NOAA Technical Report NOS CS 18 

_____________________________________________________________________ 

Solute Dispersion Modeling in New York Harbor

Eugene Wei 

Theodore Caplow 

Peter Schlosser 

Silver Spring, Maryland 

May, 2004 

noaa National Oceanic and Atmospheric Administration 

---------------------------------------------------------------------------------- 

U.S. DEPARTMENT OF COMMERCE 

National Ocean Service 

Office of Coast Survey 

Coast Survey Development Laboratory
ii

TABLE OF CONTENTS 

LIST OF FIGURES ....................................................................................................................... iii 

LIST OF TABLES...........................................................................................................................v 

EXECUTIVE SUMMARY ........................................................................................................... vi 

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

2. HYDRODYNAMIC MODEL.....................................................................................................3 

2.1. Governing Equation............................................................................................................3 

2.2. Model Grid..........................................................................................................................4 

2.3. Air-Water Gas Transfer ......................................................................................................5 

3. TRACER CONCENTRATION MODELING ............................................................................9 

3.1. July 2002 Newark Bay Field Experiment and Simulation................................................10 

3.1.1. Simulation Set-Up ..................................................................................................10 

3.1.2. Daily Averaged Concentration...............................................................................13 

3.1.3. Longitudinal Concentration Profile........................................................................13 

3.1.4. Residence Time ......................................................................................................13 

3.2. June 2003 East River Field Experiment and Simulation ..................................................22 

3.2.1. SF6 Concentration Measurement ...........................................................................24 

3.2.2. Simulation Set-Up ..................................................................................................26 

3.2.3. Longitudinal Concentration Profile........................................................................28 

3.2.4. Simulated Daily Averaged Tracer Concentration Contours...................................30 

3.2.5. Vertical Profiles......................................................................................................30 

3.2.6. Center of Mass Movement .....................................................................................37 

3.2.7. Tracer Mass Inventory............................................................................................38 

4. CONCLUSIONS AND FUTURE WORK ................................................................................42 

ACKNOWLEDGMENT................................................................................................................43 

REFERENCES ..............................................................................................................................44 
iii

LIST OF FIGURES 

Figure 1.1. Map showing New York Harbor and The Port of New York/New Jersey including 

 PORTS stations and major tributaries........................................................................................2

Figure 2.1. New York/New Jersey Harbor model grid showing locations of water level gages and 

 current meter. .............................................................................................................................6 

Figure 2.2. New York/New Jersey Harbor model bathymetry, contours in meter. .........................7 

Figure 3.1. Injection location for July 14, 2002 field experiment. ..................................................9 

Figure 3.2.A typical boat track for July, 2002 SF6 field experiment covering Newark Bay, 

Arthur Kill , and Kill Van Kull. Dots indicate the tracer measurement location. ...................10 

Figure 3.3. Observed and climatological freshwater input from Passic River, NJ (upper) and 

surface wind at Sandy Hook, NJ (bottom) for July 2002 model simulation boundary forcing. 

 ..................................................................................................................................................11 

Figure 3.4. Observed water levels and astronomical tides at Sandy Hook, NJ and Kings Point, 

NY during July, 2002 Sf6 field experiment. ............................................................................11 

Figure 3.5. Model simulated water levels and observations at Bayonne Bridge, NY and The 

 Battery, NY.............................................................................................................................12 

Figure 3.6. Hourly model simulated current velocity (light line and open arrow head) and 

 observations (heavy line and solid arrow head) at Bergen Point, Newark Bay at (a) Layer 2, 

about 3 m below the surface; and (b) Layer 5, about 9 m below the surface. .........................12 

Figure 3.7. Observed (top, Caplow, et. al., 2003) and model simulated (bottom) daily averaged 

 surface SF6 concentration contour plots for July 15, 16, and 17, 2002. Dotted lines indicate 

the survey tracks. .....................................................................................................................15 

Figure 3.8. Observed (top, Caplow, et. al., 2003) and model simulated (bottom) daily averaged 

 surface SF6 concentration contour plots for July 18, 19, and 20, 2003. Dotted lines indicate 

survey tracks. ...........................................................................................................................16 

Figure 3.9. Observed (top, Caplow, et. al., 2003) and model simulated (bottom) daily averaged 

 surface SF6 concentration contour plots for July 21, 22, and 23, 2002. Dotted lines indicate 

survey tracks. ...........................................................................................................................17 

Figure 3.10. Total measured and model simulated SF6 inventory in the inner waterways

 (Newark Bay, Arthur Kill, and Kill van Kull) over 11 days, with fitted exponential decay

curves, indicating a decay constant of 0.29 day-1 and 0.21 day-1 for observed and simulated 

 tracer dispersion......................................................................................................................18 

Figure 3.11. Boat tracks from Newark Bay to Arthur Kill and simulated SF6 longitudinal 

 concentration (solid circle) compared with observations (open triangle) for Day 1 ((a) and (c), 

July 15, 2002) and Day 2 ((b) and (d), July 16, 2002).............................................................19 

Figure 3.12. Boat tracks from Newark Bay to Arthur Kill and simulated SF6 longitudinal 

 concentration (solid circle) compared with observations (open triangle) for Day 5 ((a) and (c), 

July 19, 2002) and Day 7 ((b) and (d), July 21, 2002).............................................................20 

Figure 3.13. Contour plot of residence time for the inland waterways including Newark Bay, Kill 

van Kull, and Arthur Kill.........................................................................................................21 

Figure 3.14. Injection location at East River for June 2003 SF6 field experiment. .......................22 

Figure 3.15. Time for flood and ebb injections relative to model tidal current at injection location 

near Hell Gate a NOS tidal current reference station. .............................................................23 

Figure 3.16. Typical survey boat tracks of June 2003 SF6 field experiment, June 18 and 21. 
iv

 The survey boat covers entire East River each Day. Surveys also cover lower Hudson River 

 conducted on June 21 and 29 and Harlem River on June 21, 24, 25, and 29. .........................23 

Figure 3.17. Tidally synchronized longitudinal tracer concentration contour plots after the flood 

(top) and ebb (bottom) injections.............................................................................................25 

Figure 3.18. Observed and climatological freshwater input from Hudson River, NY (upper) and 

 surface wind at Sandy Hook, NJ (bottom) for June 2003 model simulation river and surface 

boundary forcing......................................................................................................................26 

Figure 3.19. Observed water levels and astronomical tides at Sandy Hook, NJ and Kings Point, 

NY during June 2003 SF6 field experiment. ...........................................................................27 

Figure 3.20. Model simulated water levels and observations at Bayonne Bridge and 

The Battery...............................................................................................................................28 

Figure 3.21. Observed (top) and simulated (bottom) longitudinal SF6 concentration distribution 

after the flood injection from The Battery to the Throgs Neck, heavy lines for Days 1F, 3F, 

 and 5F and light lines for Days 2E, 4E, and 6E. Note the model grid boundary location at 

Throgs Neck.............................................................................................................................29 

Figure 3.22.Observed (upper panels) and simulated (lower panels) longitudinal tracer 

 Concentration for days 1 (left panels, Days 1F and 1E, July 18 and 26) and 2 (right panels, 

 Days 2F and 2E, July 19 and 27) after the flood (open circle) and ebb injection 

 (filled circle).............................................................................................................................31 

Figure 3.23. Observed (upper panels) and simulated (lower panels) longitudinal tracer 

concentration for days 3 (left panels, Days 3F and 3E, July 20 and 28) and 4 (right panels, 

 Days 4F and 4E, July 21 and 29) after the flood (open circle) and ebb injection 

 (filled circle).............................................................................................................................32 

Figure 3.24. Simulated daily averaged tracer concentration contour plots, Days 1F (June 18) to 

6F .(June 23) after the flood injection. Tracer exiting the model domain at northern boundary 

 is apparently on the first 2 days. .............................................................................................33 

Figure 3.25. Simulated daily averaged tracer concentration contour plots for Day 0E (June 25) to 

Day 5E (June 30) after the ebb injection .................................................................................34 

Figure 3.26. Observed (left, Caplow, et. al., 2004) and model simulated (right) vertical profiles 

of ... SF6 concentrations in the East River from three regions: (a) northern, (b) injection point, 

 and (c) southern of the river. Profiles locations are shown in the map....................................35 

Figure 3.27. Observed (left (a) and (b), Caplow, et. al., 2004) and model simulated (right) 

vertical SF6 profiles in the Hudson River following the flood and ebb injections, respectively. 

 Normalized SF6 concentration vs salinity (left (c)) for all profiles indicating peak SF6

concentrations at mid-depth matches salinities in the East River............................................36 

Figure 3.28. Movement of the center of mass (COM) of SF6 in the East River; (a) observed and 

(b) model. The COM of the SF6 background has been subtracted. Note that distance 0 located 

 at the injection location (near Hell Gate) and positive distance toward north. Note that June 

18 and 26 correspond to Days 1F and 1E, respectively...........................................................37 

Figure 3.29. Location of the center of mass time series from model simulated tracer in the East 

 River, relative to the injection point (distance 0) near Hell Gate for the flood (top) and ebb 

(bottom) injection, respectively. ..............................................................................................38 

Figure 3.30. Observed and model simulated daily SF6 mass inventory within the East River from 

The .Battery to Throgs Neck following flood and ebb injections, respectively, data (circle for 
v

 flood injection and diamond for ebb injection) with regression curves for flood (solid line) 

and ebb (dot-dashed) injections also plotted. Ebb injection decays much faster than the flood 

injection. Model simulated tracer mass decay rate is less than the measurement. ..................40 

Figure 3.31. Longitudinal surveys of SF6 in the Harlem River 1 and 4 days following the flood 

and ebb injections in the East River (Caplow, et. al., 2004)....................................................41 

LIST OF TABLES 

Table 3.1. Model simulated daily tracer mass loss at model grid boundary, Throgs Neck, 

following the flood and ebb injections.........................................................................39 

Table 3.2. Residence time of observed and model simulated tracer for flood and ebb injections, 

respectively ..................................................................................................................41 
0

0 

EXECUTIVE SUMMARY 

The hydrodynamic model within the Port of New York/New Jersey Operational Forecast System 

(NYOFS) has been used to simulate the tracer dispersion in the New York Harbor. With a 

concentration model added to the NYOFS, the hydrodynamic model simulates the movement of 

the passive tracer hexafluoride (SF6) deliberately released at the Newark Bay in July, 2002 and at 

the East River in June, 2003 (two releases, one before the flood tide, flood injection, and one 

before the ebb tide, ebb injection) by Columbia University researchers. The tracer field 

experiments are used to study the dispersive characteristics of the inland waterways in the New 

York Harbor estuary, particularly at the Newark Bay, Arthur Kill, Kill van Kull, and the East 

River. 

The hydrodynamic model has been set-up for simulating the tracer movement released in the 

field experiments. The model is forced with observed water levels at lateral open boundary 

Sandy Hook, NJ and Kings Point, NY and with observed winds on the surface. Observed 

discharges at Hudson and Passaic Rivers are used as the flow input to the model instead of 

climatology in NYOFS. A one-dimensional outflow and the constant spatial gradient inflow are 

specified for the concentration boundary condition at the northern end of the East River near 

Kings Point. The simulated water levels and currents are verified with observations to ensure the 

model accuracy. Model simulated tracer concentration distribution and the mass at model surface 

layer are compared with tidally daily synchronized measurements. The comparisons include: 

longitudinal tracer concentration distribution, vertical profile, mass inventory, center of mass 

movement, and residence time. 

The simulated longitudinal tracer concentration distributions are qualitatively in agreement with 

observations. The simulated flushing rate is slower than the observations at the Arthur Kill and 

East River due to slower current velocity associated with coarse grid resolution. Since the model 

is barotropic without salinity and temperature, there is no structure in the simulated tracer 

vertical profile similar to observations found at Hudson River and northern East River. 

For the July 2002 field experiment, the residence time from the mass inventory, within the inland 

waterways of Newark bay, Arthur Kill, and Kill van Kull, was estimated about 3.4 days for the 

data and 4.5 days for the model. For the June 2003 field experiment, the residence time within 

the East River was estimated 3.8 (flood injection) and 1.7 (ebb injection) days from the data, and 

3.2 (flood injection) and 3.3 (ebb injection) days from the model, respectively.
1

1 

1. INTRODUCTION

Circulation in an estuary is the primary mechanism for transporting solute and pollutants in the 

water. The mixing process and dispersion characteristics with adjacent water parcel due to tidal 

circulation are essential to determine the short-term flushing and residence time for 

environmental and ecological management. In a coastal estuary, such as the New York Harbor 

and Galveston Bay/Houston Harbor, environmental assessment due to municipal pollutants 

requires detail transport characteristics in the area. 

The Harbor and Port of New York and New Jersey (Figure 1.1) has a complex geometry with 

narrow navigation channels interconnecting the regional bays, for example, the Kill van Kull 

between the Upper Bay and the Newark Bay; the East River between the Long Island Sound and 

the Upper Bay; the Arthur Kill between the Newark Bay and the Raritan Bay. These channels are 

important for both safe navigation and hydrodynamics in the Harbor. Tidal currents through 

these channels play an important role in determining the dispersion characteristics. Flows from 

four major river systems provide freshwater to each of the three regional bays; the Raritan River 

to the Raritan Bay, the Passaic and Hackensack Rivers to the Newark Bay, and the Hudson River 

to the Upper Bay. These river inflows associated with the eddies and current shears generated by 

interacting with tidal currents further complicate the circulation and transport in the New York 

Harbor estuary. 

The researchers in the Columbia University, New York conducted two field experiments in the 

New York Harbor to study the circulation, mixing, and the transport and the fate of solutes using 

sulfur hexafluoride (SF6). In July 2002, an approximate of 0.9 mol of SF6 was injected into 

Newark Bay, NJ. The SF6 tracer was observed over 11 consecutive days using a high-resolution 

measurement system. In June 2003, two injections of approximate of 3.9 mol SF6 each were 

made 8 days apart in the East River, NY. Measured data are processed and compiled for 

dispersion characteristics interpretation. Detailed experiment description and results are 

documented in two journal articles (Caplow, et. al., 2003 and Caplow, et. al., 2004). 

National Ocean Service (NOS) of NOAA has developed the Port of New York/New Jersey 

Operational Forecast System (NYOFS) to simulate water levels and current velocities for use by 

mariners navigating in New York Harbor. Based on the Princeton Ocean Model (POM, 

Blumberg and Mellor, 1987), this forecast system (Wei and Chen, 2001 and 2002) has been 

running operationally since February 2003 utilizing the near real-time water level and current 

information from NOS’ Physical Oceanographic Real-Time System (PORTS). The 

hydrodynamic model of this system will be used to simulate the SF6 transport in the New York 

Harbor. 

This report documents the modeling work performed to simulate the transport the SF6. The 

model set-up, simulation procedures, and results comparison with measured data are described. 

Conclusions and future work based on simulation results are discussed. 
2 

Figure 1.1. Map showing New York Harbor and The Port of New York/New Jersey including 

PORTS stations and major tributaries. 
3 

2. HYDRODYNAMIC MODEL

2.1. Governing Equation

The NYOFS hydrodynamic model is a three-dimensional barotropic circulation model, based on 

POM, for simulating water levels and current velocities. The model is forced with: water levels 

at the open boundaries at Sandy Hook, NJ and Kings Point, NY; freshwater inflows from the 

Raritan, Passaic, Hackensack, and Hudson Rivers; and surface winds. The governing equations 

in a vertical sigma coordinate are briefly given as follows. Detailed formulation is contained in 

Blumberg and Mellor (1987), and Wei and Chen (2001). 

= 0, ∂

∂

+

∂

∂

+

∂

∂

+

∂

∂

σ

η ω

y

VD

x

UD

t

 (1) 

( ), 1 2

sx bx

M

x

U

D

K

x

F fVD gD U

y

VD

x

U D

t

UD

τ τ

σ σ ρ

η

σ

ω

+ − ⎥

⎦

⎤ ⎢

⎣

⎡

∂

∂

∂

∂ = ∂∂ − − +

∂

∂

+

∂

∂

+

∂

∂

+

∂

∂ (2) 

( ), 1 2

sy by

M

y

V

D

K

y

F fUD gD V

y

V D

x

UVD

t

VD

τ τ

σ σ ρ

η

σ

ω

+ − ⎥

⎦

⎤ ⎢

⎣

⎡

∂

∂

∂

∂ = ∂∂ − + +

∂

∂

+

∂

∂

+

∂

∂

+

∂

∂

 (3) 

, 2 2

1

3 2 2 2 2 2 2 2

q

q M

F

B

U V Dq

D

q K

D

q K

y

Vq D

x

Uq D

t

q D − +

⎥

⎥

⎦

⎤

⎢

⎢

⎣

⎡ ⎟

⎠

⎞ ⎜

⎝

⎛

∂

∂ ⎟ + ⎠

⎞ ⎜

⎝

⎛

∂

∂

+⎥

⎦

⎤ ⎢

⎣

⎡

∂

∂

∂

∂ = ∂∂

+

∂

∂

+

∂

∂

+

∂

∂

σ σ σ σ σ l

ω (4) 

= ∂

∂

+

∂

∂

+

∂

∂

+

∂

∂

σ

l l l ω l 2 2 2 2q

y

Vq D

x

Uq D

t

q D

l l l W F U V

D

K E q

D

Kq M

+

⎥

⎥

⎦

⎤

⎢

⎢

⎣

⎡

⎥

⎥

⎦

⎤

⎢

⎢

⎣

⎡ ⎟

⎠

⎞ ⎜

⎝

⎛

∂

∂ ⎟ + ⎠

⎞ ⎜

⎝

⎛

∂

∂

+⎥

⎦

⎤ ⎢

⎣

⎡

∂

∂

∂

∂ 2 ~ 2 2

1

2

σ σ σ σ

 (5) 

where σ = (z-η)/(H+η), H is the mean sea level water depth, U and V are horizontal velocities, 

KM and KH are the vertical kinematic viscosity and diffusivity, respectively, Kq is vertical 

turbulence mixing coefficient, q2 is twice the turbulence kinetic energy, l is the turbulence length 

scale, ~

W =1+E2( l /k L), k = 0.4 is the von Karman constant, L-1=(η-z)-1+(H+z)-1, B1, E1, and E2

are empirical constants (B1, E1, E2)=(0.52, 1.8, 1.33), τs and τb are the wind stress and bottom 

friction, D=H+η is the total water depth, g is the acceleration due to gravity, f is the Coriolis 

parameter, ρ is the water density, and ω is the transformed vertical velocity normal to a sigma 

surface. The relationship of ω with the Cartesian vertical velocity W is 

 t t,

D

y y

D V

x x

D W U

∂

∂

+

∂

∂

+⎥

⎦

⎤ ⎢

⎣

⎡

∂

∂

+

∂

∂

+⎥

⎦

⎤ ⎢

⎣

⎡

∂

∂

+

∂

∂ = + η σ η σ η ω σ (6) 

And the horizontal viscosity and diffusion terms Fx and Fy are defined as 

2 ,⎥

⎦

⎤ ⎢

⎣

⎡

⎟

⎟

⎠

⎞

⎜

⎜

⎝

⎛

∂

∂

+

∂

∂

∂

∂

+⎥

⎦

⎤ ⎢

⎣

⎡

∂

∂

∂

∂ = x

V

y

U HA

x y

U HA

x

Fx M M (7) 
4 

⎥

⎦

⎤ ⎢

⎣

⎡

∂

∂

∂

∂ ⎥ +

⎦

⎤ ⎢

⎣

⎡

⎟

⎟

⎠

⎞

⎜

⎜

⎝

⎛

∂

∂

+

∂

∂

∂

∂ = y

V HA

x y

V

y

V HA

x

Fy 2 M M (8) 

where AM, the vertically integrated horizontal eddy viscosity, is defined by the Smagorinsky 

formula 

 

A C xy V V M N

T = ∇ +∇ Δ Δ

1

2 ( )

 (9) 

where CN, a non-dimensional parameter, is set to be 0.2 in this study; u and v are the verticallyintegrated velocities and Δx and Δy are the grid spacings in the x and y directions for each grid 

cell; 

 ( ) / 2 / 2 .

2 2 2

⎥

⎥

⎦

⎤

⎢

⎢

⎣

⎡

⎟

⎟

⎠

⎞

⎜

⎜

⎝

⎛

∂

∂

+ ⎟

⎟

⎠

⎞

⎜

⎜

⎝

⎛

∂

∂

+

∂

∂ ⎟ + ⎠

⎞ ⎜

⎝

⎛

∂

∂ ∇ + ∇ = yv

y

u

x

v

x

u V V T (10) 

For the passive tracer SF6, the concentration equation is 

F L C

D

C K

y

CVD

x

CUD

t

CD

C

M

+ − ⎥

⎦

⎤ ⎢

⎣

⎡

∂

∂

∂

∂ = ∂∂

+

∂

∂

+

∂

∂

+

∂

∂

σ σ σ

ω

 (11) 

where C is the concentration of SF6, 

 2 ,⎥

⎦

⎤ ⎢

⎣

⎡

∂

∂

∂

∂

+⎥

⎦

⎤ ⎢

⎣

⎡

∂

∂

∂

∂ = yC HA

x y

C HA

x

FC M M (12) 

and L is the loss due to the gas transfer at the water surface, described in Section 2.3. 

The boundary conditions for the continuity and momentum equations and other model parameter 

definition can be found in Wei and Chen (2001, 2002). The concentration lateral open boundary 

condition during the outflow is specified with one-dimensional advection, 

 

 n

CV

t

C

∂

∂ = ∂∂ r

 (13) 

where V

r

is the velocity in the normal direction to the boundary n. The spatial gradient is used for 

the inflow, 

 ∂ −1

∂ = ∂

∂

b n b

C

n

C (14) 

where b denotes the cell at the lateral open boundary. 
5 

2.2. Air-Water Gas Transfer 

After injection into the water column, part of the gaseous SF6 tracer exits from the water into the 

air. The tracer loss L in the concentration transport equation (2.3) cam be expressed as 

 ,⎥

⎦

⎤ ⎢

⎣

⎡

∂

∂ = D

kC L

σ

where k is the gas transfer velocity, a measure of the air-water transfer rate, can be defined as 

 k = λ g D

where λg is the first-order gas transfer loss rate for the water column (with unit t-1) and D is the 

total water depth. From many field and laboratory experiments (Ho et al., 2002, Caplow et al., 

2003), λg is found to be approximately 0.170.01 day-1. 

2.3. Model Grid

The orthogonal curvilinear model grid used in NYOFS is also adopted here for the SF6

concentration modeling. The model is constructed to cover the New York Harbor and vicinity 

estuaries from 74̊ 10' W to 73̊ 45' W and from 40̊ 24' N to 40̊ 52' N including the East River, 

Hudson River up to Poughkeepsie, Newark Bay, the Hackensack and Passaic Rivers, Arthur Kill, 

the Raritan River, and Raritan Bay (Figure 2.1). The horizontal resolution varies spatially and 

ranges from 150 to 1000 m, resulting in 134 by 73 grid points in the cross- and along- harbor 

direction. The model water depth ranges from 3 m in the shallow shoals to 25 m in the 

navigation channel near The Narrows (Figure 2.2). The Hudson River north of Spuyten Duyvil 

has been bent to take into account the river effect and to save on computational cost. For this 

simulation effort the nested fine grid in NYOFS is not included for the tracer concentration 

modeling. 

In order to fully utilize information from NOS’s Physical Oceanographic Real Time System 

(PORTS) as lateral boundary conditions, the NYOFS model grid open ocean boundary has been 

set at Kings Point, NY, and Sandy Hook, NJ. 
6 

Figure 2.1. New York/New Jersey Harbor model grid showing locations of water level gages 

and current meter. 
7 

Figure 2.2. New York/New Jersey Harbor model bathymetry, contours in meter. 
8 
9 

3. TRACER CONCENTRATION MODELING

3.1. July 2002 Newark Bay Field Experiment and Simulation

The first SF6 field experiment was conducted from July 14 to July 25, 2002. Approximately 2.4 

mol of SF6 (in which approximately 0.9 mol was dissolved in the water and the rest immediately 

escaped from the water column into the air) was injected into Newark Bay, NJ (Figure 3.1). 

After the injection, the SF6 tracer was then surveyed over 11 consecutive days using a high 

resolution measurement system (Ho et al., 2002, Caplow et al., 2003). The system includes a 

pump submerged at a depth of 1.2 m, a flow-through membrane contractor to extract gases from 

the water and a gas chromatograph equipped with an electron capture detector. A continuous 

measurement interval of 2 minutes was achieved. Figure 3.2 shows a typical survey boat track 

covering the Newark Bay, Arthur Kill, and Kill van Kull. Data were complied and processed for 

comparison with model results. 

Figure 3.1. Injection location for July 14, 2002 field experiment. 
10 

Figure 3.2. A typical boat track for July, 2002 SF6 field experiment covering Newark Bay, 

Arthur Kill , and Kill van Kull. Dots indicate the tracer measurement location.

3.1.1. Simulation Set-Up

Observed river discharge in Passaic River was about 4 m3

s

-1 during the field experiment period, 

which is much lower than the long-term average (Figure 3.3), except on July 20. The observed 

river discharges in Passaic River and long term average flows for Raritan, Hackensack, and 

Hudson rivers are used as river inflows to the model. Water level observations at Sandy Hook, 

NJ and Kings Pt, NY (Figure 3.4) from NOS water level gages are collected for open ocean 

boundary conditions at grid cells cross the harbor entrance (Sandy Hook, NJ) and the East River 

(Kings Point, NY). Detail open boundary condition specifications can be found in Wei and Chen 

(2001, 2002). The insignificant non-tidal components represent typical low river flow and 

summer winds during the experiment period. 
11 

The model was set up to simulate the SF6 tracer concentration and to study the dispersion 

characteristics in the Newark Bay and inland waterways of the New York/New Jersey estuary. 

The model simulated the water levels, currents, and SF6 concentration from July 12 to July 25, 

2002. The model was spun-up from the rest at 1600 UTC, July 12, two days before the tracer 

injection at 1600 UTC, July 14. This two-day model spun-up allows the model reaches a quasisteady state before the tracer injection. Simulated and observed water levels at the Bayonne 

Bridge and The Battery, shown in Figure 3.3, indicate that the model is accurately reproducing 

the water elevations at model interior locations. Figure 3.4 shows the simulated and observed 

current velocity in principle direction at Bergen Point at about 3 m (model layer 2) and 9 m 

(model layer 5) below the surface. Due to the insufficient model grid resolution, the model 

underestimates the maximum flood current velocity at a strong horizontal current shear location. 

However, the simulated current phase agrees with the data. 

Figure 3.3. Observed and climatological freshwater input from Passaic River, NJ (upper) and 

surface wind at Sandy Hook, NJ (bottom) for July 2002 model simulation boundary 

forcing. 

Figure 3.4. Observed water levels and astronomical tides at Sandy Hook, NJ and Kings Point, 

NY during July, 2002 Sf6 field experiment. 
12 

Figure 3.5. Model simulated water levels and observations at Bayonne Bridge, NY and The 

Battery, NY showing the model is capable of reproducing the water levels within 

the mod grid. 

Figure 3.6. Hourly model simulated current velocity (light line and open arrow head) and 

observations (heavy line and solid arrow head) at Bergen Point, Newark Bay at (a) 

Layer 2, about 3 m below the surface; and (b) Layer 5, about 9 m below the surface.
13 

3.1.2. Daily Averaged Concentration

Figure 3.7 to 3.9 shows the observed tracer concentration and simulated daily averaged surface 

SF6 concentration contours for July 15, 19, and 23, 2002. The concentration contour plots not 

only show the tracer distribution and gradient over the area but also reveal the tracer 

advancement. In general, the model simulated tracer concentration distribution is in good 

agreement with the observations. The simulated tracer leading location along Arthur Kill lags 

behind the observations, probably because of a slower simulated current velocity. One day after 

the injection, July 15, the survey reveals the tracer moving from the Kill van Kull to the Upper 

Bay. However, the model simulated tracer has extended through The Narrows to Raritan Bay, an 

area not covered by the survey. The tracer was carried by the tidal currents north of the injection 

location in the Passaic and Hackensack rivers. Transport into and through the Arthur Kill was 

much slower. In Newark Bay, maximum concentration was reduced from approximately 8000 

fmol l-1 to about 2000 fmol l-1 in two days. This behavior can also be seen from the tracer mass 

inventory plot (Figure 3.10) which shows an exponential decay of approximate total mass over 

inland waterways including the Newark Bay, Kill van Kull, and the Arthur Kill. The model 

simulated tracer exits the inland waterways slower than the observed tracer mass. 

Since the observed concentration contours shown in Figures 10 are obtained by averaging data 

measured from two boat track surveys through the inland waterways, there exists concentration 

contour errors because of the averaging process and because of the area not covered by the 

survey boat tracks. The observed total mass calculation was performed on the average over a 

Abox@ ranging from 100 m to 400 m and based on a presumed vertical distribution derived from 

limited vertical observations. The simulated total tracer mass is computed from the averaged 

tracer concentrations in each of the 3-dimensional model grids within the inland waterways at 15 

minute interval. Therefore, it is not surprising that the model simulated total mass is greater than 

the measurements. 

3.1.3. Longitudinal Concentration Profile 

Simulated SF6 concentrations in the longitudinal direction along the survey boat track were 

compared with the survey data. Figures 3.11 and 3.12 show the boat tracks along the channel 

from Newark Bay to Arthur Kill and simulated longitudinal SF6 concentration compared with 

data for Days 1, 2, 5, and 7. Distance km 0 is defined at the junction of Arthur Kill and Raritan 

Bay. Overall, the simulated tracer advanced slower than the data. The tracer gradients, however, 

match with the data. 

3.1.4. Residence Time

The residence time for SF6 in the inland waterways is defined as the time required for the total 

tracer mass to be reduced to 1/e of the original injection concentration. Therefore, the mean 

residence time is estimated as 3.4 days for the observed data and 4.7 days for the simulation 

model results. The residence time at each model grid cell in the inland waterways is assumed to 

be the time between when a grid cell is first exposed to the tracer and when the tracer 

concentration is reduced to 1/e of the peak concentration. The residence time in this definition 

refers to the relative time of tracer exposure, as an indication of flushing rate in a specific area, 

and not as a measure of the concentration history. A model-derived residence time contour plot is 
14 

shown in Figure 3.13. The figure shows that the residence time in Newark Bay and the Kill van 

Kull is on the order of one day, indicating a greater tidal current flushing rate there than in the 

Arthur Kill, where the residence time is in the order of 3 to 5 days in the lower kill. Low flushing 

rates are found upstream in the Passaic River and in channels near the marine terminals. 
15 

 

Figure 3.7. Observed (top, Caplow, et. al., 2003) and model simulated (bottom) daily averaged 

surface SF6 concentration contour plots for July 15, 16, and 17, 2002. Dotted lines 

indicate the survey tracks. 
16 

 

Figure 3.8. Observed (top, Caplow, et. al., 2003) and model simulated (bottom) daily averaged 

surface SF6 concentration contour plots for July 18, 19, and 20, 2003. Dotted lines 

indicate survey tracks. 
17 

 

Figure 3.9. Observed (top, Caplow, et. al., 2003) and model simulated (bottom) daily averaged 

surface SF6 concentration contour plots for July 21, 22, and 23, 2002. Dotted lines 

indicate survey tracks. 
18 

Figure 3.10. Total measured and model simulated SF6 inventory in the inner waterways 

(Newark Bay, Arthur Kill, and Kill van Kull) over 11 days, with fitted exponential 

decay curves, indicating a decay constant of 0.29 day-1 and 0.21 day-1 for observed 

and simulated tracer dispersion. 
19 

 (a) (b) 

 

 (c) (d) 

Figure 3.11. Boat tracks from Newark Bay to Arthur Kill and simulated longitudinal SF6

concentration (solid circle) compared with observations (open triangle) for Day 1 

((a) and (c), July 15, 2002) and Day 2 ((b) and (d), July 16, 2002). 
20 

 

 (a) (b) 

 

 (c) (d) 

Figure 3.12. Boat tracks from Newark Bay to Arthur Kill and simulated longitudinal SF6

concentration (solid circle) compared with observations (open triangle) for Day 5 

((a) and (c), July 19, 2002) and Day 7 ((b) and (d), July 21, 2002). 
21 

 

Figure 3.13. Contour plot of residence time for the inland waterways including Newark Bay, 

Kill van Kull, and Arthur Kill. 
22 

3.2. June 2003 East River Field Experiment and Simulation

The other SF6 field experiment was carried out from June 18 to June 30, 2003 in the East River, 

a tidal channel connecting Long Island Sound and New York Harbor. This field experiment was 

designed to study the dispersion and flushing characteristics of the river between The Battery and 

Throgs Neck (near Kings Point, Figure 1.1). Two initial injections were made 8 days apart in the 

East River (Figure 3.14), the first at 1230 UTC, June 17, 2003 about one hour after slack-beforeflood (flood injection) and the second at 1300 UTC, June 25, 2003, about one hour before slackbefore-ebb (ebb injection, Figure 3.15). In each injection, there was about 3.9 mol of SF6

dissolved into the water column. In addition to the determination of the dissolved material 

dispersion and flushing rate of the East River, this experiment paid particular attention to the 

effects of the tidal phase on the flushing rate. Starting on June 18, tidal synchronized boat 

surveys were conducted each day for a tidal cycle in order to measure the near surface (1.2 m 

below the water surface) SF6 concentration at 2 minute intervals. The boat track usually started 

from the City Island marina, traveled north toward Long Island Sound then turned south through 

the East River to the Upper Bay (Figure 3.16). Thus, each survey covered the entire East River, 

and often went beyond the river limits. On June 21 and 29, the survey was extended to cover the 

Hudson River from the conjunction with the Harlem River to The Battery. On June 21, 24, 25, 

and 29, SF6 concentration in the Harlem River was also measured. Concentration and salinity 

vertical profiles were also taken at several key locations in the East and Hudson Rivers in order 

to study the vertical structure (Caplow et al., 2004). 

 Figure 3.14. Injection location at East River for June 2003 SF6 field experiment. 
23 

Figure 3.15. Time for flood and ebb injections relative to model tidal current at injection 

location near Hell Gate a NOS tidal current reference station. 

 

Figure 3.16. Typical survey boat tracks of June 2003 SF6 field experiment, June 18 and 21. The 

survey boat covers entire East River each Day. Surveys also cover lower Hudson 

River conducted on June 21 and 29 and Harlem River on June 21, 24, 25, and 29. 
24 

3.2.1. SF6 Concentration Measurement

Tidally synchronized longitudinal surveys of concentration were carried out in the East River 

extended into Western Long Island Sound to the north and the Upper Bay and Raritan Bay 

through The Narrows in the south. Measurements from a portion of the survey are plotted as 

Figure 3.17 (Caplow, et. al., 2004). Daily survey concentration plots show the dispersion and 

decay of the tracer. Note the tracer spreading difference at the Upper Bay and The Narrows one 

day after the flood (Day 1F) and ebb (Day 1E) injections. Not shown in the plots is that just one 

tidal cycle after the tracer injection the tracer was carried to the lower Hudson River from the 

Upper Bay by the flooding tidal current. 
25 

 

 

 

 

Figure 3.17. Tidally synchronized longitudinal tracer concentration contour plots, in the East 

River and in the Upper Bay and The Narrows, after the flood (left) and ebb (right) 

injections (from Caplow et al., 2004). 
26 

3.2.2. Model Simulation Set-Up

The model was set up to simulate the SF6 tracer concentration movement in the East River and 

the New York/New Jersey estuary from June 15 to June 30, 2003 to study the tracer transport 

and dispersion characteristics. The observed Hudson River discharge, which is dynamically 

close to the East River (climatology for other rivers), and surface winds at Sandy Hook, NJ are 

used for model river inflow and surface boundary conditions. Figure 3.18 shows the Hudson 

River flow observations along with climatology. High flows occurred on June 22 and 23 due to 

rainfall in the upper Hudson River watershed. Open ocean boundary conditions are specified 

with observed water levels at Sandy Hook and Kings Point (Figure 3.19) comparable to the July 

2002 model simulation. 

 

Figure 3.18. Observed and climatological freshwater input from Hudson River, NY (upper) and 

surface wind at Sandy Hook, NJ (bottom) used for June 2003 model simulation. 
27 

Figure 3.19. Observed water levels and astronomical tides at Sandy Hook, NJ and Kings Point, 

NY during June 2003 SF6 field experiment. 

The injection location (Figure 14) of this experiment allows the tracer to exit the model grid open 

boundary at Kings Point (Figure 2). Therefore, the boundary condition for concentration 

equation (Eq. 11) needs to be carefully specified. There is no time series measurements at the 

model open boundary. During the outflow (flood), the concentration at the boundary is specified 

with an one-dimensional advection scheme similar to the current velocity specified at the open 

ocean boundary. During the inflow, the concentration is specified based on the concentration 

spatial gradient at the previous time step. Besides the SF6 tracer loss at the air-water interface, 

the tracer also exits from the model domain and there is a net loss of the tracer mass due to the 

way the boundary condition is treated. This loss will have to be accounted for in the total mass 

inventory calculation. 

The model simulated water levels at The Battery and Bayonne Bridge are in good agreement 

with observations (Figure 18). There were no current velocity observations available within the 

East River during the experiment. However, the coarse model grid configuration (one model grid 

cell for most of the river width) for the East River indicates the model could significantly 

underestimate the maximum current velocity in this area. The simulated tracer concentration 

accuracy may be decreased due to the inaccurate model simulated current velocity field. 

Simulated tracer concentration fields were analyzed and compared with the observed data by 

examining daily averaged concentration contours, longitudinal concentration profiles, mass 

inventory and residence time estimation, movement of the center of mass (COM), and 

concentration vertical profiles. 
28 

Figure 3.20. Model simulated water levels and observations at Bayonne Bridge and The Battery. 

3.2.3. Longitudinal Concentration Distribution 

After the tracer was injected into the water column before the flood tide, the tracer moved to the 

north with the tidal current into the Western Long Island Sound. Figure 3.21 shows the 

concentration distribution, after flood injection, in the longitudinal direction for the East River, 

from the intersection of the East River and the Upper Bay to The Battery in the south and to the 

Throgs Neck (also the model grid boundary) in the north. The concentration for days 1F, 3F, and 

5F after the flood injection are plotted as heavy lines, while lighter lines represent concentrations 

for days 2F, 4F, and 6F. The narrow width and the strong current velocities associated with the 

East River ensure a good mixing of tracer concentration in the transverse direction. The tracer 

remained maximum at Hell Gate, the injection location, and dropped sharply near The Battery, 

indicating the high dispersive characteristics where the narrow East River flows into the wider 

Upper Bay. Tracer concentrations in the river decreased daily due to flushing of the East River 

into the Upper Bay at The Battery and into the Long Island Sound at Throgs Neck, as well as 

exiting through air-sea interaction. Note the observed concentration plateau in Flushing Bay, a 

semi-enclosed bay (Figure 2.1) which serves as a solute storage area. The simulated tracer 

concentrations for the longitudinal profiles and the observations are similar. But there are distinct 

differences. The tracer loss from the model northern boundary following the flood injection on 

Days 1F and 2F results in lower concentrations than the measurements. After Day 3F, the 

simulated concentration agrees with the observations between The Battery and the Throgs Neck.
29 

 

Figure 3.21. Observed (top) and simulated (bottom) longitudinal SF6 concentration distribution 

after the flood injection from The Battery to the Throgs Neck, heavy lines for Days 

1F, 3F, and 5F and light lines for Days 2E, 4E, and 6E. Note the model grid 

boundary location at Throgs Neck. 
30 

On July 25, 2003 the tracer was injected into the water column the same location at the time 

before the ebb tide (ebb injection, Figure 3.15). Thus, simulated daily tracer longitudinal 

distributions following the ebb injection are compared with the flood injection and with 

observations shown in Figures 3.22 and 3.23. The flood injection simulated concentrations in the 

river are lower than the observations; however, the ebb injection simulated concentrations 

compare well with observations. During the ebb injection, the simulated tracer dissipates much 

slower than the measurement from The Battery to the Upper Bay. 

3.2.4. Simulated Daily Averaged Tracer Concentration Contours

The longitudinal tracer distribution following the flood and ebb injections reveals the tracer 

dispersion and decay in the East River. For the model simulation, the daily tracer concentration 

fields in 15 minutes interval are averaged to produce daily averaged concentration contour plots 

shown in Figures 3.24 and 3.25. Tracer exiting the model domain at northern boundary is 

apparent in the first 2 days. The tracer started to spread into the Upper Bay on June 18 (Day 1F) 

and then to the Hudson River by tidal excursion on June 19 (Day 2F). Instant hourly tracer 

contours (not shown here) indicate that the tracer movement is well synchronized wit the tidal 

currents. It is worth noting that a higher concentration tracer is observed in the Buttermilk 

Channel between Governors Island and Brooklyn, probably due to high current velocity. 

3.2.5. Vertical Profiles

The SF6 field survey focused on measuring longitudinal surface tracer distributions in the East 

River, the lower Hudson River, Upper Bay, The Narrows, and Western Long Island Sound. In 

addition, vertical concentration profiles at selected locations were also measured to better 

understand the tracer distribution in the vertical. Figure 3.26 shows the observed and simulated 

concentrations (normalized to the vertical average) at the injection point, and in the northern and 

southern East River (locations shown on the map). In the northern East River, the data shows a 

significant vertical gradient on Days 2F and 2E (2 days following the flood and ebb injections), 

while the model reveals a smaller vertical gradient than the observed data on Day 2E, and almost 

zero vertical gradient on Day 2F. Possible causes for these differences are the lack of density 

flow in the model, and the tidal current velocity phase discrepancy between the observations and 

model. At the injection point and in the southern East River, the tracer is well-mixed. The 

profile in the lower Hudson River, shown in Figure 27, reveals a high tracer concentration in the 

middle of the water column during the flood injection, suggesting that the tracer is trapped 

between the classic estuarine 2-layer top and bottom flows. The salinity at this depth, ranges 

from 16-22 ppt (Figure 27c) matching salinities in the East River (~20 ppt), suggesting that water 

from the East River is carried into the Hudson in the mid-depth layer. 
31 

Observations

 

 

Model

 

Figure 3.22. Observed (upper panels) and simulated (lower panels) longitudinal tracer 

concentration for days 1 (left panels, Days 1F and 1E, July 18 and 26) and 2 (right 

panels, Days 2F and 2E, July 19 and 27) after the flood (open circle) and ebb (filled 

circle) injections. 
32 

Observations

 

Model

Figure 3.23. Observed (upper panels) and simulated (lower panels) longitudinal tracer 

concentration for days 3 (left panels, Days 3F and 3E, July 20 and 28) and 4 (right 

panels, Days 4F and 4E, July 21 and 29) after the flood (open circle) and ebb 

(filled circle) injections. 
33 

Figure 3.24. Simulated daily averaged tracer concentration contour plots, June 18 (Days1F) to 

June 23 (Day 6F) after the flood injection. Tracer exiting the model domain at 

northern boundary is especially apparent during the first 2 days. 
34 

Figure 3.25. Simulated daily averaged tracer concentration contours for June 25 (Day 0E) to 

June 30 (Day 5E) after the ebb injection. 
35 

 

 

 

 

 

 

 

Figure 3.26. Observed (left, Caplow, et. al., 2004) and model simulated (right) vertical profiles 

of SF6 concentrations (normalized to the vertical average) in the East River from 

three regions: (a) northern, (b) injection point, and (c) southern of the river. 

Profiles locations are shown on the map. 
36 

Figure 3.27. Observed (left column (a) and (b), Caplow, et. al., 2004) and model simulated 

(right column) vertical SF6 profiles in the Hudson River following the flood and 

ebb injections, respectively. Normalized SF6 concentration vs salinity (left (c)) for 

all profiles indicating peak SF6 concentrations at mid-depth matches salinities in 

the East River. 
37 

3.2.6. Center of Mass Movement

The movement of the center of mass (COM) was calculated from the survey mass inventory each 

day in the East River. Figure 3.28(a) shows the observed COM movement for the flood and ebb 

injections (Caplow, et. al., 2004). The mean displacement was northward for both injections 

although initially it is southward for the flood injection. Although the distribution of background 

SF6 from the survey has been subtracted before the COM calculation, the calculation could result 

in a significant error due to unknown background variability (Caplow et al., 2004). The model 

simulated tracer COM can be calculated at any model output time by a two-dimensional moment 

method, as the simulated tracer concentration is available over the entire model grid. Figure 3.29 

shows surface layer COM time series at the model output interval (15 minutes) for flood (top) 

and ebb (bottom) injections. The COM locations coincide with a semi-diurnal tidal current, and a 

southward net movement for the flood injection can be seen. To calculate the COM net 

movement for comparison with the observations, the daily averaged COM calculated based on 

the model surface layer tracer concentration is presented in the right plot of Figure 3.28(b). In 

contrast to the data, the COM movement in the model is southward for the flood injection. The 

cause of discrepancy between the model and the observations is probably due to the mass loss at 

the model northern boundary in the model. For the ebb injection, the simulated net COM 

movement is northward, consistent with the observations because the flushing rate is higher than 

the flood injection from the East River to the Upper Bay (Figures 3.22 and 3.23). 

(a) (b) 

Figure 3.28. Movement of the center of mass (COM) of SF6 in the East River; (a) observed and 

(b) model. The COM of the SF6 background has been subtracted. Note that 

distance 0 located at the injection location (near Hell Gate) and positive distance 

toward north. Note that June 18 and 26 correspond to Days 1F and 1E, respectively. 
38 

Figure 3.29. Location of the center of mass time series from model simulated tracer in the East 

River, relative to the injection point (distance 0) near Hell Gate for the flood (top) 

and ebb (bottom) injection. 

3.2.7. Tracer Mass Inventory

The tracer injected into the water column in the experiment eventually either exits through the 

water surface into the air or flushes out to the Western Long Island Sound to the north and the 

Upper Bay to the south. The tidal flushing rate in the East River can be estimated from the total 

mass inventory. Some of the tracer that moves out of the East River (from The Battery to Throgs 

Neck) to the Long Island Sound will move back into the East River by the flooding tidal current. 

However, there are no data to evaluate the tracer inflow into the East River at the northern open 

boundary (near Throgs Neck) during the ebb tide (toward the south). There will be errors 

associated with the inflow boundary condition specified in the model. For this model simulation 

experiment, the tracer mass loss due to the difference between the outflow and the A 

concentration spatial gradient inflow boundary condition specified at Throgs Neck, can be 

estimated from the velocity and concentration information at the model boundary. Daily mass 

loss following the flood and ebb injections is calculated and tabulated in Table 3.1. There is 

significant mass loss during the first 2 days following the flood injection. Daily mass loss 

following the ebb injection is almost invariant after day one. Figure 3.30 shows the total mass 

decay for flood and ebb injections. For the observed data the ebb injection flushing rate is greater 

than the flood injection flushing rate. For the model, the tracer flushes out of the East River to 

the Upper Bay so quickly on the first two days that the mass decay in the ebb injection (square) 

is greater than the flood injection (triangle) despite the tracer mass loss at the northern boundary. 

For the ebb injection, the mass loss for the model (square) is much less than the data (diamond) 
39 

probably due to: (1) significantly underestimating mixing in the Upper Bay by the mode, (2) low 

simulated current velocities caused by the coarse grid resolution; and (3) no Harlem River 

configuration in the model. Significant amounts of tracer were found in Harlem River from the 

survey (Figure 3.31, from Caplow et al., 2004). 

The residence time is defined as the time it takes for the mass to decay to 1/e. Table 3.2 shows 

the residence time between the data and the model for the flood and ebb injections, respectively, 

based on the mass inventory decay curve in Figure 3.30. As mentioned previously, the model 

residence time is slightly less than that for the data following the flood injection because of the 

mass loss at the northern boundary. The model residence time is much greater than that of the 

data following the ebb injection. 

Table 3.1. Model simulated daily tracer mass loss at model grid boundary, Throgs Neck, 

following the flood and ebb injections. 

 Flood Injection Ebb Injection 

Day Loss (mod) % of Total Loss (mol) % of Total 

1 0.050 9.4 0.010 1.9 

2 0.039 10.4 0.015 4.0 

3 0.022 8.7 0.013 4.8 

4 0.013 7.3 0.009 5.0 

5 0.008 6.4 0.007 5.1 

6 0.005 5.6 

 
40 

Figure 3.30. Observed and model simulated daily SF6 mass inventory within the East River 

from The Battery to Throgs Neck following flood and ebb injections. Observed 

data (circle for flood injection and diamond for ebb injection) with regression 

curves for flood (solid line) and ebb (dot-dashed) injections are also plotted. Ebb 

injection decays are much faster than the flood injection. 
41 

 

Figure 3.31. Longitudinal surveys of SF6 in the Harlem River 1 and 4 days following the flood 

and ebb injections in the East River (Caplow, et. al., 2004). 

Table 3.2. Residence time of observed and model simulated tracer for flood and ebb injections, 

respectively. 

 Flood Injection Ebb Injection 

Data 3.8 day 1.7 day 

Model 3.2 day 3.3 day 
42 

4. CONCLUSIONS AND FUTURE WORK

The estuarine dispersion characteristics of inland waterways in the New York Harbor have been 

investigated by the movement of a deliberately released gaseous SF6 tracer at Newark Bay (July, 

2002) and the East River (June, 2003). The flushing rate and residence times were estimated by 

tracer concentration data collected at the surface by tidally synchronized boat surveys for about 

two weeks following the tracer release. 

With the addition of a concentration subroutine to the NYOFS hydrodynamic model and forcing 

with proper boundary condition, the model has been set up to simulate the tracer movement 

during the two field experiments. The simulated SF6 concentration characteristics not only have 

been verified with observations collected from the field experiments but also extended beyond 

the area covered by the field survey. The simulated longitudinal tracer concentration 

distributions are qualitatively in agreement with observations obtained field experiments 

(Caplow et al., 2003 and Caplow et al., 2004). In the Newark Bay experiment, the simulated and 

observed maximum concentration and distribution shapes are similar but have mismatches in the 

phase. The simulated tracer advances less than the observed tracer in the Arthur Kill and the East 

River, probably due to slower current velocity associated with the coarse grid resolution. A finer 

model grid resolution such as the nested fine grid in NYOFS for Kill van Kull and Newark Bay 

is needed to improve the current velocity accuracy in these channels. In the East River 

experiment, the simulated maximum longitudinal concentration for the flood injection is less 

than the observed data due to the tracer loss at the northeastern boundary. Extending the model 

grid to the Western Long Island Sound would cover the entire tracer movement for this 

experiment. The vertical profiles observed in the Hudson and East Rivers in the East River 

experiment show peak SF6 concentrations at the mid-depth associated with classic two layer 

estuarine flow. The model is barotropic without salinity and temperature components, so there is 

no structure in the simulated tracer vertical profile comparable to the observed data. The model 

requires the density effect and fully 3-D baroclinic structure in order to produce accurate 

concentration structure in the vertical. 

The residence time can be defined as the time it takes for the tracer mass to decreases to 1/e of 

the original mass, i.e., the e-folding. In the Newark Bay experiment, the simulated residence time 

for the inland waterways including the Newark Bay, Arthur Kill, and Kill van Kull is about 4.7 

days, compared with 3.4 days for the observed data. Again, the slower current velocity 

associated with the coarse grid is the probable cause. For the East River experiment, the 

residence time following the flood injection in the model is about the same as the data (3.8 days 

for the observed data and 3.2 days for the model). However, the residence time following the ebb 

injection from the observed data (1.7 days) is much shorter than that from the model (3.3 days). 

This is probably due to the mixing in the Upper Bay is significantly underestimated by the model. 

Slower simulated current velocities and the lack of a Harlem River configuration in the model 

may also contribute the tracer out flushing from the East River. The grid resolution needs to be 

increased in the East River and the grid needs to be extended beyond the present boundary to 

more accurate tracer simulation. The Harlem River should also be included in the model 

configuration. 

Analysis of the survey data reveals a high flushing rate from the East River to the Upper Bay 

following the tracer ebb injection, suggesting the optimal outfall time for wastewater 
43 

management. However the model shows about the same residence time in the East River 

between flood and ebb injection. The model performance accuracy needs to be improved with 

model grid modification and more thorough verification of transport. By then, the verified model 

can be efficient and cost effective tool for environmental and ecological management in the New 

York Harbor estuary. For example, the model can be used to effectively study the dispersion of 

multiple pollutant sources, to evaluate their long term impacts, and for sensitivity studies of the 

forcing variables including river discharge, surface winds, and the coastal signal at the harbor 

entrance. 

Concentration modeling is a cost effective tool for characterizing the dispersion features of a 

soluble substance in an estuary. For other pollutants, particle tracking may be a more appropriate 

approach. This report only documents the model simulation of the SF6 tracer dispersion using 

the concentration approach. Lagrangian trajectory modeling, for example the 4th order RungeKutta method (Wei, 1994), can also be applied to study the SF6 tracer dispersion experiments 

and to compare with results from the concentration modeling. 

The model grid configuration to match the shoreline is very important for conserving mass and 

momentum. An un-structured grid is capable of matching the shoreline with higher accuracy than 

curvilinear grids. The finite volume models such as FVCOM (Chen et al., 2003), UnTRIM 

(Casulli et al., 2000), or ELCIRC (Zhang et al., 2004) using un-structured grids have been 

proven to be more accurate in circulation modeling than the orthogonal grid models in a complex 

estuary. Such model applications should improve the accuracy required for environmental 

management. 

ACKNOWLEDGMENT

The solute model work has been carried out in the Coast Survey Development Laboratory 

(CSDL) of NOS’s Office of Coast Survey with the encouragement from CSDL’s Chief, Dr. 

Bruce Parker and the Chief of CSDL’s Marine Modeling and Analysis Programs, Dr. Frank 

Aikman. Mr. Ferdi Hellweger of Columbia University has kindly provided the concentration 

subroutine for the water surface tracer loss. 
44 

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