objectives 

As described in the Section 1.1, the hydrodynamic and water quality models were required to be extended 

to the mouth of the Delaware Bay to obtain the better temporal and spatial gradients of the chemicals of 

concern for the rest of the Estuary. The major objectives for this study are described below. 

1. Development of the model segmentation to cover the Zone 6 of the Delaware Bay. 

2. Calibration of the hydrodynamic model against the tidal heights to ensure that the model correctly 

simulates the advective water movements within the Estuary. 

3. Calibration of the water quality model, linked with hydrodynamic model, against chloride to ensure 

that the model simulates the dispersive movement properly. 

2. CONCEPTUAL APPROACH FOR THE MODEL CALIBRATION 

The calibration of the hydrodynamic model basically requires two steps followed by a link with the water 

quality model to complete the calibration process. The detailed description of the two step calibration 

approach is discussed in this section. 

Step 1 

The DYNHYD5 model was calibrated against tidal heights. The hydrodynamic model was set up with all 

the forcing tides at the open boundaries and inflows from the tributaries and discharges. Groups of 

Manning’s coefficients were determined to obtain the best match with the observed tidal heights at the gaging 

stations. Because of the lack of velocity data, the current velocities were not a calibration parameter in this 

calibration process. Rather, the current velocities and flows were checked and confirmed using best 

professional judgement and the limited available data. At the end of this process, the advective movements 

are set and calibrated. 

Step 2 

Once the hydrodynamic model is calibrated, the outputs of the calibrated hydrodynamic model are then linked 

with the water quality model as a part of the hydrodynamic model calibration process. The main purpose of 

this process is to set the proper dispersion coefficients and also to find the proper computational time step of 

the water quality model. It was almost inevitable that certain levels of the numerical dispersions were 

introduced into the water quality model because of the size of the segments and the computational time step. 

Dispersion coefficients and the advection factor were adjusted until the water quality model results were well 

matched with known, spatially and temporally varying, observed conservative chemical concentrations. Like 

many other estuary model calibration processes, chloride (or salinity) concentrations were used as a 

calibration parameter. The major sources of chloride were the two open boundaries. The dispersion 

coefficients between segments and an advection factor were then adjusted to obtain the best fit with the 

observed data sets. Calibrated dispersion coefficients and the advection factor were thus established at the 

end of this step. Utilizing the hydrodynamic model results along with these dispersion coefficients properly 

2
simulated both the advective and dispersive movement of the chemicals of concern in the water column. 

Iterative approach using step one and two might be required to finalize the hydrodynamic model calibration, 

which was the case for this study. 

2.1 Constraints for the Extension of the Model Segments 

Version 1.0 of the DYNHYD5 hydrodynamic model consists of 94 junctions and 100 channels. The 

downstream boundary was extended to the mouth of the Delaware Bay (Zone 6) in the newer version of the 

hydrodynamic model. The extended model comprises a total of 105 junctions and 111 channels. A number 

of constraints were considered in this model domain extension. The major constraints of the inclusion of the 

Delaware Bay into the model domain are the stability of the model, the data availability, and overall 

simulation time. Because the PCB water quality model will have additional sediment layers, and there is a 

slower interaction between sediment layer and water column chemical exchanges, the overall simulation time 

was one of the critical elements in determining the number of extended portions of the model segments. 

Because the purpose of the inclusion of the Delaware Bay was to generate reasonable temporal variations of 

chemical concentrations at the intersection of the Zones 5 and 6, it was not required to have a relatively fine 

scale of segmentation in Zone 6. It was determined that nine segments would cover the Zone 6. This coarse 

segmentation will fulfill the main purpose of this work while minimizing the overall computational time in 

both hydrodynamic and water quality model simulations. 

2.2 Concept of the Rolling Calibration and the Calibration Period 

The newly segmented hydrodynamic model was then calibrated against tidal heights and chloride by utilizing 

the water quality model over a longer time period than used with Version 1.0. The final calibration covers 

the period from September 1, 2001 to March 31, 2003, which lasted for 19 months or 577 days. The concept 

of rolling calibration was used. In rolling calibration, as more data becomes available, the simulation period 

of the model is sequentially extended, and the model is re-calibrated or validated to the full available data set 

for each extension. Thus, rather than splitting the time period for the model calibration and validation period, 

a longer and single time period was used as a calibration time period. In consequence, a number of sensitivity 

runs performed before March 31, 2003 did not cover the whole calibration time period. 

3. OVERVIEW OF THE MODELS 

3.1 Overview of DYNHYD5 Hydrodynamic Model 

The DYNHYD5 hydrodynamic model solves the one dimensional equations of continuity and momentum 

for a branching or channel-junction (link-node), computational network. The resulting unsteady 

hydrodynamics are averaged over larger time intervals and stored for later use by the water quality model 

(Ambrose et. al., 1993a). 

3.1.1 Governing Equations 

Even though more detailed descriptions of the governing equations for the DYNHYD5 hydrodynamic model 

are available from the User’s Manual (Ambrose et. al, 1993a), a number of key equations are listed in this 

section to help understand the DYNHYD5 model. The hydrodynamic model solves one-dimensional 

equations describing the propagation of a long wave through a shallow water system while conserving both 

momentum and volume. The equation of motion, based on the conservation of momentum, predicts water 

3
velocities and flows. The equation of continuity, based on the conservation of volume, predicts water heights 

(heads) and volumes. This approach assumes that flow is predominantly one- dimensional, Coriolis and other 

accelerations normal to the direction of flow are negligible, channels can be adequately represented by a 

constant top width with a variable hydraulic depth, wave length is significantly greater than the depth, and 

that bottom slopes are moderate. 

3.1.2.1 The Equation of Motion 

The equation of motion is given by: 

∂ U ∂ U

∂ t = −U ∂ x

+ ag,λ + af + aw,λ

where, 

∂ U

∂ t

= the local inertia term, or the velocity rate of change with respect to time, m/sec2 

∂ U

U ∂ x

= the Bernoulli acceleration, or the rate of momentum change by mass transfer; also defined as 

the conservative inertial term from Newton’s second law, m/sec2 

ag,λ = gravitational acceleration along the λ axis of the channel, m/sec2 

af = frictional acceleration, m/sec2 

aw,λ = wind stress acceleration along axis of channel, m/sec2 

x = distance along axis of channel, m 

t = time, sec 

U = velocity along the axis of channel, m/sec 

λ = longitudinal axis 

Gravitational acceleration is driven by the slope of the water surface. The acceleration along the longitudinal 

axis is 

ag,λ = − g sin S

where, 

g = acceleration of gravity = 9.81 m/sec2 

S = water surface slope, m/m 

with small water surface slope (S), the term [sin S] can be replaced with S. The slope can be expressed as 

the water surface elevation changes along the distance of the channel. The gravitational acceleration term 

can be now expressed as: 

∂ H

ag,λ = − g ∂ x

where, 

H = water surface elevation, or head (height above an arbitrary datum), m 

4 
The frictional acceleration term can be expressed using the Manning equation for steady uniform flow: 

/ R23 ∂ H1/2 

U = n ∂ x

where, 

R = hydraulic radius (approximately equal to the depth for wide channel), m 

n = Manning roughness coefficient, sec/m1/3 

∂ H

∂ x

= the energy gradient, m/m 

The wind effect was not considered in the hydrodynamic model calibration for the Delaware River Estuary. 

3.1.2.2 The Equation of Continuity 

The equation of continuity is given by: 

∂ A = − ∂ Q

∂ t ∂ x

where, 

A = cross sectional area, m2 

Q = flow rate m3/sec 

For rectangular channels of constant width B, the equation of continuity can be expressed as: 

∂ H = − 1 ∂ Q

∂ t B ∂ x

where, 

B = width, m 

H = water surface elevation (head), m 

∂ H

∂ t = rate of water elevation change with respect to time, m/sec 

1 ∂ Q

B ∂ x

= rate of water volume change with respect to distance per unit width, m/sec

3.1.2 Model Network 

The solutions of the equations give velocities (U) and heads (H) throughout the water body over the duration 

of the simulation. The “link-node (or channel-junction)” network solves the equations of motion and 

continuity at alternating grid points. At each time step, the equation of motion is solved at the links, giving 

velocities for mass transport calculations, and the equation of continuity is solved at the nodes, giving heads 

for pollutant concentration calculations. 

3.2 Overview of TOXIWASP5 

(see DRBC, 2003a, b, c; Ambrose et. al., 1993b, c; for the detailed model description) 

5
4. CALIBRATION OF THE HYDRODYNAMIC MODEL 

4.1 Model Bathymetry and Geometry 

4.1.1 Bathymetry 

The bathymetry data for the extended portion was downloaded from the National Ocean Service (NOS) web 

site (http://spo.nos.noaa.gov/servlet/BuildPage?template=bathy.txt&parm1=M090). This hydrographic 

information for the Zone 6 was established using the Digital Elevation Model (DEM) and GIS. The 

downloaded bathymetry data was based on the mean low water (MLW) datum whereas, the existing model’s 

datum was National Geodetic Vertical Datum of 1929 (NGVD1929). Because of lack of a information on 

the relationship between MLW and NGVD29 for the Bay area, limited station information was used to 

convert the datum of the downloaded bathymetry to NGVD29 datum. Another note to the downloaded 

bathymetry data was that the bathymetry data were derived from seventeen hydrographic surveys conducted 

between 1945 and 1993. On the other hand, the existing model’s bathymetry was derived from single shore 

to shore survey performed by U.S. Army Corps of Engineers (USACE) in late 1980s to early 1990s. The 

bathymetry data for the Version 2.0 of the hydrodynamic model was from the USACE for the Zones 2 

through 5 and from the NOS for the Zone 6. 

4.1.2 Model Geometry and the Segmentation

The newer version of the hydrodynamic model extends the downstream boundary to the mouth of the

Delaware Bay (Zone 6), and consists of 105 junctions and 111 channels. The minimal number of junctions

were added to represent the Zone 6 of the Delaware River Estuary to improve the simulation results and to

minimize impacts on the overall computational time. 

Minor modifications were also performed to junctions and channels of the Version 1.0 model to improve the

model stability. Most of the numbering systems were kept to maintain the comparability between the models.

One of modifications in Version 2.0 model was the addition of boundary junctions for all four drinking water

intake withdrawals. By assigning the boundary junctions for the intake withdrawals, the mass of chemical

of concern would be withdrawn along with the water mass in the hydrodynamic and water quality modeling.

Another modification to the Version 1.0 hydrodynamic model was the relocation of the Chesapeake and

Delaware Canal (C&D Canal) downstream boundary. The downstream boundary for the C&D Canal was

at the Old Town Point Wharf, MD in the earlier version of the model. In this version, the boundary was

moved about 9 km east from the Old Town Point to the Chesapeake City, MD for several reasons. First, the

Chesapeake City location has a more confined channel configuration compared to the location at the Old

Town Point Wharf, which is potentially influenced by the Elk River. Second, tidal heights were not gaged

for both of the locations, rather, relationships to estimate the tidal heights for both locations were already

developed by NOAA. The tidal heights for the Old Town Point Wharf were derived from the observed tidal

heights at Baltimore, MD, which is over 80 km away. Whereas, the tidal heights for the Chesapeake City

were derived from the Reedy Island Station’s observed data, which is only about 21 km apart. Therefore,

Chesapeake City would be based on more accurate tidal height calculations. Junctions and channels of the

C&D Canal were redefined, while the total number of segments and the numbering system remained same

as the Version 1.0 Model.

The finalized segmentation for the Version 2.0 of the DYNHYD5 hydrodynamic model for each Zone is

presented in Figure 4-1 (a) to (e). The schematic diagram of segmentation for the entire Delaware Estuary

is presented in Figure 4-1 (f). The individual junction information for the model input is summarized in Table

4-1 and the channel geometries are summarized in Table 4-2.

6
Figure 4-1(a): Schematic diagram of the segmentation for the DYNHYD5 hydrodynamic model (Version

2.0): Zone 2

7
Figure 4-1(b): Schematic diagram of the segmentation for the DYNHYD5 hydrodynamic model (Version

2.0): Zone 3

8
Figure 4-1(c): Schematic diagram of the segmentation for the DYNHYD5 hydrodynamic model (Version

2.0): Zone 4

9
Figure 4-1(d): Schematic diagram of the segmentation for the DYNHYD5 hydrodynamic model (Version

2.0): Zone 5

10
Figure 4-1(e): Schematic diagram of the segmentation for the DYNHYD5 hydrodynamic model (Version

2.0): Zone 6

11
RM Trenton RM

133.3

132.0

130.6

129.0 

67 

53 

41 

39 

37 

35 

21 20 

18 

19 

13 14 

90 

76 

75 

74 

72 

71 

70 

69 

68 

64 

63 

62 

55 

2 

60 

59 

58 

56 

51 

49 

48 

44 

43 

38 

42 

23 

36 

77 

34 

33 

32 

31 

66 

52 

22 

12 

78 

11 

25 

24 

92 

95 

96 

97 

17 

102 

100

98 

99 

101 

73 89 Crosswicks

127.3

124.9

Lower Bucks Intake 105 122.6

120.7

Bristol & Burlington Intake 104 118.6 119.0 

Zone 2 Neshaminy 88 65 116.8 

115.0 

113.2 

61 87 

57 86 

54 85 

Torresdale Intake 103 111.5 Rancocas 

109.5 

107.8 

105.4 Penskn 

104.0 

Zone 3 101.6 101.7 Cooper 

99.4 

96.9 50 84 Newton 

95.5 

Schuylkill 83 47 46 45 92.3 

89.7 

87.7 87.0 

Zone 4 Darby 82 40 86.5 

84.8 

82.2 82.0 

81.0 93 94 Raccoon 

80.0 

81 

30 

80 29 28 27 26 

Brandywine 77.3 

75.1 

72.2 

Christina 70.8 

Zone 5 68.1 

65.5

63.0

60.6 60.6

60.2

60.1 

C&D Canal 91 1 3 4 5 6 7 8 9 10 58.6 58.7 15 16 79 Salem 

54.9 

53.3 

51.9 

50.5 

48.3 

46.9 

45.0 

42.6 

39.6 

35.8 

28.7 

Zone 6 18.6 

13.5

8.0 

1.2 

Mouth of Bay 

Figure 4-1(f) : Schematic diagram of the segmentation for the DYNHYD5 hydrodynamic model (Version 

2.0) for all Zones: Boundaries are marked in red colored letters and drinking water intakes 

are marked in green colored letters. 

12 
Table 4-1: Summary of the junction data. 

Node 

No. 

River 

Mile 

Surface Area 

(m2) 

Bottom 

Elevationa 

(m) 

1 58.6 558800 -8.64 

2 48.3 11926900 -5.54 

3 58.6 438900 -8.64 

4 58.6 375980 -8.91 

5 58.6 336160 -9.18 

6 58.6 429880 -9.23 

7 58.6 523600 -9.28 

8 58.6 583660. -9.24 

9 58.6 664180. -9.25 

10 58.6 685410. -9.23 

11 51.9 9341080. -5.52 

12 54.9 12758070. -5.08 

13 58.6 8766871. -6.45 

14 58.7 5064157. -1.35 

15 58.6 2351584. -2.18 

16 58.6 6374031. -1.23 

17 45.0 24912800. -5.07 

18 60.2 5167297. -3.97 

19 60.1 5177611. -1.33 

20 60.6 6157438. -5.61 

21 63.0 7034125. -2.14 

22 63.0 10221140. -5.04 

23 65.5 9519791. -5.59 

24 68.1 7735475. -5.64 

25 70.8 7384800. -5.99 

26 70.8 660094. -5.01 

27 70.8 587896. -2.29 

Node 

No. 

River 

Mile 

Surface Area 

(m2) 

Bottom 

Elevationa 

(m) 

54 101.6 330047. -1.48 

55 104.0 2898224. -6.41 

56 105.4 2508300. -6.93 

57 105.4 190491. -1.86 

58 107.8 2487769. -7.40 

59 109.5 2735115. -7.09 

60 111.5 2526880. -6.46 

61 111.5 693730. -3.18 

62 113.2 2186401. -4.89 

63 115.0 1672200. -7.19 

64 116.8 1791112. -5.70 

65 116.8 255475. -3.19 

66 118.6 1435770. -8.05 

67 119.0 417771. -3.29 

68 120.7 1435770. -7.76 

69 122.6 1219777. -7.16 

70 124.9 1575120. -6.93 

71 127.3 1672200. -6.74 

72 129.0 1207700. -5.16 

73 129.0 156351. -1.29 

74 130.6 969504. -3.86 

75 132.0 650300. -4.81 

76 133.3 646500. -1.67 

77 50.5 9839210. -5.22 

78 53.3 8672718. -5.30 

79 58.6 7173807. -1.68 

80 70.8 8500. -1.20 

13
Node 

No. 

River 

Mile 

Surface Area 

(m2) 

Bottom 

Elevationa 

(m) 

Node 

No. 

River 

Mile 

28 70.8 

29 70.8 

30 70.8 

31 72.2 

32 75.1 

33 77.3 

34 80.0 

35 81.0 

36 82.2 

37 82.0 

38 84.8 

39 86.5 

40 86.5 

41 87.7 

42 87.0 

43 89.7 

44 92.3 

45 92.3 

46 92.3 

47 92.3 

48 95.5 

49 96.9 

50 96.9 

51 99.4 

52 101.6 

53 101.7 

567268. 

587896. 

206279. 

7993324. 

7065067. 

6704078. 

5517972. 

1897769. 

3228271. 

1165478. 

4352494. 

1392385. 

515698. 

1443955. 

2980736. 

4548459. 

5507658 

711663. 

825117. 

433186. 

3733656. 

2887910. 

268163. 

2722887. 

2403154. 

1340552. 

-1.20 81 70.8 

-1.20 82 86.5 

-3.24 83 92.3 

-5.30 84 96.9 

-5.93 85 101.6 

-5.43 86 105.4 

-5.83 87 111.5 

-2.82 88 116.8 

-8.32 89 129.0 

-1.07 90 134.0 

-5.46 91 58.6 

-2.42 92 46.9 

-2.80 93 82.2 

-2.38 94 82.2 

-6.46 95 39.6 

-8.41 96 35.8 

-7.17 97 28.7 

-7.43 98 18.6 

-7.21 99 8.0 

-5.13 100 13.5 

-6.42 101 1.2 

-10.67 102 42.6 

-1.87 103 111.5 

-8.95 104 118.6 

-6.70 105 122.6 

-1.67 

Surface Area 

(m2) 

Bottom 

Elevationa 

(m) 

11900. -3.24 

9100. -2.80 

16900. -5.13 

5100. -1.87 

9100. -1.48 

9100. -1.86 

18300. -3.18 

10200. -3.19 

10200. -1.29 

26300. -1.67 

655600. -8.25 

14443000. -5.01 

433547. -1.87 

495482. -1.87 

45906200. -5.51 

86887700. -5.02 

286164000. -4.24 

401974000. -5.79 

462987600. -8.83 

335131600. -2.64 

92928860. -12.57 

31825000. -5.32 

10000. -6.50 

10000. -6.50 

10000. -6.50 

a- The datum for the bottom elevations was NGVD1929. 

14
Name Channel 

No. 

Length 

meter 

C&D 1 2093 

MAIN 2 1889 

C&D 3 1528 

C&D 4 1528 

C&D 5 2380 

C&D 6 2380 

C&D 7 2926 

C&D 8 3111 

C&D 9 2285 

C&D 10 2285 

MAIN 11 4570 

MAIN 12 3120 

MAIN 13 5890 

MAIN 14 4000 

Salem 15 2742 

Salem 16 2742 

MAIN 17 4163 

MAIN 18 4164 

MAIN 19 2742 

MAIN 20 4164 

MAIN 21 3250 

MAIN 22 2945 

MAIN 23 3352 

MAIN 24 4265 

MAIN 25 4164 

Christina 26 3656 

Christina 27 3656 

Christina 28 2844 

Christina 29 2844 

Table 4-2: Summary of the channel geometry. 

Width Angle 

meter degree 

Name 

220 90 

220 90 

220 90 

220 90 

220 90 

220 90 

220 90 

220 90 

4381 330 

3796 15 

2347 5 

1372 90 

518 40 

7129 320 

305 60 

1320 50 

1625 355 

1158 315 

1410 320 

1036 320 

1871 320 

1494 280 

2316 30 

1189 330 

2747 45 

2501 30 

2080 20 

239 315 

230 255 

Pennsauken 57 1930 427 

MAIN 58 2742 53 

MAIN 59 3656 932 

MAIN 60 2437 762 

Rancocas 61 2949 871 

MAIN 62 2745 65 

MAIN 63 2949 851 

MAIN 64 2949 966 

Neshaminy 65 2949 848 

MAIN 66 2745 181 

MAIN 67 2745 766 

MAIN 68 2745 712 

MAIN 69 2898 652 

MAIN 70 1930 89 

MAIN 71 2898 649 

MAIN 72 3356 466 

Crosswicks 73 2389 296 

MAIN 74 2389 307 

MAIN 75 2949 433 

MAIN 76 3305 415 

MAIN 77 3660 433 

MAIN 78 2745 406 

Salem 79 1830 91 

Christina 80 2288 430 

Brandywine 81 2438 363 

Darby 82 2438 239 

Schuylkill 83 2980 220 

Newton 84 2714 5664 

Cooper 85 3000 6530 

15

Channel 

No. 

Length Width 

meter meter 

Angle 

degree 

110 

150 

60 

45 

80 

90 

75 

85 

75 

90 

80 

85 

90 

300 

90 

70 

90 

10 

40 

125 

90 

70 

60 

355 

330 

355 

90 

330 

325 
Name Channel 

No. 

Length 

meter 

Width 

meter 

Angle 

degree 

Name Channel 

No. 

Length 

meter 

Width 

meter 

Angle 

degree 

Brandywine 30 2844 169 225 Pennsauken 86 1472 102 255 

MAIN 31 2844 102 225 Rancocas 87 1472 179 320 

MAIN 32 2844 179 320 Neshaminy 88 1421 98 20 

MAIN 33 3656 2086 10 Crosswicks 89 1675 142 45 

MAIN 34 3656 2225 30 Trenton 90 1421 37 105 

MAIN 35 3656 2107 40 C&D 91 1421 53 150 

MAIN 36 4062 2095 45 MAIN 92 1422 65 90 

MAIN 37 3656 1236 45 Raccoon 93 1422 181 90 

MAIN 38 3250 1185 60 Raccoon 94 1015 89 300 

MAIN 39 3656 1320 45 MAIN 95 965 91 60 

Darby 40 2234 754 60 MAIN 96 1269 239 355 

MAIN 41 2234 1059 25 MAIN 97 2285 4816 330 

MAIN 42 1930 792 45 MAIN 98 2285 3795 15 

MAIN 43 3656 1506 90 MAIN 99 2438 203 315 

MAIN 44 2742 98 20 MAIN 100 9754 102 315 

Schuylkill 45 1930 417 90 Mouth of the 

Bay 

101 5000 7794 320 

Schuylkill 46 3656 417 90 MAIN 102 6900 8636 320 

Schuylkill 47 3656 1248 80 Torresdale 

Intake 

103 10880 15362 322 

MAIN 48 4750 1156 60 Bristol Intake 104 14941 22981 336 

MAIN 49 3250 195 330 LowBucks 

Intake 

105 16803 25824 330 

Newton 50 3250 173 10 MAIN 106 11167 25025 325 

MAIN 51 3250 142 45 MAIN 107 24041 14351 29 

MAIN 52 3656 1152 90 MAIN 108 21563 13281 253 

MAIN 53 3656 912 35 MAIN 109 4563 581 270 

Cooper 54 2742 37 105 MAIN 110 4563 581 270 

MAIN 55 3656 786 350 MAIN 111 4563 581 270 

MAIN 56 3148 1014 10 

16
4.2 Data Compilation 

4.2.1 Tidal Height 

Available water surface elevation (tidal height) data were obtained from National Oceanic Atmospheric 

Administration (NOAA) web-site (http://www.co-ops.nos.noaa.gov/data_res.html) for the period from 

September 1, 2001 to March 31, 2003, which coincides with the calibration period of the PCBs water quality 

model. Seven tide gaging stations were available with the verified hourly tidal heights within the model 

domain (Figure 4-2). Hourly tidal heights were downloaded based on Local Standard Time (LST), units of 

meters, and Mean Lower Low Water (MLLW) datum. Retrieved water surface elevation data sets were then 

converted to the NGVD1929 datum. The data for the water surface elevation at Burlington, New Jersey were 

obtained from the US Geological Survey (USGS) by personal contact (personal contact with Robert 

Schopp,USGS, NJ District, 2003). A summary of the available water surface elevation data with model node 

information is contained in Table 4-3. 

Figure 4-2: Map of locations of the tide gage stations in the Delaware River Estuary. 

17
Table 4-3: Summary of available water surface elevation data from NOAA and USGS for the Delaware 

River Estuary. 

Station 

ID 

River 

Mile 

Station 

Name 

Available Period NODE 

No. 

MLLW - NGVD29 

meter 

Lewes 8557380 1.5 9/1/01 ~ 3/31/03 101 0.6523 

Brandywine 

Shoal 8555889 15 7/1/02 ~ 3/31/03 99 0.6800a 

Reedy Point 8551910 58 9/1/01 ~ 3/31/03 10 0.7681 

Philadelphia 8545240 100 9/1/01 ~ 3/31/03 51 0.7010b 

TaconyPalmyra 

Bridge 

8538886 107 6/11/02 ~ 3/31/03 58 0.8400a 

Burlington 01464598 119 6/20/02 ~ 1/16/03C 

3/1/03 ~ 3/31/03 66 Reported with 

NGVD29 datum

Newbold 8548989 127 11/15/01 ~ 3/31/03 71 0.9700a 

a - Information on the difference between mean lower low water (MLLW) and NGVD1929 was not 

available. The difference was assumed to correct the NOAA’s verified data into the model’s datum of 

NGVD1929. 

b - There were two tidal stations for Philadelphia under NOAA’s web site. One station (Station ID 

8545240) contained tidal height data for the modeling period and the other station (Station ID 8545530) 

only contained the MLLW to NGVD29 relationship. The station 8545240 had NAVD88 height related 

to MLLW. A downloadable software (called VERTCON) was used to calculate the relationship between 

NAVD88 and NGVD29 using the latitude and longitude. Using the location information and the 

‘VERTCON’, the vertical relationship between NAVD88 and NGVD29 was calculated to be 0.332 

meters. NAVD88 from MLLW for this station was reported as 1.033 meters. Thus, the calculated 

relationship between MLLW and NGVD29 became 0.701 meters. 

c - The data gap was caused by an ice jam at the gaging station. 

4.2.2 Inflows 

4.2.2.1 Inflows from Tributaries 

Daily flows from twenty-two (22) tributaries, including the Delaware River at Trenton and Schuylkill River, 

were input into the model. Daily average flows for the Delaware River at Trenton for the entire calibration 

period are shown in Figure 4-3. The flow at Trenton varied from 69 to 2,237 m3

 /sec (or 2,420 to 79,000 

ft3

/sec) during the calibration period. The annual average freshwater inflows from Trenton makeup more than 

60% of total freshwater inflows into the Delaware River Estuary. Daily flows for the ungaged tributaries 

18
2500 

m^3/sec ft^3/sec 

90,000 

Flow, m3/sec 

80,000 

2000 70,000 

60,000 

1500 

50,000 

40,000 

1000 

30,000 

500 20,000 

10,000 

0 -

09/01/01 11/01/01 01/01/02 03/03/02 05/03/02 07/03/02 09/02/02 11/02/02 01/02/03 03/04/03 

Date 

Figure 4-3: Daily average flow for the Delaware River at Trenton during the model calibration period. 

were extrapolated from nearby gaging stations with drainage area adjustments. Detailed methods and 

assumptions on tributary flow calculations are summarized in DRBC (2003b). 

4.2.2.2 Inflows from Discharges 

Seventeen (17) NPDES permittees with discharges that contribute to the top 90 percent of the cumulative Flow, ft3/sec

flows among 144 discharges were requested to submit the daily average effluent flows. These daily average 

inflows (577 data points per discharge) were used in the model for the calibration period. For the rest of the 

discharges, a mean flow value per discharge for the entire calibration period was calculated using the Permit 

Compliance System (PCS) data, and used in the model. More detailed description can be found in the model 

calibration report (DRBC, 2003b). Four water intake withdrawals were also incorporated into the model. 

Those four intakes were: the City of Philadelphia, Torresdale; City of Burlington; Bristol Borough; and 

Lower Bucks County JMUA. Daily average intake flow data were obtained from the City of Philadelphia 

for the Torresdale intake and incorporated into the model. The other, three intakes were assigned their 

average intake flow rate value. 

4.2.3 Current Velocity 

Limited current velocity data were available during the model calibration period. The Acoustic Doppler 

Current Profiler (ADCP) was deployed in the mid section of the Estuary to measure the current velocity 

19
profiles in a number of transects by the University of Delaware. The data were obtained through the personal 

contact and used to confirm the performance of the model. (Personal communication with Dr. Christopher 

Sommerfield). 

4.3 Calibration of the DYNHYD5 Hydrodynamic Model 

4.3.1 Code Modification 

The original DYNHYD5 source codes had been modified to reduce the simulation time in the earlier version 

of DYNHYD5 model for the Delaware River Estuary. Most of the modifications were performed to comment 

out the linkage with the graphic output processing subroutines. In this version, additional modifications were 

required to incorporate the larger number of junctions and channels, larger number of variable inflows, and 

longer time series inputs. The dimensions of the corresponding variables in ‘Dynhyd.CMN’ file were 

therefore updated. 

4.3.2 Assignment of Open Boundaries With Forcing Tides and the Computational Time Step 

Two downstream boundaries were assigned with the forcing tidal heights. One was located at the Mouth of 

the Bay (Lewes, DE) and the other was at the Western end of C & D canal (Chesapeake City, MD). A 

combination of the measured high and low tidal heights and hourly observed tidal heights were input into the 

model along with the corresponding times for the mainstem downstream boundary at Lewes, DE. The 

derived hourly tidal heights from the hourly observed data at the Reedy Island gaging station were assigned 

as forcing tides at the C&D Canal boundary. The relationship for tidal heights at Chesapeake City from 

Reedy Island station was obtained from the NOAA (International Marine, 2001). The average phase lag was 

about 55 minutes (high and low tides at Chesapeake City were 55 minutes ahead of Reedy Is. Station’s) and 

amplitude correction factor was 0.5 (multiply 0.5 to the Reedy Is. Station’s tidal heights). The forcing tidal 

heights at both boundaries were adjusted to NGVD1929 datum before incorporated into the model. 

The computational time step for the DYNHYD5 hydrodynamic model was set to 30 seconds to maintain the 

stability of the model. 

4.3.3 Determination of Manning’s Coefficients 

The Manning’s coefficient (n) plays an important role on water movement in the DYNHYD5 hydrodynamic 

model. Manning’s coefficient was the key factor in calibrating the advective movement of the water mass. 

The basic sensitivity of the model’s responses to the assigned Manning’s coefficients revealed that assigning 

a larger Manning’s coefficient slowed down the tidal propagation and decreased the tidal amplitude. Smaller 

Manning’s coefficients resulted in faster tidal propagation and increased tidal amplitude, as expected. 

Assignment of too large or too small of Manning’s coefficients could cause the instability of the model. 

To have a better fit in the regression between the simulated and the observed tidal heights, numerous 

combinations of Manning’s coefficients sets were tested. From these, acceptable values were assigned for 

the sections of the model’s domain. The assigned Manning’s coefficients are summarized graphically in 

Figure 4-4. 

20
Lower Bucks Intake

Bristol & Burlington Intake

Neshaminy

Zone 2 

Torresdale Intake 

Zone 3 

Schuylkill 

Darby 

Zone 4 

Brandywine 

Christina 

Zone 5 

C&D Canal 

Zone 6 

RM 

Crosswicks 

67 

Rancocas 

Pensauken 

53 Cooper 

Newton 

41 

39 

37 

35 Raccoon 

21 20 

18 

19 

13 14 Salem 

101 

98 

100

99 

102 

95 

96 

97 

77 

2 

92 

17 

22 

12 

78 

11 

31 

25 

24 

23 

36 

34 

33 

32 

44 

43 

42 

38 

52 

51 

49 

48 

59 

58 

56 

55 

64 

63 

62 

60 

69 

68 

66 

74 

72 

71 

70 

90 

76 

75 

Trenton Manning's n 

133.3 Sec/m1/3

132.0

130.6

129.0

127.3 0.040 

124.9 

122.6 

120.7 

118.6 

116.8 

115.0 

113.2 0.035 

111.5 

109.5 

107.8 

105.4 

104.0 

101.6 

99.4 

96.9 

95.5 

92.3 0.020 

89.7 

87.7 

86.5 

84.8 

82.2 

80.0 

77.3 

75.1 0.016 

72.2 

70.8 0.010 

68.1

65.5

63.0 0.015

60.6

60.2

58.6

54.9

53.3 0.010 

51.9 

50.5 

48.3 

46.9 

45.0 

42.6 

39.6 

35.8 

28.7 0.017 

18.6 

8.0 

1.2 

Mouth of Bay 

Figure 4-4: Assigned Manning’s coefficients for the main channel of the model segments. Only the 

main stem of the Delaware Estuary is shown. 

21
4.3.4 Influence of the C&D Canal

While calibrating the hydrodynamic model, it was found that the C&D Canal played a very important role

in chloride concentration profiles in the lower part of the Delaware Estuary. The direction and the magnitude

of the net flow between the Chesapeake and Delaware Estuary made a significant impact on the chemical

transport in the Delaware Estuary. The Manning’s coefficient for the channels within the C&D Canal was

assigned with a value of 0.030, which was comparable with the earlier study result (n=0.026) performed by

Gardner and Pritchard (1974). In addition, the predicted amplitude of the tidal velocity was maintained at

about 1.0 m/sec within the C&D Canal and this was confirmed by Dr. Kuo-Chuin Wong of the University

of Delaware and Dr. William Boicourt of the University of Maryland (personal communications).

4.3.4.1 Issue Statement

Direction of net flow and magnitude

During the early stage of the calibration process, the direction of the net flow within the C&D Canal was

predicted to be westward (from the Delaware into the Chesapeake Estuary) with an average flow rate of about

300 m3

/sec by the model. These results were contradictory to the number of earlier study results (Gardner

and Pritchard, 1974; Pritchard and Gardner, 1974; Thatcher and Najarian, 1981; Johnson et. al., 1999). All

of the previous field and modeling study results revealed that the long-term net flow within C&D Canal had

eastward flow direction with net flow rates ranging from 30 to 259 m3

/sec in their studies. 

Chloride Gradient in the Delaware Estuary

The water quality model was run with the hydrodynamic model output which contained the westward C&D

net flow condition. Dispersion coefficients in the water quality model were set to zero for the whole estuary

in this run. The chloride concentration for the downstream boundary at Lewes, DE was set at 16,000 mg/L.

Note that the simulation period was from August 2001 to November 2002 for these calibration runs (See the

Section 2.2 of the concept of the rolling calibration regarding the differences in the simulation period). 

The temporal variations of the simulated chloride concentrations at River Mile (RM) 54 were plotted along 

with the daily freshwater inflows at Trenton, NJ (Figure 4-5). As shown in Figure 4-5, the chloride 

concentrations in the Delaware Estuary were greatly influenced by the upstream freshwater inflows. During 

the low freshwater inflow period, a significant ocean water intrusion was simulated. The chloride 

concentrations were dropped significantly during the high freshwater inflow conditions, as expected. The 

simulated chloride concentrations were compared with the observed data at River Mile 54 (Figure 4-6). The 

model over-predicted the chloride concentrations, especially during the low freshwater inflow period. One 

of the main reasons was that the C&D Canal withdrew water from the Delaware Estuary, causing water from 

the ocean moving up during the low freshwater inflow period. Because the model was already set with zero 

dispersion coefficients, there was no other mechanisms to depress the chloride intrusion from the ocean. 

22
23

-

2,000

4,000

6,000

8,000

10,000

12,000

14,000

8/1/01 10/1/01 12/1/01 1/31/02 4/2/02 6/2/02 8/2/02 10/2/02 12/2/02

Chloride Conc., mg/L

-

200

400

600

800

1,000

1,200

1,400

Flow at Trenton, m3/sec

Simulated chloride concentration Daily flow at Trenton, NJ

0

2000

4000

6000

8000

10000

12000

14000

16000

8/1/01 10/1/01 12/1/01 1/31/02 4/2/02 6/2/02 8/2/02 10/2/02 12/2/02

Chloride Conc., mg/L

Observed_USGS Simulated

Figure 4-5: Temporal variations of the simulated chloride at RM 54 related to the inflows at Trenton.

Figure 4-6: Temporal variations of the simulated and the observed chloride concentration at RM 54.
24

0

2000

4000

6000

8000

10000

12000

14000

8/1/01 10/1/01 12/1/01 1/31/02 4/2/02 6/2/02 8/2/02 10/2/02 12/2/02

Chloride Conc., mg/

L

0cm shift 10cm Shift 20cm Shift

4.3.4.2 Approach and Modification to the Tidal Datum at Chesapeake City, MD

Because the manipulation of dispersion coefficients could not resolve the intrusion of chloride, an advective

movement correction was performed within the C&D Canal. adjustment was required to

correctly simulate the direction and magnitude of the net flow through the C&D Canal. The major

components that determined the direction and the magnitude of the flows within the C&D Canal were the

tidal heights at both ends of the Canal, Chesapeake City and Reedy Point, in this model. 

adjustments on the tidal heights at the Chesapeake City would be made and not to make any adjustment on

tidal heights at Reedy Point Station, because the tidal heights at Reedy Point were actually observed. On the

other hand, the tidal heights at the Chesapeake City were derived from the Reedy Point station’s observed

data. To force the net flow direction eastward (from Chesapeake to Delaware Estuary), the tidal heights at

the west end (Chesapeake City) were raised. datum at Chesapeake City was shifted up at different

levels and compared to the results of the sensitivity simulations on chloride concentrations (Figure 4-7). 

(10) centimeters up-shift of the tidal datum at the Chesapeake City was chosen based upon the simulated

chloride concentration profiles.

Figure 4-7: Sensitivity simulation results: Impact on chloride concentrations by the datum shift at the

Chesapeake City. 

A certain level of 

It was decided that

The tidal

Ten
4.3.4.3 Confirmation of the Datum Adjustment 

Even though the monitoring of the long-term flow, or the actual tidal heights at Chesapeake City with a 

survey of the station’s datum would be the only way to clearly justify this adjustment, a number of previous 

studies and the modeling results reenforced the approach we took in this modeling work. 

With 10 centimeter of up-shift of the datum at Chesapeake City, the model simulated the net flow direction 

of eastward. This result agreed with the earlier studies described in the Section 4.3.4.1. In addition, Thatcher 

and Najarian (1981) applied same approach to force the net flow direction to east in their previous modeling 

work. Lastly, a crucial justification may be observed in the setup in the recently developed Chesapeake Bay 

Model (Wang and Johnson, 2002). In their model, the C&D Canal was treated as a river boundary and a 

constant flow rate of 21.24 m3

/sec was assigned. The direction of flow was from the Chesapeake toward the 

Delaware Bay. The sensitivity simulation results on datum shift for the entire calibration period (577 days) 

are summarized in Table 4-4. The direction of the long-term net flow changes at a point between 5 and 10 

centimeters datum shift. With 10 centimeter shift, the net flow amount for the entire calibration period was 

simulated to be 20.6 m3

/sec, which was almost exact amount of flow rate assigned in Chesapeake Bay Model. 

Table 4-4: The direction and magnitude of the simulated, long-term net flow in C&D Canal with 

various amount of datum shift. 

Scenario 

Direction of net flow 

Magnitude of the net flow (m3

/sec) 

Datum Up-shift amount 

cm 

Calibration period 

(577 days) 

Feb 2002 to Jan 2003 

(365 days) 

0 West 246 257 

5 West 114 126 

10 East 20.6 19.1 

15 East 158 148 

20 East 298 297 

25
4.4 Calibration Results 

The input file for DYNHYD5 hydrodynamic model for the calibration period is provided in Appendix A. 

Because of the file size, portions of the daily inflows and forcing tide input sections were shortened. 

4.4.1 Comparisons with Current Velocity 

ADCP results from eleven transects were selected to compare with the hydrodynamic model outputs. The 

current velocity profile data for those 11 transects were post-processed to obtain the average velocity and then 

the results were compared with the simulated current velocity. Review of the plots and results of regression 

(a) 

(b) 

Figure 4-8: Comparison between the observed and the simulated current velocity: (a) Spatial plot; (b) 

Linear regression results. 

26
analyses confirms that the model reproduces the current velocity relatively well both spatially and temporally 

(Figures 4-8 (a) and (b)). 

4.4.2 Calibration Results of the Tidal Heights 

The simulated tidal heights are compared with the observed tidal heights at six tide gaging stations. The 

observed data and the simulated tidal heights are presented in four types of plots per station. The four plots 

are: (a) temporal plot for the entire calibration period; (b) temporal plot for the last 3 weeks of the calibration 

period; (c) linear regression plot; (d) cumulative frequency distribution plot. Figures 4-9 a, b, c and d 

represent the comparison plots at the Reedy Point Station as an example. The tidal height comparison plots 

for the rest of the stations are presented in the Appendix C. The temporal comparison plots showed good 

agreement between the observed data and the simulated results for both the amplitudes and the phases of the 

tidal heights. The results of the linear regression between the observed data and the simulated tidal heights 

are summarized in Table 4-5. If simulated and observed data are equal, then the slope would be one and 

intercept would be zero. The slopes were ranged from 0.945 to 1.027 and the intercepts were ranged from 

-0.087 to 0.035. The square of the correlation coefficients (R2

) were varied from 0.930 to 0.994. The 

cumulative frequency distribution plots show a good agreement between the simulated and the observed tidal 

heights throughout the ranges of the tidal heights. 

Table 4-5: The summary of the regression results between the observed data and the simulated tidal 

heights. 

Station Name River Mile Slope Intercept R2 

Brandywine Shoal 8.0 0.973 0.005 0.994 

Reedy Point 58.6 0.961 0.035 0.937 

Philadelphia 99.4 1.027 -0.087 0.941 

Tacony-Palmyra 107.8 1.026 0.012 0.934 

Burlington 118.6 0.979 -0.075 0.942 

Newbold 127.3 0.945 0.010 0.930 

The calibrated DYNHYD5 hydrodynamic model successfully reproduced the tidal heights. The model 

generated the tidal heights reasonably well on both the amplitudes and the phases of the tidal heights. Along 

with the current velocity confirmation results and tidal height comparison results, the calibrated DYNHYD5 

hydrodynamic model for the Delaware River Estuary correctly generates the advective movement of the water 

mass. 

27
28

Tidal height comparison at Reedy Point (Node 10: RM 58.6)

-1.5

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

2.5

09/01/01 11/01/01 01/01/02 03/03/02 05/03/02 07/03/02 09/02/02 11/02/02 01/02/03 03/04/03

Date

Tidal height, meter

Observed (NOAA) Simulated

Tidal height comparison at Reedy Point (Node 10: RM 58.6)

-1.5

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

2.5

03/10/03 03/12/03 03/14/03 03/16/03 03/18/03 03/20/03 03/22/03 03/24/03 03/26/03 03/28/03

Date

Tidal height, meter

Observed (NOAA) Simulated

(a)

(b)

Figure 4-9: The observed and the simulated tidal heights at Reedy Point (River Mile 58.6): (a) for the

entire calibration period; (b) from the period March 10, 2003 to March 31, 2003.
29

Obsrved vs. Simulated Tidal Height at Reedy Point (Node 10: RM 58.6)

y = 0.9608x + 0.0347

R2

 = 0.9374

-1.5

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

-1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0

Observed tidal height, m

Simulated tidal height, 

m

Simulated 1:1 Line Linear (Simulated)

Cumulative Plot of Tidal Heights 

at Reedy Pt. (Node 10: RM 58.6)

-2

-1

0

1

2

3

0% 20% 40% 60% 80% 100%

Cumulative Percentage, %

Tidal Height, meter

Observed Simulated

(c)

(d)

Figure 4-9: The observed and the simulated tidal heights at Reedy Point (River Mile 58.6): (c) Linear

regression results (n=13,777); (d) cumulative frequency distribution curve.
5 CALIBRATION OF WATER QUALITY (CHLORIDE) MODEL 

As a part of the hydrodynamic model calibration, the original TOXI5 model was linked with the outputs from 

the calibrated DYNHYD5 model. Fifteen (15) minutes of the computational time step was used for the water 

quality model. TOXI5 model was then calibrated against the chloride concentrations to determined the 

dispersive mixing within the Estuary. Chloride concentrations were traced throughout the model domain and 

compared with the observed data with various sets of assigned dispersion coefficients. The main objective 

in this calibration process was to determine a set of advection factor and dispersion coefficients for the water 

quality model. 

5.1 Water Quality Model Segmentation 

The segmentation of the water quality model was established through one to one mapping with the 

segmentation of the DYNHYD5 hydrodynamic model. Because the water quality model (TOXI5) required 

boundary flows from outside its network, one junction above each of the TOXI5 boundary segments was not 

mapped. Thus, the total number of segments for the water quality model became 87. The schematic diagram 

of the water quality model segmentation is depicted in Figure 5.1. 

30
RM Trenton RM 

133.3 

132.0 

130.6 

129.0 

Zone 2 127.3 

124.9 

122.6 

120.7 

119.0 118.6 

Neshaminy 65 116.8 

115.0 

113.2 

111.5 

109.5 

107.8 

105.4 

Zone 3 104.0 

101.6 

67 

53 

41 

39 

37 

35 

21 20 

18 

19 

13 14 

76 

75 

17 

74 

72 

71 

70 

69 

68 

66 

64 

63 

62 

60 

59 

58 

56 

55 

52 

51 

49 

48 

44 

43 

42 

38 

36 

34 

33 

32 

31 

25 

24 

23 

80 

81 

87 

22 

12 

78 

11 

82 

83 

84 

86

85 

77 

2 

101.7 

99.4 

96.9 

95.5 

92.3 

89.7 

Schuylkill 47 46 45 

Zone 4 87.7 

Darby 40 86.5 87.0 

84.8 

82.2 82.0 

81.0 

80.0 

77.3 

Brandywine 75.1 

72.2 

70.8 

30 

Christina 29 28 27 26 

Zone 5 68.1 

65.5 

63.0 

60.7 60.6 

60.2 

60.1 

58.6 58.7 

54.9 

53.3 

51.9 

50.5 

48.3 

46.9 

45.0 

42.6 

39.6 

35.8 

C&D Canal 1 3 4 5 6 7 8 9 10 

Zone 6 28.7 

18.6 

13.5

8.0 

Mouth of Bay 

Figure 5-1: Schematic diagram of the segmentation for the water quality model. 

73 Crosswicks 

61 Rancocas 

57 Pensauken 

54 Cooper 

50 Newton 

79 Raccoon 

15 16 Salem 

31
5.2 Data Compilation and Processes 

One of the biggest merits in calibrating a hydrodynamic model in an estuarine system is the existence of the 

natural conservative chemical. Salt content is usually used as a part of the hydrodynamic model calibration 

process in an estuarine system. Because of our rolling calibration approach (i.e., longer time period), using 

the salt content as a calibration parameter seemed to be a logical choice rather than performing a dye study. 

The salt content can be expressed in a number of ways. The direct expression of the salt content, salinity, was 

usually in units of parts per thousand (ppt). The chloride concentration in milligrams per liter is another way 

of expressing the salt content. The chloride concentration is typically obtained by laboratory testing. On the 

other hand, the specific conductance (or conductivity) is another way to express salinity. The specific 

conductance is basically a measurement of the electrical transmisivity (in a unit of micro Siemens per 

centimeter), which can be affected by other minerals in ambient water. However, in highly saline water 

environment, the impact from other mineral content is much smaller than that from the chloride content. The 

limitation of using the specific conductance as a surrogate measurement for salinity is not clearly defined. 

All three types of available salt content data were compiled for the Delaware Estuary from late 90s to March 

2003. The chloride concentration was chosen to be the form of salt content in this model calibration, thus 

all the compiled data were converted into chloride concentration before use. 

5.2.1 DRBC (BoatRun) Monitoring Data 

Boatrun data, which is the water quality monitoring program run by DRBC throughout the Estuary, were used 

in the chloride calibration. Water samples were collected at a depth of three feet below the water surface and 

were targeted for the slack tide conditions. Because of slack tide sampling, it could be assumed that the 

collected data represented the full range of chloride concentrations for the monitoring station. A total of 

twenty-two (22) stations were monitored and the sampling frequency was either 12 or 7 times per year, 

depending on the location of the station. The benefit of these data sets was that chloride concentration was 

actually measured in the laboratory. Therefore, any conversion process was not required. The observed 

chloride data sets were used as calibration targets and also used to assign the mainstem upstream and 

downstream boundary conditions. 

5.2.2 USGS Continuous Monitoring Stations 

Water temperature and specific conductance were measured using automatic monitors hourly at four locations 

along the Estuary by USGS. Those four stations are: (1) Reedy Is. Station (RM 54); (2) Chester Station (RM 

82); (3) Fort Mifflin Station (RM 92); and (4) Ben Franklin Station (RM 100). No data were collected during 

the winter season with exception of the Reedy Island Station. Hourly specific conductance and water 

temperature data were downloaded from the USGS Automated Data Processing System (ADAPS). The 

hourly observed specific conductance were then converted into chloride concentration for use with the 

hydrodynamic model calibration. 

5.2.3 Other Sources of Data 

1. Chloride data collected in Schuylkill River by Academy of the Natural Science: Measured chloride 

data for the Schuylkill River were available for the time period of 1999 and 2000. These data sets 

were used to assign the boundary conditions at the Schuylkill River. 

2. The chloride concentration data within the C&D Canal were provided by DNREC (Richard Greene, 

DNREC, personal communication), and these data sets were used in assigning the C&D Canal 

boundary. 

32
5.2.4 Data Process 

DRBC’s (BoatRun) chloride concentration data were directly compared with the model outputs without any 

data manipulation. However, the continuous monitored data collected by USGS required conversions. Using 

time series specific conductivity and water temperature data, the salinity was calculated using a relationship 

provided by DNREC (Greene, 1998). This specific conductance to salinity relationship was claimed to be 

valid over a wide range of the salinity (0 to 40 ppt). The calculated salinity values were then converted into 

chloride concentration by applying the simple relationship (APHA, 1995). 

Chloride concentration (mg/L) = Salinity (ppt) x 1000 / 1.80655 

These converted time series chloride data at four USGS stations were then compared with the observed 

BoatRun chloride concentration data to validate the conversion relationship. The comparison results are 

provided in the Figures 5-2 through 5-5. Note that the y-axis scales are different in all four figures. The 

derived and observed chloride concentrations show a good agreement for the data collected at the Reedy 

Island station. Because the locations did not coincide between the DRBC and the USGS stations, the 

observed data from two DRBC monitoring stations were used to bound the derived data for both Chester 

(Figure 5-3) and Fort Mifflin (Figure 5-4) USGS stations. During the high flow period (March to June 2002), 

both the observed and derived chloride concentrations were below 200 mg/L except at the Reedy Island 

station. The conversion relationship between chloride concentration and salinity appeared to breakdown 

where the chloride concentrations are less than 200 mg/L. The derived chloride concentrations were 

systematically higher than the concentrations observed by DRBC monitoring program (Figures 5-3, 5-4 and 

5-5). For this reason, a caution is needed in interpreting the model performance when the converted chloride 

data are used to compare with the model outputs. Both the derived and observed chloride concentrations were 

below 200 mg/L at all time for the Ben Franklin Bridge Station. Figure 5-5 shows a clear discrepancy 

between the derived and the observed chloride concentrations collected at Ben Franklin Bridge station. With 

this observation, the derived chloride concentration data at the Ben Franklin Bridge station were not used in 

this model calibration. 

Further development of a relationship is required between salinity and chloride concentration in low regime 

of chloride concentrations in order to utilize all the data collected at the four USGS stations in the Delaware 

Estuary. 

33
12000 

10000 

8000 

6000 

4000 

2000 

0

8/1/01 10/1/01 12/1/01 1/31/02 4/2/02 6/2/02 8/2/02 10/2/02 12/2/02

Chloride Conc. converted from Reedy Is. Station DRBC Monitored Data 

Figure 5-2: Temporal comparison of chloride concentrations derived from the USGS monitored specific 

conductance data and the monitored chloride data at the Reedy Island station. 

1800 

1600 

1400 

1200 

1000 

800 

600 

400 

200 

0

8/1/01 10/1/01 12/1/01 1/31/02 4/2/02 6/2/02 8/2/02 10/2/02 12/2/02

Chloride Conc. converted from Chester Station Boatrun-84.0 Boatrun-78.1 

Figure 5-3: Temporal comparison of chloride concentrations derived from the USGS monitored specific 

conductance data and the monitored chloride data at the Chester station. Chloride Conc., mg/L Chloride Conc., mg/L 

34
500 

450 

400 

350 

300 

250 

200 

150 

100 

50 

0

8/1/01 10/1/01 12/1/01 1/31/02 4/2/02 6/2/02 8/2/02 10/2/02 12/2/02

Chloride Conc. converted from Ft. Mifflin Station Boatrun-93.2 Boatrun-87.9 

Figure 5-4: Temporal comparison of chloride concentrations derived from the USGS monitored specific 

conductance data and the monitored chloride data at the Fort Mifflin station. 

180 

160 

140 

120 

100 

80 

60 

40 

20 

0

8/1/01 10/1/01 12/1/01 1/31/02 4/2/02 6/2/02 8/2/02 10/2/02 12/2/02

Chloride Conc. converted from Ben Franklin Station Boatrun-100.2 

Figure 5-5: Temporal comparison of chloride concentrations derived from the USGS monitored specific 

conductance data and the monitored chloride data at the Ben Franklin station. Chloride Conc., mg/L Chloride Conc., mg/L 

35
5.3 Calibration of the Chloride Water Quality Model 

5.3.1 Assignment of the Boundary Conditions 

Because of the lack of observed time series chloride concentration data, constant values were assigned at the 

boundaries throughout the calibration period. Detailed descriptions of determining the boundary conditions 

are listed below. 

1. The segment for the downstream boundary of the main stem Delaware Estuary occupied 

from River Mile 3 to 12.6, which is a relatively large size. The observed chloride 

concentration temporally varied from 9,000 to 18,000 mg/L within the downstream boundary 

segment according to the DRBC’s four years of monitoring data. With the lack of the time 

series data points at the boundary, the median value of 15,000 mg/L of chloride 

concentration was assigned. 

2. The boundary condition for the C&D Canal was set at 550 mg/L after reviewing the 

available data and the previous modeling work. 

3. The observed chloride data at the most upstream sampling station of the DRBC’s monitoring 

program (BoatRun) were used to determined the upstream boundary condition. The data was 

tightly bounded with median chloride concentration of 21 mg/L. For the mainstem upstream 

boundary, the Delaware River at Trenton, the boundary chloride concentration was assigned 

with 21 mg/L. 

4. The chloride concentration at Fairmount Dam, the upstream boundary for the Schuylkill 

River, varied from 20 to 59 mg/L with a median value of 34 mg/L. The upstream boundary 

chloride concentration for the Schuylkill River was assigned with 34 mg/L. 

5. The rest of the minor tributaries were assigned with the chloride concentrations ranging from 

7 to 24 mg/L after reviewing the previous modeling works (DRBC, 1998; HydroQual, Inc., 

1998). 

5.3.2 Determination of the Advection Factor (ADF) and Dispersion Coefficients 

Two parameters were adjusted during the calibration process, the advection factor and longitudinal dispersion 

coefficients. The advection factor (0 to 0.5) is used by TOXI5 model to modify the finite difference 

approximation of the advection term in the mass balance differential equation. A non-zero ADF reduces the 

numerical dispersion produced by a particular velocity, channel length, and time step combination. However, 

assignment of non-zero ADF could cause instability of the model. ADF of 0.3 was assigned in the Version 

1.0 model, while 0.37 was assigned for this version of the model to reduce the numerical dispersion. The 

increase of the ADF was necessary to reduce the numerical dispersion in the Bay (Zone 6) segments with 

large segment sizes. The computational time step was determined to be 15 minutes. 

Along with the advection factor adjustment, sets of the dispersion coefficients were tested. The assigned 

dispersion coefficients for the TOXI5 model are graphically summarized in Figure 5-6. Because of the large 

segment sizes, zero dispersion coefficient was assigned for the segments in the lower portion of the Bay. 

36
RM Trenton RM 

133.3 

132.0 

130.6 

Crosswicks 

67 119.0 

Rancocas 

Pensauken 

53 101.7 Cooper 

Newton 

41 

39 

37 82.0 

35 81.0 Raccoon 

21 20 60.6 

18 

19 60.1 

13 14 58.7 Salem 

76 

75 

74 

72 

71 

70 

69 

68 

66 

64 

63 

62 

60 

59 

58 

56 

55 

52 

51 

49 

48 

44 

43 

42 87.0 

38 

36 

34 

33 

32 

31 

25 

24 

77 

2 

80 

23 

22 

12 

78 

83 

84 

86 13.5

85 

17 

87 

81 

82 

11 

Dispersion Coefficients,

m

2

/sec 

129.0 

127.3 

124.9 

Lower Bucks Intake 122.6

120.7

Bristol & Burlington Intake 118.6

Neshaminy 116.8 

115.0 

Zone 2 113.2 

Torresdale Intake 111.5 

109.5 

107.8 30 105.4 

104.0

Zone 3 101.6 

99.4

96.9

95.5

Schuylkill 92.3

89.7

87.7

Darby 86.5

Zone 4 84.8

82.2

80.0

77.3

75.1 50 Brandywine 72.2 

Christina 70.8 

68.1 

Zone 5 65.5 

63.0

60.6

60.2 100

C&D Canal 58.6 

54.9 

53.3 

51.9 

50.5 250 48.3

46.9

45.0

42.6 140

39.6

35.8

Zone 6 28.7 

18.6 0 

8.0 

Mouth of Bay 

Figure 5-6: Assigned dispersion coefficients for the water quality model. The main stem of Delaware 

Estuary is only shown in the schematic. 

37
5.4 Calibration Results of Chloride Concentrations 

5.4.1 Comparison with the DRBC Data 

The model input file for the chloride calibration is provided in Appendix B. The simulated chloride 

concentrations at 19 segments were compared with the observed DRBC Boatrun data . The temporal chloride 

comparisons are presented in the Appendix D. Figures D-3 and D-4 show that the model tends to over-predict 

the chloride concentrations in a lower portion of the Bay (River Miles between 20 and 36). This overprediction might be associated with the coarse grid segmentation in the lower portion of the Bay. Numerical 

dispersion is believed to be the main cause for this over-prediction. However, the main objective in the 

development of Version 2.0 of the hydrodynamic model were (1) to generate an acceptable temporal chemical 

trend at the Zone 5 / Zone 6 interface; (2) to simulate proper advective and dispersive transport of chemical 

mass within the Estuary. The simulated chloride results at the Liston Point (River Mile 48.2; boundary 

between Zones 5 and 6) show a strong positive relationship with the observed chloride data (Figure D-5). 

Cumulative frequency distributions for the observed and the simulated chloride concentrations were 

calculated for the segments around the Zones 5 and 6 interface. The three segments used in calculations were 

node 17 (RM 45), node 2 (RM 48), and node 12 (RM 55) and their corresponding observed data from Smyrna 

R., Liston Pt., and Reedy Is. monitoring stations. The calculated results were then plotted in Figure 5-7. 

Figure 5-7 clearly shows that the model reproduces the observed chloride concentrations around the Zones 

5 and 6 interface correctly. As shown in the Figures D-6 through D-19 from the Appendix D, there was a 

good agreement between the simulated chloride concentrations and the observed data at the individual 

100,000 

10,000 

1,000 

100 

10 

1 

0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 

Cumulative Percentage 

Observed Simulated 

Figure 5-7: Cumulative frequency distributions of the observed and the simulated chloride 

concentrations: Data from three segments (Node 2, 12 and 17) were combined. 

Chloride Concentration, mg/L 

38
monitoring stations throughout the Estuary. The observed and the simulated chloride concentration data were 

re-organized to check the model performance on the spatial scale. The monitoring data and the minimum, 

maximum and median values of the model outputs for the main channel segments of the Estuary are compared 

in Figure 5-8. River Mile (RM) zero indicates the Mouth of the Delaware Bay at Lewes, DE., and RM 133 

is the location of head of the tide at Trenton, NJ. The observed chloride data were well bounded by the 

minimum and maximum values of the model outputs, and the median values of model outputs generally split 

the observed data. 

All of the comparison plots between the observed and the simulated chloride concentrations indicated that 

the model was able to reproduce the temporal and spatial trends, and the magnitude of the chloride 

concentrations within a reasonable range throughout the tidal portion of the Delaware River. The calibrated 

model therefore properly simulates the advective and dispersive movement of the chloride for the entire 

Estuary. 

20000 

18000 

16000 

14000 

12000 

10000 

8000 

6000 

4000 

2000 

0 

0 10 20 30 40 

Simulated (Minimum) 

chloride conc., mg/L 

Zone 6 Zone 5 Zone 4 Zone 3 Zone 2 

50 60 70 80 90 100 

River Mile 

Simulated (Maximum) Simulated (Median) 

110 120 130 140 

Observed (01-02) 

Figure 5-8: Spatial comparison between the observed data (DRBC_BoatRun) and the simulated chloride 

concentrations throughout the Estuary. 

39
5.4.2 Comparison with USGS Data 

Simulated chloride concentrations were compared with chloride concentrations which were derived from the 

hourly observed specific conductance data measured by USGS. Because the data obtained from USGS 

stations are long-term continuous (hourly interval) measurements, the comparison with model outputs 

provides the performance check on the phase of the chloride movement in the estuary. The derived chloride 

concentration data from Ben Franklin Bridge station were not used in this comparison because of the low 

chloride concentration and the conversion issues described in the section 5.2.4. For the same reason, only 

the graphical comparison was performed for two stations: Fort Mifflin (River Mile 91.8) and Chester (River 

Mile 82.4). The comparisons of the simulated and the derived chloride concentrations over time are presented 

on Figure 5-9 for Fort Mifflin station and Figure 5-10 for Chester Station. The model successfully reproduces 

the temporal trend of the chloride concentrations in both locations. Again, the model tends to over-predict 

above 200 mg/L of chloride concentration regime and under-predict when the chloride concentrations were 

below 200 mg/L. A further investigation is required on the conversion issue to assess the model output results 

in a lower regime of chloride concentrations. Still, the model generally matches the peaks, as shown on 

Figures 5-9(b) and 5-10(b). 

The derived and the simulated chloride concentrations were presented in four types of comparisons for the 

Reedy Island station. The four plots were: (a) temporal plot for the entire calibration period; (b) temporal plot 

for the first week of September, 2002; (c) linear regression plot; (d) cumulative frequency distribution plot. 

Figures 5-11, 5-12, 5-13, and 5-14 represent the comparison plots at the Reedy Island station which is located 

at River Mile 54.2. Figures 5-11 and 5-12 are the comparison plots to check the performance of the model 

on temporal variations of chloride concentrations. As shown on Figure 5-11, the model predicted the general 

trend of the temporal variation properly. In addition, Figure 5-12 shows a reasonable prediction on the 

magnitude and the phase of the chloride variation. The linear regression result is shown on Figure 5-13 with 

slope of 1.036, intercept of -130 mg/L and R2

 of 0.87. Compared to the wide range of chloride concentrations 

(60 to 9,500 mg/L) during the calibration period, an intercept of -130 mg/L is a negligible bias. The 

cumulative frequency distribution plot shows a good agreement between the observed and the predicted 

results (Figure 5-14). The model slightly under-predicted in the low chloride range and over-predicted in 

high chloride concentration range. The median value for the USGS station at Reedy Is. was 3,000 mg/L while 

the model predicted 2,840 mg/L for the calibration period. This result yields -5.3 percent of relative error in 

the median chloride concentration prediction at the Reedy Is. station. 

Overall, the calibrated model successfully reproduces the temporal trend of the chloride concentration at three 

USGS continuous monitoring stations. 

40
41

0

100

200

300

400

500

600

9/1/01 12/1/01 3/2/02 6/1/02 8/31/02 11/30/02 3/1/03

Chloride Conc., mg/l

Derived_USGS Simulated

0

100

200

300

400

500

600

9/1/02 9/2/02 9/3/02 9/4/02 9/5/02 9/6/02 9/7/02 9/8/02

Chloride Conc., mg/l

Derived_USGS Simulated

(a)

(b)

Figure 5-9: Temporal comparison between the observed data (derived from specific conductance from

USGS Fort Mifflin Station) and the simulated chloride concentrations for (a) entire

simulation period; (b) first week of September 2002.
(a) 2,000 

1,800 

1,600 

Chloride Conc., mg/L

Chloride Conc., mg/l 

1,400 

1,200 

1,000 

800 

600 

400 

200 

-

9/1/01 12/1/01 3/2/02 6/1/02 8/31/02 11/30/02 3/1/03 

Simulated Derived_USGS 

(b) 2000 

1800 

1600 

1400 

1200 

1000 

800 

600 

400 

200 

0

9/1/02 9/2/02 9/3/02 9/4/02 9/5/02 9/6/02 9/7/02 9/8/02

Derived_USGS Simulated 

Figure 5-10: Temporal comparison between the observed data (derived from specific conductance from 

USGS Chester Station) and the simulated chloride concentrations for (a) entire simulation 

period; (b) first week of September 2002. 

42
43

-

2,000

4,000

6,000

8,000

10,000

12,000

9/1/01 12/1/01 3/2/02 6/1/02 8/31/02 11/30/02 3/1/03

Chloride Conc., mg/L

Derived_USGS Simulated

-

2,000

4,000

6,000

8,000

10,000

12,000

9/1/02 9/2/02 9/3/02 9/4/02 9/5/02 9/6/02 9/7/02 9/8/02

Chloride Conc., mg/L

Derived_USGS Simulated

Figure 5-11: Temporal comparison between the observed data (derived from specific conductance from

USGS Reedy Is. Station) and the simulated chloride concentrations for the calibration period.

Figure 5-12: Temporal comparison between the observed data (derived from specific conductance from

USGS Reedy Is. Station) and the simulated chloride concentrations for the first week of

September, 2002.
44

y = 1.0357x - 130.36

R2

 = 0.8733

-

2,000

4,000

6,000

8,000

10,000

12,000

- 2,000 4,000 6,000 8,000 10,000 12,000

Observed chloride concentration., mg/L

Simulated chlor. Conc., mg/

L

Reedy Is Linear (Reedy Is)

-

2,000

4,000

6,000

8,000

10,000

12,000

0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

Cumulative percentage, %

Chloride Conc., mg/L

Derived_USGS Simulated

Figure 5-13: Linear regression results between derived and simulated chloride concentrations at Reedy

Is. USGS station (n=13,660). oth data sets were hourly time interval throughout the

calibration period.

Figure 5-14: Cumulative frequency distributions of the observed and the simulated chloride

concentrations for the Reedy Island station.

B
6. FUTURE REFINEMENTS 

The performance of the Version 2.0 DYNHYD5 hydrodynamic model will be increased by incorporating 

following future works: 

1. Refinement of the segmentation in Zone 6. Use of smaller segmentation in zone 6 to reduce the 

numerical dispersion and increase the resolution of the concentration gradients. 

2. Use of the observed tidal heights at the C&D Canal boundary for forcing tides. 

3. Measurements of the long-term flow in C&D Canal to identify the direction and magnitude of 

exchanges between Chesapeake and Delaware Estuary. 

4. More frequent time series data collection of chloride concentrations at the major boundaries. 

5. Development of the relationship between the chloride and salinity to cover the low regime of salinity 

information derived from specific conductance data. 

6. Measurements of current velocities and incorporating into the calibration process. 

45
7 REFERENCES 

Ambrose, R.B., Wool, T.A., and Martin, J.L. 1993a. The Dynamic Estuary Model Hydrodynamics Program, 

DYNHYD5 Documentation and User Manual. US Environmental Protection Agency. 

Ambrose, R.B., Wool, T.A., and Martin, J.L. 1993b. The Water Quality Analysis Simulation Program, 

WASP5. Part A: Model Documentation. US Environmental Protection Agency. 

Ambrose, R.B., Wool, T.A., and Martin, J.L. 1993c. The Water Quality Analysis Simulation Program, 

WASP5. Part B: The WASP5 Input Dataset. US Environmental Protection Agency. 

American Public Health Association. 1995. Standard Methods for the Examination of Water and Wastewater. 

APHA, Washington, DC. 

DRBC. 1995. Calibration and Validation of the DYNHYD5 Hydrodynamic Model for the Delaware River 

Estuary. Estuary Toxics Management Program. Delaware River Basin Commission. West Trenton, New 

Jersey. December 1995. 

DRBC. 1998a. Calibration and Validation of a Water Quality Model for Volatile Organics and Chronic 

Toxicity in the Delaware River Estuary. Estuary Toxics Management Program. Delaware River Basin 

Commission. West Trenton, New Jersey. December 1998. 

DRBC. 1998b. Wasteload Allocations for Volatile Organics and Toxicity: Phase I TMDLs for Toxic 

Pollutants in the Delaware River Estuary. Estuary Toxics Management Program. Delaware River Basin 

Commission. West Trenton, New Jersey. December 1998. 

DRBC. 2003a. PCB Water Quality Model for Delaware Estuary (DELPCB). Delaware River Basin 

Commission. West Trenton, New Jersey. 

DRBC. 2003b. Calibration of the PCB Water Quality Model for the Delaware Estuary for Penta-PCBs and 

Carbon. Delaware River Basin Commission. West Trenton, New Jersey. 

DRBC 2003c. Total Maximum Daily Loads for Polychlorinated Biphenyls (PCBs) for Zones 2 - 5 of the 

Tidal Delaware River. Delaware River Basin Commission. West Trenton, New Jersey. 

Gardener, G.B. and Pritchard, D. W. 1974. Technical Report 87: Hydrographic and Ecological Effects of 

Enlargement of the Chesapeake and Delaware Canal: Appendix XV. Verification and Use of a Numerical 

Model of the C & D Canal. Final Report to The Philadelphia District, U.S. Army Corps of Engineers. 

Greene, R.W. 1998. Procedure for Computing Salinity from Temperature and Conductance Measurements. 

Delaware Department of Natural Resources and Environmental Control. 

HydroQual, Inc. 1998. Development of a Hydrodynamic and Water Quality Model for the Delaware River. 

Delaware River Basin Commission, West Trenton, N.J. 

International Marine. 2001. Tide Tables 2002: East Coast of North and South America. 

Johnson, B. H., Heath, R. E., Hsieh, B. B., Kim, K. W., and Martin, B. L. 1999. Assessment of Channel 

46
Deepening in the Chesapeake and Delaware Canal and Approach Channels in Upper Chesapeake Bay: 

Three-Dimensional Numerical Model Study. Draft Report. Waterways Experiment Station. Prepared for 

U.S. Army Engineer District, Philadelphia. 

National Ocean Service. Estuarine Bathymetry Data.

URL: http://spo.nos.noaa.gov/servlet/BuildPage?template=bathy.txt&parm1=M090

National Oceanic and Atmospheric Administration. Retrieve Observed Water Levels and Associated 

Ancillary Data. URL: http://www.co-ops.nos.noaa.gov/data_res.html 

Pritchard, D. W., Gardner, G. B. 1974. Technical Report 85: Hydrography of the Chesapeake and Delaware 

Canal. Chesapeake Bay Institute, The Johns Hopkins University. U.S. Army Corps of Engineers Contract 

No. DACW 67-71-C-0062. Philadelphia, PA. February 1974. 

Thatcher, L. M., Najarian, T. O. 1981. Comparison of Salt Intrusion in the Delaware Estuary Under the 

Influence of Pre- and Post- Enlargement Flows in C & D Canal. U.S. Army Corps of Engineers Contract 

No. DACW 61-80-C-0080. Najarian, Thatcher & Associates Inc. Closter, NJ. March 1981. 51pp. 

Wang, H. V., Johnson, B. H. 2002. Validation and Application of the Second Generation Three Dimensional 

Hydrodynamic Model of Chesapeake Bay. Water Quality and Ecosystem Modeling, 1., Kluwer Academic 

Publishers. The Netherlands. 2002. pp. 51-90. 

Wong, K-C, Garvine, R. W. 1984. Observations of Wind-Induced, Subtidal Variability in the Delaware 

Estuary. Journal of Geophysical Research, Vol. 89, No. C6. pp. 10589-10597. 

47
APPENDIX

A. Input File of the Calibrated DYNHYD5 Hydrodynamic Model (Version 2.0) 

B. Input File of the Calibrated Water Quality (chloride) Model

C. Calibration Results of the DYNHYD5 Hydrodynamic Model for the Delaware River Estuary 

D. Calibration Results of the Water Quality (chloride) Model for the Delaware River Estuary 

48