U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2011–5203

Prepared in cooperation with the Onondaga Lake Partnership

Improvement in Precipitation-Runoff Model 

Simulations by Recalibration With Basin-Specific 

Data, and Subsequent Model Applications,

Onondaga Lake Basin, Onondaga County, New York
Cover. Background image showing aerial view of downtown Syracuse, N.Y., taken by William Hecht. Photographs of streams in the 

Onondaga Lake Basin. 
Improvement in Precipitation-Runoff 

Model Simulations by Recalibration With 

Basin-Specific Data, and Subsequent 

Model Applications, Onondaga Lake Basin, 

Onondaga County, New York

By William F. Coon

Prepared in cooperation with the Onondaga Lake Partnership

Scientific Investigations Report 2011–5203

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

U.S. Geological Survey, Reston, Virginia: 2011

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reproduce any copyrighted materials contained within this report.

Suggested citation:

Coon, W.F., 2011, Improvement in precipitation-runoff model simulations by recalibration with basin-specific data, and 

subsequent model applications, Onondaga Lake Basin, Onondaga County, New York: U.S. Geological Survey Scientific 

Investigations Report 2011–5203, 37 p., at http://pubs.usgs.gov/sir/2011/5203/.
iii

Acknowledgments

Thanks are extended to Jeanne Powers, Antonio Deskins, and Janaki Suryadevara of the 

Onondaga County Department of Water Environment Protection (OCWEP) for their assistance in 

providing water-quality data from sites in OCWEP’s Ambient Monitoring Program and miscellaneous data on chloride concentrations in the Onondaga Lake Basin. Mark Murphy, manager 

of the Onondaga County Water Authority water-treatment plant near Marcellus, New York, 

provided data on Otisco Lake water levels and withdrawals, as well as precipitation data. Greg 

Crysler, operator of the Marcellus wastewater-treatment plant, provided water-quality data for 

Ninemile Creek near the plant. 

Lisa Senior and Rheannon Hart, both of the U.S. Geological Survey, conducted technical reviews 

of the report.
THIS PAGE INTENTIONALLY LEFT BLANK
v

Contents

Abstract...........................................................................................................................................................1

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

New Data for Model Recalibration.............................................................................................................2

Model Revisions.............................................................................................................................................5

Extension of Input Datasets ................................................................................................................5

Structural Changes...............................................................................................................................5

New Otisco Lake Tributary Subbasin .......................................................................................5

Revisions to Land-Use and Land-Cover Acreages ................................................................7

Changes to Hydrologic Response Units...................................................................................7

Elimination of Unique Row-Crop PERLND ......................................................................7

Creation of New Landslide PERLND................................................................................8

Creation of New PERLNDs in Harbor Brook Basin .......................................................8

Mitigative Effects of the Onondaga Reservoir........................................................................8

Mitigative Effects of Otisco Lake ..............................................................................................9

Changes to Model Parameter Values and Comparison of 2003 and 2008 Simulation 

Results.......................................................................................................................................9

Changes to the Hydrologic Components of the Model........................................................10

Changes to the Sedimentological Components of the Model............................................13

Basinwide Particle-Size Analyses.................................................................................13

Suspended Sediment and Total Suspended Solids.....................................................13

Changes to the Water-Quality Components of the Model ..................................................17

Orthophosphate Concentrations....................................................................................17

Phosphorus Concentrations ...........................................................................................17

Chloride Concentrations in Onondaga Creek...............................................................22

Model Applications......................................................................................................................................22

Sediment and Phosphorus Loading Rates......................................................................................22

Subbasin Loads of Sediment and Phosphorus ..............................................................................24

Watershed-Management Analysis..................................................................................................26

Chloride Loads in Onondaga Creek .................................................................................................34

Precolonization (Forested) Scenario...............................................................................................34

Summary........................................................................................................................................................35

References Cited..........................................................................................................................................36
vi

Figures

1. Map showing locations of streamflow- and water-quality-monitoring sites in the 

Onondaga Lake Basin, Onondaga County, New York, 2005–08.............................................3

2. Map showing subbasins and major hydrologic subdivisions used in the 2008 version 

of the precipitation-runoff model of the Onondaga Lake Basin, Onondaga County, 

New York ........................................................................................................................................6

3. Graphs showing streamflows simulated by the 2003 and 2008 versions of the 

Onondaga Lake Basin model, Onondaga County, New York, for selected headwater 

subbasins, 2005–08: A, Onondaga Creek (reach 102), B, Rattlesnake Gulf (reach 109), 

C, North Branch Ley Creek (reach 302), D, South Branch Ley Creek (reach 304), and 

E, Willow Brook (reach 405)......................................................................................................11

4. Graphs showing streamflows simulated by the 2003 and 2008 versions of the 

Onondaga Lake Basin model, Onondaga County, New York, at the mouths of major 

tributaries to the lake, 2005–08: A, Onondaga Creek (reach 137), B, Harbor Brook 

(reach 206), C, Ley Creek (reach 312), and D, Ninemile Creek (reach 443).......................12

5. Graphs showing flow-duration curves simulated by the 2003 and 2008 versions of the 

Onondaga Lake Basin model, Onondaga County, New York, at the mouths of major 

tributaries to the lake: A, Onondaga Creek (reach 137), B, Harbor Brook (reach 206), 

C, Ley Creek (reach 312), and D, Ninemile Creek (reach 443).............................................14

6. Graph showing paired concentrations of total suspended solids and suspended 

sediment in water samples collected in Onondaga Lake Basin, Onondaga County, 

New York, 2005–08......................................................................................................................15

7. Graphs showing suspended-sediment concentrations simulated by the 2003 and 

2008 versions of the Onondaga Lake Basin model, Onondaga County, New York, for 

selected headwater subbasins, 2005–08: A, Onondaga Creek (reach 102), B, Rattlesnake Gulf (reach 109), C, North Branch Ley Creek (reach 302), D, South Branch Ley 

Creek (reach 304), and E, Willow Brook (reach 405).............................................................16

8. Graphs showing suspended-sediment concentrations simulated by the 2003 and 

2008 versions of the Onondaga Lake Basin model, Onondaga County, New York, at 

the mouths of major tributaries to the lake, 2005–08: A, Onondaga Creek (reach 137), 

B, Harbor Brook (reach 206), C, Ley Creek (reach 312), and D, Ninemile Creek 

(reach 443) ...................................................................................................................................18

9. Graphs showing concentrations of orthophosphate, as phosphorus (P), simulated by 

the 2003 and 2008 versions of the Onondaga Lake Basin model, Onondaga County, 

New York, for selected headwater subbasins, 2005–08: A, Onondaga Creek (reach 

102), B, Rattlesnake Gulf (reach 109), C, North Branch Ley Creek (reach 302), D, South 

Branch Ley Creek (reach 304), and E, Willow Brook (reach 405).......................................19

10. Graphs showing concentrations of orthophosphate, as phosphorus (P), simulated by 

the 2003 and 2008 versions of the Onondaga Lake Basin model, Onondaga County, 

New York, at the mouths of major tributaries to the lake, 2005–08: A, Onondaga Creek 

(reach 137), B, Harbor Brook (reach 206), C, Ley Creek (reach 312), and D, Ninemile 

Creek (reach 443)........................................................................................................................20

11. Graphs showing phosphorus concentrations simulated by the 2003 and 2008 versions 

of the Onondaga Lake Basin model, Onondaga County, New York, for selected 

headwater subbasins, 2005–08: A, Onondaga Creek (reach 102), B, Rattlesnake Gulf 

(reach 109), C, North Branch Ley Creek (reach 302), D, South Branch Ley Creek 

(reach 304), and E, Willow Brook (reach 405)........................................................................21
vii

12. Graphs showing phosphorus concentrations simulated by the 2003 and 2008 versions 

of the Onondaga Lake Basin model, Onondaga County, New York, at the mouths of 

major tributaries to the lake, 2005–08: A, Onondaga Creek (reach 137), B, Harbor 

Brook (reach 206), C, Ley Creek (reach 312), and D, Ninemile Creek (reach 443) ...........23

13. Graphs showing observed and simulated chloride concentrations along Onondaga 

Creek, Onondaga County, New York: A, near Cardiff (site 04237962), B, at Dorwin 

Avenue (site 04239000), C, at Spencer Street (site 04240010), and D, at Kirkpatrick 

Street (site 04240011) .................................................................................................................24

14. Graph showing average annual yields of suspended sediment from subbasins 

simulated by the precipitation-runoff model of Onondaga Lake Basin, Onondaga 

County, New York........................................................................................................................27

15. Graphs showing average annual yields of A, orthophosphate, as phosphorus (P), 

and B, phosphorus from subbasins simulated by the precipitation-runoff model of 

Onondaga Lake Basin, Onondaga County, New York ...........................................................28

16. Maps showing orthophosphate, as phosphorus (P), A, average annual subbasin 

yields and B, estimated subbasin yields that enter Onondaga Lake, Onondaga 

County, New York........................................................................................................................30

17. Maps showing phosphorus A, average annual subbasin yields and B, estimated 

subbasin yields that enter Onondaga Lake, Onondaga County, New York .......................32

18. Graph showing annual chloride loads simulated at four sites along Onondaga Creek 

by the precipitation-runoff model of Onondaga Lake Basin, Onondaga County, 

New York ......................................................................................................................................34

Tables

1. Streamflow- and water-quality-monitoring sites in the Onondaga Lake Basin, 

Onondaga County, New York, 2005–08 ......................................................................................4

2. Estimated removal efficiencies for selected constituents for the Onondaga Reservoir 

on Onondaga Creek, Onondaga County, New York, 2006–08.................................................9

3. Selected headwater subbasins for comparison of output from the 2003 and 2008 

versions of the Onondaga Lake Basin models, Onondaga County, New York..................10

4. Model-performance statistics for 1997–2003 streamflows simulated by the 2008 

version of the Onondaga Lake Basin model, Onondaga County, New York, at the 

mouths of major tributaries to the lake ...................................................................................15

5. Average annual sediment and phosphorus loading rates for water years 1998–2008 

from pervious and impervious land types in five major subdivisions of the Onondaga 

Lake Basin simulated by the 2008 version of the precipitation-runoff model of the 

Onondaga Lake Basin, Onondaga County, New York ...........................................................25

6. Average annual sediment and phosphorus loading rates for water years 1998–2008 

from pervious land types in five major subdivisions of the Onondaga Lake Basin 

simulated by the 2003 and 2008 versions of the precipitation-runoff model of the 

Onondaga Lake Basin, Onondaga County, New York ...........................................................26

7. Average annual orthophosphate, as phosphorus (P), and phosphorus loads simulated 

in tributaries to Onondaga Lake by the precipitation-runoff model of Onondaga Lake 

Basin, Onondaga County, New York, under current (1998–2008) and precolonization 

(forested) conditions ..................................................................................................................35
viii

Conversion Factors, Datum, Abbreviations, and Acronyms

Inch/pound to SI

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

inch (in.) 25.4 millimeter (mm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

acre 4,047 square meter (m2)

acre 0.4047 hectare (ha)

square mile (mi2) 259.0 hectare (ha)

square mile (mi2) 2.590 square kilometer (km2)

Volume

gallon (gal) 3.785 liter (L)

acre-foot (acre-ft) 1,233 cubic meter (m3)

Flow rate

cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s)

Mass

pound, avoirdupois (lb) 0.4536 kilogram (kg)

ton, short (2,000 lb) 0.9072 megagram (Mg)

Concentrations of chemical constituents in water are given either in milligrams per liter (mg/L) 

or micrograms per liter (μg/L).

Vertical coordinate information is referenced to the National Geodetic Vertical Datum of 1929 

(NGVD 29).

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83).

Elevation, as used in this report, is the distance above the vertical datum.

Water year is the 12-month period October 1 through September 30 and is designated by the 

calendar year in which it ends and which includes 9 of the 12 months.
ix

List of Abbreviations and Acronyms

AGWO HSPF active-groundwater-outflow volume

AGWRC HSPF active-groundwater-recession coefficient

AOQC HSPF concentration of constituent in groundwater outflow

BMPRAC HSPF best-management practice module

GIS geographic information system

HRU hydrologic response unit

HSPF Hydrological Simulation Program–Fortran

IMPLND HSPF impervious land segment

IOQC HSPF concentration of constituent in interflow outflow 

LOADEST USGS Load Estimation Program

NEXRAD next-generation radar

NLCD National Land Cover Data

NWS National Weather Service

NPS nonpoint source

OCWA Onondaga County Water Authority

OCWEP Onondaga County Department of Water Environment Protection

OLP Onondaga Lake Partnership

PERLND HSPF pervious land segment

RCHRES HSPF stream reach or reservoir

USGS U.S. Geological Survey

Chemical Abbreviations

Cl chloride

NH3 ammonia nitrogen

NOx nitrate-plus-nitrite nitrogen

OP orthophosphate, dissolved

OrgN organic nitrogen

OrgP organic phosphorus

SS suspended sediment

TKN ammonia-plus-organic nitrogen (total Kjeldahl nitrogen)

P phosphorus

TSS total suspended solids
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Improvement in Precipitation-Runoff Model Simulations 

by Recalibration With Basin-Specific Data, and 

Subsequent Model Applications, Onondaga Lake Basin, 

Onondaga County, New York

By William F. Coon

Abstract

Water-resource managers in Onondaga County, New 

York, are faced with the challenge of improving the water 

quality of Onondaga Lake, which has the distinction of being 

one of the most contaminated lakes in the United States. To 

assist in this endeavor, during 2003–07 the U.S. Geological 

Survey (USGS), in cooperation with the Onondaga Lake 

Partnership, developed a precipitation-runoff model of the 

285-square-mile Onondaga Lake Basin with the computer 

program Hydrological Simulation Program–Fortran (HSPF). 

The model was intended to provide a tool whereby the 

processes responsible for the generation of loads of sediment 

and nutrients that are transported to Onondaga Lake could 

be better understood. This objective was only partly attained 

because data for calibration of the model were available 

from monitoring sites only at or near the mouths of the 

major tributaries to Onondaga Lake; no calibration data 

from headwater subbasins, where the loads originated, were 

available. To address this limitation and thereby decrease the 

uncertainty in the simulated results that were associated with 

headwater processes, the USGS conducted a 3-year (2005–08) 

basinwide study to assess the quality of surface water in 

the Onondaga Lake Basin. The study quantified the relative 

contributions of nonpoint sources associated with the major 

land uses and land covers in the basin and also monitored 

known sources and presumed sinks of sediment and nutrient 

loads, which previously had not been evaluated. The use of the 

newly acquired data to recalibrate the HSPF model resulted in 

improvements in the simulation of processes in the headwater 

subbasins, including suspended-sediment, orthophosphate, and 

phosphorus generation and transport. 

Simulation of streamflows in small subbasins was 

improved by adjusting model parameter values to match base 

flows, storm peaks, and storm recessions more precisely than 

had been done with the original model. Simulated recessional and low flows were either increased or decreased as 

appropriate for a given stream, and simulated peak flows 

generally were lowered in the revised model. The use of 

suspended-sediment concentrations rather than concentrations 

of the surrogate constituent, total suspended solids, resulted 

in increases in the simulated low-flow sediment concentrations and, in most cases, decreases in the simulated peak-flow 

sediment concentrations. Simulated orthophosphate concentrations in base flows generally increased but decreased for peak 

flows in selected headwater subbasins in the revised model. 

Compared with the original model, phosphorus concentrations 

simulated by the revised model were comparable in forested 

subbasins, generally decreased in developed and wetlanddominated subbasins, and increased in agricultural subbasins. 

A final revision to the model was made by the addition of the 

simulation of chloride (salt) concentrations in the Onondaga 

Creek Basin to help water-resource managers better understand the relative contributions of salt from multiple sources in 

this particular tributary. The calibrated revised model was used 

to (1) compute loading rates for the various land types that 

were simulated in the model, (2) conduct a watershedmanagement analysis that estimated the portion of the total 

load that was likely to be transported to Onondaga Lake from 

each of the modeled subbasins, (3) compute and assess chloride loads to Onondaga Lake from the Onondaga Creek Basin, 

and (4) simulate precolonization (forested) conditions in the 

basin to estimate the probable minimum phosphorus loads to 

the lake.

Introduction

During 2003–07, the U.S. Geological Survey (USGS), 

in cooperation with the Onondaga Lake Partnership (OLP), a 

consortium of Federal, State, and local agencies, developed a 

basinwide precipitation-runoff model of the 285-square mile 

(mi2

) Onondaga Lake Basin, Onondaga County, New York 

(Coon and Reddy, 2008). The objective of the model was 

to assist water-resource managers in making management 

decisions regarding nonpoint-source (NPS) contaminant 

loads that were contributing to water-quality problems in 

Onondaga Lake; in 2010, the lake was still identified as one 
2 Improvement in Precipitation-Runoff Model Simulations by Recalibration and Model Applications, Onondaga Basin, N.Y.

of the most contaminated lakes in the United States owing 

to industrial and wastewater-treatment discharges, combined 

storm-and-sanitary-sewer overflows, and rural and urban 

nonpoint sources of pollution (Effler and Hennigan, 1996; 

Upstate Freshwater Institute, 2010). A complementary report 

(Coon, 2008) provided guidance on applications of the model 

to create and simulate scenarios of changes in the watershed. 

The simulated results could be compared with those from the 

calibrated model representing current conditions. 

The model, which simulated the period from October 

1997 through September 2003, was created by using the 

computer program Hydrological Simulation Program–Fortran 

(HSPF; Bicknell and others, 2001). The Onondaga Lake Basin 

was divided into 107 subbasins, and within these subbasins, 

the land area was apportioned among 16 pervious and 3 

impervious land types on the basis of land use and land cover, 

hydrologic soil group, and aspect. The land uses and land 

covers included forest, pasture hay, row crops, farmsteads 

(that is, livestock or dairy farms), urban or recreational grass, 

wetlands and ponds, low- and high-intensity residential areas, 

and commercial-industrial-transportation areas. Pervious and 

impervious components of the residential and commercialindustrial-transportation land uses were simulated separately. 

Precipitation data that were used as input to the model were 

available from three sources—the National Weather Service 

(NWS) (A.T. DeGaetano, Northeast Regional Climate Center, 

written commun., 2008), the USGS (U.S. Geological Survey, 

2008), and the Onondaga County Water Authority (OCWA) 

(M.J. Murphy, Onondaga County Water Authority, written 

commun., 2008). The model simulated streamflow, water temperature, concentrations of dissolved oxygen, and concentrations and loads of sediment, orthophosphate (OP), phosphorus 

(P), nitrate, ammonia, and organic nitrogen in the four major 

tributaries to Onondaga Lake—Onondaga Creek, Harbor 

Brook, Ley Creek, and Ninemile Creek (fig. 1). Additional 

background information on the Onondaga Lake Basin and 

development of the 1997–2003 version of the Onondaga Lake 

Basin model are presented in Coon and Reddy (2008).

The model was calibrated to flows and constituent 

concentrations and loads that were associated with long-term 

monitoring sites at or near the mouths of the major tributaries 

to Onondaga Lake. No streamflow or water-quality data 

associated with the sources of contaminants in the headwater 

areas of the basin were available for model calibration. 

Therefore, parameter values that would best reproduce the 

observed data at the downstream monitoring sites were 

estimated for the entire basin. Many assumptions regarding 

runoff processes and sediment- and nutrient-loading rates were 

made to calibrate the model. Although the model simulated 

observed flows and constituent loads at the mouths of the 

streams reasonably well, uncertainty in regard to the processes 

that generated flows and loads in the headwater subbasins 

limited the utility of the model. “Good” model results (as 

defined by Donigian, 2002) at the mouths of the tributaries 

could not have supported a claim that headwater processes 

were being simulated accurately.

During 2005–08, the USGS, again in cooperation with 

the OLP, conducted an NPS assessment study at 25 surfacewater sites in the Onondaga Lake Basin that included (1) small 

subbasins ranging in size from 0.09 to 12.6 mi2 to characterize 

the load contributions from areas dominated by a single land 

use and (or) subbasins with previously identified water-quality 

problems, and (2) locations along the major streams in the 

basin to document changes in constituent concentrations as 

loads were carried downstream toward the lake (Coon and 

others, 2009). Flows were measured and water samples were 

analyzed for nutrients and suspended sediment. The newly 

acquired data were used to update and improve the Onondaga 

Lake Basin model by decreasing the uncertainty in the loadgeneration processes in the headwater areas of the basin and 

thereby increasing the likelihood that the model was simulating the correct results at the mouths of the tributaries for the 

correct reasons. 

This report documents the changes in model structure 

and parameter values that were required to recalibrate the 

original version of the Onondaga Lake Basin model (with a 

simulation period 1997–2003) to flow and water-quality data 

collected during 2005–08. The report compares the results 

of simulations of flow and concentrations of suspended 

sediment (SS), OP, and P in selected head-water subbasins, 

as well as at the long-term monitoring sites on the major 

tributaries to Onondaga Lake, by the original (2003) and 

revised (2008) models for the period from October 1, 2005, 

through September 30, 2008. The report then presents several 

applications of the model and a scenario comparison that 

demonstrates the utility of the model as a water-resources 

management tool for the members of the OLP.

New Data for Model Recalibration

The NPS study (2005–08; Coon and others, 2009) 

included periodic measurements of streamflow and collection 

of water-quality samples at 22 surface-water sites in the basin; 

water-quality samples also were collected at three long-term 

streamflow-monitoring sites (table 1; fig. 1). Continuous flow 

records from nine USGS streamflow-monitoring sites (U.S. 

Geological Survey, 2009) and water-quality data from seven 

of the nine sites and two additional sites, which were operated by Onondaga County Department of Water Environment 

Protection (OCWEP; Antonio Deskins, Onondaga County 

Department of Water Environment Protection, written commun., 2008), also were available for recalibration of the 

model. Water-quality constituents that were analyzed for the 

NPS study included ammonia nitrogen (NH3), nitrite nitrogen 

(NO2), nitrate-plus-nitrite nitrogen (NOx), ammonia-plusorganic nitrogen (TKN; unfiltered and filtered), orthophosphate (OP), phosphorus (P; unfiltered and filtered), and suspended sediment (SS). Selected samples also were analyzed 

for total suspended solids (TSS). Measured streamflows and 

concentrations of SS, OP, and P were used to recalibrate the 

appropriate modules of the model.
New Data for Model Recalibration 3

CAYUGA COUNTY

ONONDAGA COUNTY

CORTLAND COUNTY

ONONDAGA COUNTY

Harbor

Brook

Onondaga

Creek

Ley

Creek

Creek

Ninemile

Brook

Geddes

Furnace

Brook

Doust Creek

West

Branch

Onondaga Creek

Onondaga

Creek

Creek

Spafford

Willow

Brook

Rice Brook

Gulf Rattlesnake

Creek.

Rainbow

North

Branch

South

Branch

Onondaga

Reservoir

Sawmill Creek

Bloody Brook

Creek

Ninemile

Onondaga Lake

Otisco Lake

Marietta

Marcellus

Camillus

Lakeland

Tully Valley

Cardiff

Tully

South

Onondaga

Otisco

Borodino

Spafford

Marcellus Falls

Fairmount

Nedrow

East Syracuse

Collamer

Liverpool

Rice Grove

Williams Grove

Indian

Village

Otisco Valley

20

80

11A

81

173

5

174

175

174

80

11

481

690

695

90

5

90

11

81

20

81

173

175

20

Syracuse

Onondaga

Nation

Syracuse Hancock

International Airport

Mudboils

04240011

04240010

04239000

04240100

04240300

04240470

04237962

04237956

04240145

04240170

04238550

04240152

04240158

04240180

04240253

04240200

04240182

04240108

04239800

04237995

04237955

04237953

04237952

04237950

04237917 04240150

 04238000

0424011445

0424015305

0423013502

430415076055901

430317076054201

04240105

04240120

EXPLANATION

Drainage area of sewered site

Municipality and name

Onondaga Lake Basin

Cardiff

04240180 Nonpoint-source-study water-qualitymonitoring site and site number

04239000 U.S. Geological Survey streamflow

and(or) Onondaga County water-qualitymonitoring site and site number

Base from U.S. Geological Survey, Seamless Data Distribution System,

accessed in 2006 at http://seamless.usgs.gov 

Universal Transverse Mercator projection, Zone 18, NAD 83

Location Map

Onondaga Lake

Basin

NEW

YORK

0 5 MILES

0 5 KILOMETERS

76°20' 76°10' 76°

43°

42°50'

Figure 1. Locations of streamflow- and water-quality-monitoring sites in the Onondaga Lake Basin, Onondaga County, New York, 

2005–08.
4 Improvement in Precipitation-Runoff Model Simulations by Recalibration and Model Applications, Onondaga Basin, N.Y.

Table 1. Streamflow- and water-quality-monitoring sites in the Onondaga Lake Basin, Onondaga County, New York, 2005–08.

[Site locations are shown in figure 1. mi2, square miles; USGS, U.S. Geological Survey; OCWEP, Onondaga County Department of Water Environment Protection; Site type: NPS, periodic streamflow measurements and water-quality sampling by USGS as part of nonpoint source study, 2005–08 (Coon and others, 

2009); LT, long-term streamflow monitoring by USGS and water-quality sampling by OCWEP; LT-Q + NPS-QW, long-term streamflow monitoring and periodic 

water-quality sampling (2005–08) by USGS; LT-QW, long-term water-quality sampling by OCWEP; --, no data]

Site-identification

number Site name and location

Drainage 

area 

(mi2)

Reach

number

Site type

NPS LT

LT-Q 

+

NPSQW

LTQW

04237917 Onondaga Creek northwest of Tully 6.40 102 X -- -- --

04237950 Onondaga Creek at Tully Valley 16.4 106 X -- -- --

04237952 Rainbow Creek at Route 11A at Tully Valley 2.37 105 X -- -- --

04237953 Rattlesnake Gulf at Otisco 2.77 107 X -- -- --

04237955 Rattlesnake Gulf at Tully Farms Road near Cardiff 9.06 109 X -- -- --

04237956 Onondaga Creek north of Tully Valley 28.9 110 X -- -- --

04237962 Onondaga Creek near Cardiff 33.9 111 -- -- X X

04237995 West Branch Onondaga Creek near South Onondaga 12.6 114–115 X -- -- --

04238000 West Branch Onondaga Creek at South Onondaga 22.1 118 X -- -- --

04238550 Onondaga Creek at Indian Village 69.9 122 X -- -- --

04239000 Onondaga Creek at Dorwin Avenue, Syracuse1 88.5 128 -- X -- --

04239800 Furnace Brook at Syracuse 3.71 133 X -- -- --

04240010 (04240011) Onondaga Creek at Spencer Street (Kirkpatrick Street), Syracuse1,2 110 137 -- X -- --

04240100 Harbor Brook (above Holden Street) at Syracuse1 10.1 205 -- X -- --

04240105 Harbor Brook at Hiawatha Boulevard, Syracuse1 12.1 206 -- X -- --

04240108 North Branch Ley Creek at Collamer 4.15 302 X -- -- --

0424011445 South Branch Ley Creek at Exeter Street at East Syracuse 3.73 304 X -- -- --

04240120 Ley Creek at Park Street, Syracuse 29.9 312 -- X -- --

0424013502 Bloody Brook above mouth at Liverpool 3.86 501 -- -- -- X

04240145 Spafford Creek at Bromley Road near Spafford 3.14 400 X -- -- --

04240150 Spafford Creek at Sawmill Road at Otisco Valley 8.06 402 X -- -- --

04240152 Otisco Lake tributary at Williams Grove 0.56 499 X -- -- --

0424015305 Rice Brook at Rice Grove 2.44 404 X -- -- --

04240158 Willow Brook near Borodino 1.95 405 X -- -- --

04240170 Otisco Lake at Marietta 42.3 409 X -- -- --

04240180 Ninemile Creek near Marietta 45.1 410 -- -- X --

04240182 Doust Creek near Marcellus 1.01 412 X -- -- --

04240200 Ninemile Creek at Camillus 84.3 430 -- -- X --

04240253 Geddes Brook at Fairmount 8.29 441 X -- -- --

04240300 Ninemile Creek at Lakeland1 115 443 -- X -- --

04240470 Sawmill Creek at Liverpool 2.34 502 -- -- -- X

430317076054201 Erie Boulevard outfall to South Branch Ley Creek, Syracuse 0.10 304 X -- -- --

430415076055901 Lamson Street outfall to South Branch Ley Creek tributary, Syracuse 0.09 305 X -- -- --

1

Suspended-sediment samples were collected periodically at this site as part of the nonpoint source study (Coon and others, 2009).

2

Streamflow is monitored at Spencer Street (04240010), but water-quality samples are collected at Kirkpatrick Street (04240011), 0.15 mile downstream.
Model Revisions 5

Model Revisions

A major change to the 1997–2003 version of the 

Onondaga Lake Basin model, hereafter referred to as the 2003 

model, was the lengthening of the simulation period from an 

end date of September 2003 to an end date of September 2008; 

this change was the basis for the revised model, hereafter 

referred to as the 2008 model. The addition of this 5-year 

period necessitated the extension of all the model input files, 

including the meteorological datasets and known inflows 

and point sources of sediment and nutrients. Although the 

simulation period of the 2008 model was from October 1997 

through September 2008, the recalibration period was only 

from October 2005 through September 2008, which coincided 

with the period of the NPS study. Calibration of the 2008 

model resulted in structural and parameter-value changes to 

the model.

Extension of Input Datasets

Three precipitation records, one each from the National 

Weather Service (NWS) station north of Syracuse, N.Y., at the 

Syracuse Hancock International Airport, a USGS station near 

Tully Valley in the upper part of the Onondaga Creek Basin, 

and an Onondaga County Water Authority (OCWA) station at 

the north end of Otisco Lake (fig. 2), were used in the 2003 

model. These records were applied to three areas of the 

Onondaga Lake Basin as approximately defined by Thiessen 

(1911) polygons. The precipitation records from the NWS, 

USGS, and OCWA stations were targeted to areas B and C, 

area A, and areas D and E, respectively, as shown in figure 2. 

The NWS station at the Hancock Airport also provided hourly 

time series of air temperature, dew-point temperature, wind 

speed, and percentage of cloud cover. Time series of solar 

radiation and potential evapotranspiration were computed 

from the NWS-furnished data. These additional meteorological datasets were applied to the entire Onondaga Lake Basin. 

All the meteorological-data time series were extended to the 

end of the new simulation period, September 30, 2008. 

Time series of daily precipitation from Next-Generation 

Radar (NEXRAD) data (DeGaetano and Wilks, 2008) were 

obtained through the Northeast Regional Climate Center 

(A.T. DeGaetano, Northeast Regional Climate Center, Ithaca, 

N.Y., written commun., 2008). Because these data were 

unavailable prior to January 1, 2005, and therefore did not 

span the entire simulation period, the data were not incorporated into the model. Instead, the NEXRAD data were used to 

fill in periods of erroneous or questionable data that resulted 

from periodic equipment malfunction at the Tully Valley rain 

gage. The NEXRAD data were substituted for the rain-gage 

data from January 2005 through April 2006 and from April 

through September 2008 at this site.

Other time series of input data were extended and added 

to the model. Daily sediment loads from mudboils, volcanolike cones of fine sand and silt, near Tully Valley, N.Y., in the 

upper Onondaga Creek Basin (fig. 1; Kappel and McPherson, 

1998; Kappel, 2009) were computed from daily streamflows 

and weekly sediment concentrations with the USGS Load 

Estimation (LOADEST) program (Runkel and others, 2004). 

Because the sediment from the mudboils is derived from 

groundwater under confined conditions moving upward 

through a dense layer of silt and clay, fluctuations in loads 

result from the opening of new or the clogging of old mudboil 

vents rather than from surface runoff and erosional processes. 

Bias in the sediment-load estimates was minimized by using 

the minimum-variance unbiased estimator in the maximumlikelihood estimation method (Cohn, 1988; Cohn and 

others, 1992).

Hourly loads of P, TKN, NH3

, and organic nitrogen 

(OrgN) from the Village of Marcellus, N.Y., wastewatertreatment plant in the Ninemile Creek Basin were estimated 

from once-monthly instantaneous flows and constituent 

concentrations (Greg Crysler, Marcellus wastewater-treatment 

plant operator, written commun., 2008) that were assumed 

to be representative of flows and concentrations for a given 

month. Discharges documented by seasonal measurements 

from springs in the carbonate-rock aquifers of the Onondaga 

and Bertie Limestone to Onondaga Creek in the southern part 

of the city of Syracuse and Ninemile Creek near Marcellus 

Falls (fig. 1) were used to correct discrepancies in base flows 

measured at the monitoring sites downstream from the springs. 

These discrepancies in base flows arose because the springs, a 

localized source of water, were not accurately simulated by the 

groundwater-discharge processes for the pervious land types in 

the model.

Structural Changes

Structural changes were made to the model by the subdivision of an existing subbasin and by revisions to the areas 

of specific land types in selected subbasins to reflect updated 

land-use and land-cover data. Changes to hydrologic response 

units (HRUs) were required. An existing HRU (row crops in 

lacustrine silt-and-clay soils) was removed from the model, 

and new HRUs to simulate large sediment loads from landslides and temporal changes in orthophosphate loads in the 

Harbor Brook Basin were added. Finally, the water-quality 

effects of Onondaga Reservoir at the confluence of Onondaga 

Creek and West Branch Onondaga Creek were incorporated 

into the model. The mitigative effects of Otisco Lake on water 

quality were also evaluated, but no structural changes to the 

model were required to simulate these effects.

New Otisco Lake Tributary Subbasin

A small 0.56-mi2 subbasin of the Otisco Lake Basin 

was included in the 2005–08 NPS study. To permit direct 

calibration of the effects of a farmstead, which dominated the 

water-quality characteristics of this subbasin, the subbasin was 

delineated, assigned a unique subbasin number (499; fig. 2), 
6 Improvement in Precipitation-Runoff Model Simulations by Recalibration and Model Applications, Onondaga Basin, N.Y.

Subbasin boundary and number

409

503

417

121

127

111

137

108

303

112

434

130

501

401

304

405

406

116

306

125

104

439

115

422

436

123

118

428

310

113

402

400

129

408

442

204

117

502

301

410

407

302

102

110

427

418

423

107

429

100

433

435

119

101

404

103

106

438

440

202

105

441

124

305

122

126

132

136

120

205

308

114

403

206

437

133

425

109

415

430

131

419

128

201

432

414

416

424

421

412

413

311

312

411

203

135

207

134

134

420

313 307

138

309

443

499

444

426

431

409

100

0 5 MILES

0 5 KILOMETERS

Syracuse Hancock

International Airport

Tully Valley

Otisco Lake

EXPLANATION

A. Upper and middle Onondaga Creek Basins

B. Ley Creek and lower Onondaga and

Ninemile Creek Basins

C. Harbor Brook Basin

D. Otisco Lake Basin

E. West Branch Onondaga Creek and middle Ninemile Creek Basins

Precipitation station

Lake

Onondaga

Lake

Otisco

HarborBrook

Onondaga

Creek

Ley Creek

Creek

Ninemile

West

Branch OnondagaCreek

Onondaga

Creek

Creek Spafford

Ninemile

Creek

Base from U.S. Geological Survey, Seamless Data Distribution System,

accessed in 2006 at URL http://seamless.usgs.gov

Universal Transverse Mercator projection, Zone 18, scale 1:250,000

76°20' 76°10' 76°

43°

42°50'

C

D

A

B B

E

Figure 2. Subbasins and major hydrologic subdivisions used in the 2008 version of the precipitation-runoff model of the Onondaga 

Lake Basin, Onondaga County, New York.
Model Revisions 7

and incorporated into the model. The parameter values that 

were selected to calibrate sediment and nutrient concentrations 

measured in this subbasin—Otisco Lake tributary at Williams 

Grove (station number 04240152; fig. 1)—were used to 

simulate farmstead land types elsewhere in the Onondaga 

Lake Basin.

Revisions to Land-Use and Land-Cover Acreages

Land uses and land covers classified by the 1992 and 

2001 National Land Cover Data datasets (NLCD; U.S. 

Geological Survey, 1999, 2005) were both available during 

the development of the 2003 model (Coon and Reddy, 2008), 

but only the 1992 NLCD were used because the 2001 NLCD 

had not been finalized at the time. The 2001 NLCD were 

reviewed during calibration of the 2008 model to identify 

any substantial changes in land uses between 1992 and 2001. 

Direct comparison of the two datasets was hindered because 

land types were defined differently in 2001 than in 1992. 

Nevertheless, comparisons showed that land types for almost 

96 percent of the basin remained unchanged between 1992 

and 2001. 

The two largest differences in land use from 1992 to 

2001 were the apparent conversion of agricultural land to 

wetlands (1,946 acres) and forest (4,201 acres); however, 

these results more likely reflected misclassification of land 

types by one of the surveys rather than real changes in 

land types. For instance, wetlands that were erroneously 

classified as row crops in the 1992 NLCD (Coon and Reddy, 

2008) were correctly identified in the 2001 NLCD, which 

incorporated freshwater wetlands regulated by the New York 

State Department of Environmental Conservation (1999) and 

wetlands from the National Wetland Inventory (U.S. Fish and 

Wildlife Service, 2000). Wetlands from these two datasets 

were included in the wetland geographic information system 

(GIS) layer that was developed for and used to correct this 

land-type error in the 2003 model. Forested areas, as defined 

by the 2001 NLCD, are characterized by woody vegetation 

that is generally greater than about 20 feet (ft) (6 meters) tall, 

a tree height that could not be attained in 9 years on land that 

was formerly classified as agricultural land. For this reason, 

the 1992 NLCD classification was retained for HRUs where 

the 2001 NLCD indicated conversion of agricultural to 

forested land.

Although areas of row-crop and pasture-hay land in 

the 1992 NLCD might have changed in specific locations 

identified in the 2001 NLCD, the total area covered by these 

land uses in a given subbasin did not change substantially, and 

therefore the acreages associated with these land uses were not 

revised in the 2008 model. Areas of urban development were 

scrutinized to assess the extent of urban expansion, especially 

in the northern third of the Onondaga Lake Basin. Acreages 

of developed land uses were adjusted in 13 subbasins where 

at least 9 acres (an arbitrary size) of forested and wetland land 

were converted to developed land. Areas of urban developed 

land increased the most in the headwater subbasins of North 

Branch Ley Creek (subbasins 301–303 and 310; fig. 2) and 

the subbasins that drain directly to Onondaga Lake (subbasins 

501–503; fig. 2).

Changes to Hydrologic Response Units

Within the 2003 model of the Onondaga Lake Basin, 

the land area was segmented into 22 HRUs, which included 

16 pervious land types (PERLNDs) and 6 impervious land 

types (IMPLNDs). Each PERLND (which was defined on the 

basis of land use or land cover, hydrologic soil group, and 

aspect) and each IMPLND (which was defined on the basis 

of land use) was assumed to show homogeneous hydrologic 

and water-quality responses to meteorological inputs. The 

data that were collected during the NPS study indicated that 

one PERLND that simulated row crops grown in lacustrine 

silt-and-clay soils was unnecessary and that a new PERLND 

that simulated landslide processes was required. PERLNDs to 

simulate high and seasonally variable concentrations of OP in 

the Harbor Brook Basin also were added to the model.

Elimination of Unique Row-Crop PERLND

Paschal and Sherwood (1987) monitored the water quality of the five main tributaries of Otisco Lake during 1981–83, 

estimated sediment and nutrient loads from each subbasin, 

and related these loads to land use, geology, and soil type. 

They identified a disproportionately large sediment load from 

Spafford Creek (subbasins 400–403; fig. 2), the largest of the 

five tributaries, and concluded that the source of this sediment 

was the lacustrine silt-and-clay soils in row-crop use in the 

valley bottom. Spafford Creek carried 72 percent of the total 

sediment load that was transported to Otisco Lake during the 

1982–83 water years; the annual yield (load per unit area) was 

0.52 short ton per acre compared to 0.05 to 0.12 ton per acre 

for other tributaries. On the basis of this analysis, the 2003 

model was set up to mimic this sediment load in the Spafford 

Creek subbasin as well as in other locations with similar conditions throughout the Onondaga Lake Basin. Loading rates 

for row-crop areas that were not in lacustrine silt-and-clay 

soils were calibrated to the low rates in the other Otisco Lake 

subbasins. A unique PERLND—row crops in lacustrine siltand-clay soils—was created for the Spafford Creek subbasin 

and calibrated in the 2003 model to make the final basinwide 

yield approximate the computed rate of 0.52 ton per acre per 

year. In fact, the loading rate for this PERLND was increased 

to more than 15 tons per acre per year, which seemed excessive and produced a basinwide yield of only 0.38 ton per 

acre per year. Additional increases in the loading rate for this 

PERLND were not pursued for the 2003 model. 

During the 2005–08 NPS study (Coon and others, 

2009), three of the five major tributaries to Otisco Lake, 

including Spafford Creek, were monitored. The results of 

this study indicated that although Spafford Creek still had 

the largest yield of suspended sediment, the yield was not 

4 to 10 times larger than the yields at the other sites as the 
8 Improvement in Precipitation-Runoff Model Simulations by Recalibration and Model Applications, Onondaga Basin, N.Y.

data from Paschal and Sherwood (1987) seemed to indicate. 

Presumably agricultural-management practices in the Spafford 

Creek subbasin decreased sediment loads subsequent to 1983. 

Recalibration of the model indicated that all row-crop land 

uses could be simulated with a single PERLND, and that 

the unique PERLND—row crops in lacustrine silt-and-clay 

soils—was unnecessary. For this reason, the unique PERLND 

was removed from the model.

Creation of New Landslide PERLND

Rainbow Creek (subbasin 105, fig. 2) and Rattlesnake 

Gulf (subbasins 107–109, fig. 2), two tributaries to Onondaga 

Creek in the headwater area of that basin, are known 

sources of large sediment loads (Coon and others, 2009). 

The magnitudes of these loads, which are derived from the 

erosion of landslide materials within their respective basins, 

were undocumented prior to the 2005–08 NPS study. Model 

parameter values that controlled sediment processes—soil 

detachment, washoff, and scour—were adjusted in the 2008 

model to match the suspended-sediment concentrations 

measured in these streams. These adjustments to parameter 

values for existing PERLNDs, however, failed to produce 

the desired results in Rainbow Creek and Rattlesnake Gulf 

without also adversely affecting SS concentrations simulated 

in other streams. Therefore, a new PERLND (no. 17) with 

exceptionally high values for the soil-detachment, washoff, 

and scour parameters was created for these two subbasins in 

the 2008 model. The areal extents of the landslide areas were 

determined by Tamulonis and others (2009).

Creation of New PERLNDs in Harbor Brook Basin

Observed OP concentrations in Harbor Brook (area C 

in fig. 2) were much higher near the mouth of the stream (at 

Hiawatha Boulevard, site 04240105) than concentrations 

farther upstream (above Holden Street, site 04240100; table 1; 

fig. 1) and in other streams in the Syracuse urban area. Also, 

base-flow concentrations of OP increased during the 2003–08 

simulation period, which violated the modeling assumption 

that basin processes were relatively constant during the 

simulation period and made matching simulated and observed 

OP concentrations unlikely with a single parameter set in the 

2008 model. Eighty-six percent of the Hiawatha Boulevard 

subbasin (no. 206, fig. 2) is classified as having developed 

land uses, and storm runoff from the entire subbasin flows into 

a combined sanitary-and-storm sewer system. Additionally, 

Harbor Brook flows through a tunnel for about half the 

distance between Holden Street and Hiawatha Boulevard 

(sites 04240100 and 04240105 in fig. 1). Plausible reasons 

for the high and gradually increasing OP concentrations were 

sought, but data were unavailable to support any proposed 

explanation. 

Because HSPF, as structured for the Onondaga Lake 

Basin model, is designed to simulate average or representative conditions in a basin during the period of simulation, 

parameter values that control OP concentrations could not 

be adjusted to mimic the observed data. Attempts to resolve 

the simulation discrepancies at Hiawatha Boulevard failed 

because improvements in OP simulations in this subbasin 

resulted in degraded simulated-to-observed relations at other 

calibration sites. The solution to this problem was to create a 

new set of PERLNDs to permit simulation of high-OP contributions from pervious land in the combined sanitary-andstorm sewered areas of the Harbor Brook Basin and to add 

instructions to the special-actions module of HSPF to permit 

simulation of the increasing trend in the OP concentrations 

during the simulation period. These changes permitted high 

and seasonally variable concentrations of OP to be simulated 

at Hiawatha Boulevard without affecting the simulation results 

for other urban areas of the Onondaga Lake Basin.

Mitigative Effects of the Onondaga Reservoir

The Onondaga Reservoir on Onondaga Creek 

downstream from the confluence with West Branch Onondaga 

Creek (fig. 1) was constructed by the U.S. Army Corps of 

Engineers in 1949 to control flooding in Syracuse. This dam, 

which has a capacity of 18,200 acre-feet and can create an 

860-acre pool at the spillway crest elevation of 504.5 ft (U.S. 

Army Corps of Engineers, 1945), controls flows from a 

67.7-mi2 drainage area. Although this dam is a flow-through 

structure with an open tunnel but without gates or any other 

mechanism to retain storm runoff, by design it does attenuate 

stormflows and temporarily detains water and, depending on 

water levels, disperses stormwater across the flood plain. 

The two major inflows to the reservoir—Onondaga 

Creek near Cardiff, N.Y. (site 04237962) and West Branch 

Onondaga Creek at South Onondaga, N.Y. (site 04238000)—

and the outflow from the reservoir—Onondaga Creek at 

Indian Village, N.Y. (site 04238550, table 1; fig. 1)—were 

monitored during the NPS study. On the basis of instantaneous 

loads computed from limited data collected at these three 

sites (Coon and others, 2009; table 2), constituent removal 

efficiencies that could be attributed to the combined effects 

of the reservoir and the low-gradient channel upstream from 

the reservoir were estimated. These removal efficiencies 

were found to be related to flow regime. For all measured 

constituents except NH3, the reservoir had small or no effects 

on constituent loads during base-flow periods; NH3 loads in 

base-flow outflows decreased compared to inflows. Loads 

of all constituents decreased during storm-runoff periods 

when the constriction of the tunnel caused water to back up, 

disperse, and deposit sediment onto the flood plain. These 

results were simulated in the model by splitting the inflow to 

the reservoir between low flows, which were routed directly 

to the downstream reach, and high flows, which were routed 

to the HSPF best-management practice module (BMPRAC). 

Removal fractions were calibrated to reproduce the removal 

efficiencies estimated from data for water years 2007–08. 
Model Revisions 9

Table 2. Estimated removal efficiencies for selected constituents 

for the Onondaga Reservoir on Onondaga Creek, Onondaga County, 

New York, 2006–08.

[Removal efficiencies were computed from limited data collected during 

2006–08 (Coon and others, 2009). A negative (positive) value indicates a 

decrease (increase) in the constituent loads from inflow to outflow]

Constituent

Estimated removal efficiency,

in percent

Base flow Stormflow All flows

Ammonia nitrogen -33 -52 -50

Ammonia-plus-organic nitrogen 13 -65 -62

Nitrate-plus-nitrite nitrogen 15 -38 -32

Orthophosphate 3 -54 -52

Phosphorus 25 -64 -63

Suspended sediment 1 -39 -39

Mitigative Effects of Otisco Lake

Otisco Lake, with a surface area of 2.93 mi2 and an 

average depth of 33.5 ft, holds 21 billion gallons of water at 

its mean elevation of 788 ft (Bloomfield, 1978). The large 

volume and relatively long detention time of the lake mitigate 

the loads of sediment and nutrients that enter the lake. This 

mitigative effect was assessed by comparing data collected 

during the NPS study (2005–08) for inflows from three of 

the major tributaries to the lake—Spafford Creek at site 

04240150, Rice Brook at site 0424015305, and Willow Brook 

at site 04240158 (fig. 1; table 1), which collectively drain 

43 percent of the Otisco Lake Basin—with data for outflow 

from the lake at Marietta, N.Y., site 04240170 (fig. 1; table 1; 

Coon and others, 2009). 

Outflows, which are regulated by the dam at the north end 

of the lake, do not reflect time-specific hydrologic and waterquality processes in the Otisco Lake Basin. In other words, 

the magnitude and quality of the lake’s outflow are not related 

to the magnitude and quality of concurrent flows entering the 

lake because of the storage and mixing characteristics of the 

lake. For this reason and because flow data were unavailable 

to compute loads, median concentrations of nutrients and 

SS were compared between inflows and outflow to assess 

the lake’s mitigative effects on these constituents (Coon and 

others, 2009). The concentrations in Otisco Lake outflow were 

much lower than in the inflows for all constituents, except 

NH3

, for which concentrations were similar in magnitude. 

Median outflow concentrations of TKN, NOx

, and OP were 

65, 83, and 85 percent lower than the respective averages of 

the median concentrations in inflows from the three monitored 

tributaries to the lake. The most striking differences were for 

P and SS, for which median outflow concentrations were only 

9 and 4 percent, respectively, of the average of the three inflow 

median concentrations. 

For the 2003 model, water-quality loads in Otisco Lake 

outflow were computed from average summertime epilimnion 

concentrations (Callinan, 2001; C.W. Callinan, New York 

State Department of Environmental Conservation, written 

commun., 2004) and daily lake outflows (M.J. Murphy, 

Onondaga County Water Authority, written commun., 2004), 

and were input to the receiving stream reach (RCHRES) 

as point sources of constituent loads (Coon and Reddy, 

2008). Calibration of the 2008 model was achieved by 

simulating Otisco Lake as a flow-through RCHRES; that 

is, outflow constituents were routed directly from the lake 

to the downstream reach. Neither input of constituent loads 

as point sources nor simulation of constituent removals by 

a BMPRAC, as was done with Onondaga Reservoir, were 

necessary. The simulated loads of P and OP in the outflow 

from Otisco Lake were 14 and 12 percent, respectively, 

of the combined inflow loads to the lake, which included 

the simulated loads from the five major tributaries and the 

estimated loads from the areas that drain directly to the lake.

Changes to Model Parameter Values and 

Comparison of 2003 and 2008 Simulation Results

Model parameter values were changed on the basis 

of recalibration of simulated flows and concentrations and 

loads of sediment and nutrients on the basis of instantaneous 

measured flows, daily streamflows (where available), and all 

chemical-concentration data that were collected during 2005–

08 at the 25 NPS sites (Coon and others, 2009). In addition, 

continuous flow records from nine USGS streamgages (U.S. 

Geological Survey, 2009) and water-quality data from seven 

colocated and two additional water-quality monitoring sites, 

which were operated by the OCWEP (Antonio Deskins, 

Onondaga County Department of Water Environment 

Protection, written commun., 2008), also were available for 

recalibration of the model. All data from these latter sites, 

including the 1997–2003 data that had been used to calibrate 

the 2003 model, as well as new data that had been collected 

during 2003–08, were used to calibrate the 2008 model.

The results from simulations by the 2003 and 2008 

versions of the model were compared for the period October 1, 

2005 through September 30, 2008. Five reaches that represent 

subbasins dominated by a particular land type were selected 

to compare results for the headwater areas of the basin; 

the names of the streams, reach and subbasin numbers, 

monitoring-site identification numbers, and the dominant 

land types in the subbasins are listed in table 3. In addition, 

the results for the four long-term monitoring sites near the 

mouths of the major tributaries to Onondaga Lake—Onondaga 

Creek (site 04240010), Harbor Brook (site 04240105), Ley 

Creek (site 04240120), and Ninemile Creek (site 04240300; 

fig. 1; table 1)—were also compared to assess changes in 

simulated flows and constituent concentrations as a result of 

model recalibration. 
10 Improvement in Precipitation-Runoff Model Simulations by Recalibration and Model Applications, Onondaga Basin, N.Y.

Table 3. Selected headwater subbasins for comparison of output from the 2003 and 2008 versions of the Onondaga Lake Basin 

models, Onondaga County, New York.

[Values in parentheses under “Dominant land types” are percentages of the total area in each subbasin]

Stream

Model-reach 

subbasin 

number

Monitoring-site 

identification 

number

Drainage area, 

in square 

miles

Dominant land types

Onondaga Creek 102 04237917 6.40 Forest (62) and agriculture (33).

Rattlesnake Gulf 109 04237955 9.06 Forest (47) and agriculture (47), but water quality is 

dominated by erosion of landslide materials.

North Branch Ley Creek 302 04240108 4.15 Mixed uses: forest (37), agriculture (25), and developed 

(10), but water quality is dominated by wetland (27).

South Branch Ley Creek 304 0424011445 3.73 Residential (47) and commercial, industrial, and 

transportation (27).

Willow Brook 405 04240158 1.95 Agriculture (79).

Changes to the Hydrologic Components of the 

Model

Changes made to parameter values controlling hydrologic 

components from the 2003 to the 2008 model had noticeable 

effects on the simulated hydrographs of streams in the 

small headwater subbasins (fig. 3). The active-groundwaterrecession coefficient (AGWRC) controls the rate at which 

groundwater discharges to streams. On the basis of flow 

data recorded on South Branch Ley Creek (fig. 3D) and 

Geddes Brook (model results not shown), the values of 

AGWRC were decreased for the developed HRUs in these 

subbasins in the 2008 model. Conversely, in the Harbor Brook 

Basin, the AGWRC values for residential and commercialindustrial-transportation uses were increased slightly. The 

groundwater-outflow modifier (KVARY) was adjusted by land 

type in the 2008 model rather than by the major hydrologic 

subdivisions that were defined by precipitation records (fig. 2) 

in the 2003 model. On the basis of simulation results for the 

agriculture-dominated Willow Brook Basin, the lower-zone 

evapotranspiration value (LZETP) was increased for row 

crops during the summer months in the 2008 model (see 

fig. 3E). The timing and magnitude of wintertime peak flows 

were improved by lowering the wet-bulb air temperature, 

below which precipitation occurs as snow under saturated 

conditions (TSNOW).

On the basis of flow data recorded on North Branch Ley 

Creek (fig. 3C), which drains a low-gradient area of which 

27 percent is covered by wetlands, the length of the assumed 

overland flow plane was increased and the slope of the overland flow plane was decreased to delay the response time to 

overland runoff. To decrease summer flows, water losses due 

to evapotranspiration were increased by doubling the potential 

evapotranspiration associated with wetlands and increasing the 

values for evapotranspiration from active groundwater storage (AGWETP). This adjustment was considered reasonable 

given that (1) potential evapotranspiration was computed by 

the Hamon (1961) method, which is solely a function of daily 

mean air temperature and the number of possible hours of sunshine, and makes no allowance for different vegetation types, 

and (2) wetland vegetation, such as cattails, have an unlimited 

supply of water and a large ratio of leaf-surface area to land 

area, which would maximize transpiration rates.

As a result of these revisions, simulated recessional and 

low flows were either increased or decreased as appropriate 

for a given stream. Of the five headwater sites selected for 

comparison (table 3), peak flows simulated by the 2008 model 

generally were lower than those simulated by the 2003 model 

(fig. 3); only the peak flows for Willow Brook (fig. 3E) were 

consistently higher with the 2008 model than with the 

2003 model.

At the calibration sites near the mouths of the major 

tributaries to Onondaga Lake, the effects of the hydrologic 

revisions to the model were mixed (fig. 4). In most instances 

for these downstream sites, the simulated flows from the two 

versions of the model were reasonably close. This outcome 

was not unexpected, because streamflow data were available 

and used to calibrate flows at these sites in both versions 

of the model. Nevertheless, differences in simulated low 

flows were noticeable for Onondaga Creek (fig. 4A), Harbor 

Brook (fig. 4B), and Ninemile Creek (fig. 4D). Peak flows 

in Harbor Brook simulated by the 2008 model generally 

decreased, whereas those in Ninemile Creek generally 

increased. Simulated peak flows in Onondaga Creek either 

decreased or increased; whereas those in Ley Creek (fig. 4C) 

were essentially unchanged from those simulated by the 
Model Revisions 11

0

1

10

100

1,000

10,000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

0

1

10

100

1,000

10,000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

0

1

10

100

1,000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

0

1

10

100

1,000

10,000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

0

1

10

100

1,000

10,000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

EXPLANATION

Observed streamflow

2003 model

2008 model

Streamflow, in cubic feet per second

Streamflow, in cubic feet per second

B

C D

E

A

Figure 3. Streamflows simulated by the 2003 and 2008 versions of the Onondaga Lake Basin model, Onondaga County, New York, for 

selected headwater subbasins, 2005–08: A, Onondaga Creek (reach 102), B, Rattlesnake Gulf (reach 109), C, North Branch Ley Creek 

(reach 302), D, South Branch Ley Creek (reach 304), and E, Willow Brook (reach 405).
12 Improvement in Precipitation-Runoff Model Simulations by Recalibration and Model Applications, Onondaga Basin, N.Y.

10

100

1,000

10,000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

1

10

100

1,000

10,000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

1

10

100

1,000

10,000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

10

100

1,000

10,000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

EXPLANATION

Observed streamflow

2003 model

2008 model

Streamflow, in cubic feet per secondStreamflow, in cubic feet per second

B

C D

A

Figure 4. Streamflows simulated by the 2003 and 2008 versions of the Onondaga Lake Basin model, Onondaga County, New York, at the 

mouths of major tributaries to the lake, 2005–08: A, Onondaga Creek (reach 137), B, Harbor Brook (reach 206), C, Ley Creek (reach 312), 

and D, Ninemile Creek (reach 443).
Model Revisions 13

2003 model. Despite these discrepancies, agreement and 

even overall improvement in streamflow simulations by the 

2008 model compared to those generated by the 2003 model 

were noted. For example, the flow durations computed by 

the 2003 model for the 1997–2003 simulation period and by 

the 2008 model for the 1997–2008 period were both close to 

the respective flow durations of observed daily streamflows

(fig. 5). In addition, model-performance statistics (table 4) 

indicated that the 2008 model simulated daily and monthly 

mean streamflows at the mouths of at least three of the four 

major tributaries to Onondaga Lake with less bias, higher 

correlation, and better model fit than did the 2003 model. 

Daily streamflows in Ninemile Creek at Lakeland were not 

simulated as well by the 2008 model as were done by the 2003 

model; however, simulated monthly streamflows were slightly 

improved by the revisions to the 2008 model. 

Changes to the Sedimentological Components of 

the Model

Particle-size analyses that were performed on SS 

samples collected during the NPS study (Coon and others, 

2009) enabled refinement of the proportions of the simulated 

sediment load into its three components—sand, silt, and 

clay. In addition, comparison of SS and TSS concentrations 

in concurrently collected water samples documented that 

TSS concentrations were poor calibration surrogates for SS 

concentrations simulated by the 2003 model. This comparison 

justified major revisions to the sedimentological components 

of the 2008 model.

Basinwide Particle-Size Analyses

Particle-size analyses of SS in water samples collected 

by Paschal and Sherwood (1987) from Otisco Lake tributaries 

during 1981–83 indicated a sediment composition that, on 

average, was 10 percent sand, 55 percent silt, and 35 percent 

clay. In the absence of other data from the Onondaga Lake 

Basin, these percentages were used to apportion sediment 

loads from PERLNDs and IMPLNDs to the receiving 

RCHRESs in the 2003 model. During 2005–08, particle sizes 

were analyzed in storm samples of SS that were collected 

from 18 sites throughout the Onondaga Lake Basin as part of 

the NPS study (Coon and others, 2009). The data confirmed 

an approximate 10- to 90-percent split between sand and siltplus-clay (fines) in water samples collected from Otisco Lake 

tributaries as well as from other sites but showed that these 

percentages were not applicable across the entire Onondaga 

Lake Basin. Some samples had sand-fine splits as high as 

40 to 60 percent. Therefore, three combinations of sediment 

proportions were used in the 2008 model—the original lowsand-percentage composition (10, 55, and 35 percent sand, silt, 

and clay, respectively), a high-sand-percentage composition 

(40, 35, and 25 percent sand, silt, and clay, respectively), and 

an average composition (23, 47, and 30 percent sand, silt, and 

clay, respectively). Lacking the percentages of silt and clay 

in the fines fraction of the 2005–08 particle-size analyses, the 

relative percentages of silt and clay in the 1981–83 analyses 

were used to estimate the silt and clay fractions in the 2005–08 

samples. The low- and high-sand compositions were applied to 

the PERLNDs in the basins from which the particle-size data 

were collected. The average values were applied to PERLNDs 

in all other basins, as well as to all IMPLNDs. 

Suspended Sediment and Total Suspended Solids

Except for data available from the 1981–83 study of the 

tributaries to Otisco Lake by Paschal and Sherwood (1987), no 

sediment-concentration or load data were available to calibrate 

the 2003 model. TSS data were used as a surrogate constituent, but comparison of TSS and SS concentrations in samples 

that were collected during the 2005–08 NPS study (Coon 

and others, 2009) indicated a large negative bias in the TSS 

concentrations—that is, TSS concentrations usually were less 

than SS concentrations (fig. 6). Therefore, major changes to 

the simulated land-segment and instream processes related to 

transport, deposition, and scour of the suspended fractions of 

sand, silt, and clay were required to calibrate the 2008 model. 

The first major revision to the model to mimic observed 

SS concentrations was the simulation of a base-flow load. 

HSPF simulates SS loads primarily as a storm-related process; that is, sediment loads are derived from the detachment 

and washoff of soil from land surfaces during rainfall events. 

Channel scour can be simulated, but this process is controlled 

by the mean flow velocity in a given RCHRES. Therefore, 

during base flows, no sediment inputs from land surfaces are 

simulated, and channel scour commonly is near zero. Contrary 

to these modeling limitations, the NPS study documented that 

SS concentrations were sustained in base flows at higher levels 

than could be simulated by the HSPF algorithms (fig. 7). To 

rectify this shortcoming, a base load of sediment was tied to 

the groundwater outflow volume (AGWO) from pervious land 

segments. Because AGWO is a constant source of water to 

streams, tying sediment inputs to AGWO ensured a constant 

supply of sediment to base flows. Different multiplication 

factors were used to target these sediment inputs to the silt and 

clay components of the SS input loads to each RCHRES.

One subbasin, Rattlesnake Gulf (subbasin no. 109; 

fig. 2), has a continuous and elevated base-flow SS load, 

which is derived from unstable lacustrine silt and clay deposits 

that periodically slump from the steep valley side into the 

channel along a high-gradient reach of the stream (Tamulonis 

and others, 2009). To increase the simulated base-flow SS 

concentrations to the observed levels in this stream, constant 

loads of silt and clay sediment fractions (in addition to the 

AGWO-associated inputs) were added to the modeled reach 

through the HSPF external sources module; the results of this 

step are shown in figure 7B. Simulated peak SS concentrations 

were calibrated to observed concentrations by adjusting the 

model parameters that control soil detachment and sediment 

washoff and scour during periods of storm runoff. In the case 

of Rattlesnake Gulf, the creation of a unique PERLND (see 
14 Improvement in Precipitation-Runoff Model Simulations by Recalibration and Model Applications, Onondaga Basin, N.Y.

D. Ninemile Creek

C. Ley Creek

B. Harbor Brook

A. Onondaga Creek

2003 MODEL 2008 MODEL

Percent chance flow exceeded Percent chance flow exceeded

1,000

100

10

1

0.5 2 5 10 20 30 50 70 80 90 95 98 99.5

10,000

1,000

100

10

0.5 2 5 10 20 30 50 70 80 90 95 98 99.5

10,000

1,000

100

10

0.5 2 5 10 20 30 50 70 80 90 95 98 99.5

1,000

100

10

1

0.5 2 5 10 20 30 50 70 80 90 95 98 99.5

1,000

100

10

1

0.5 2 5 10 20 30 50 70 80 90 95 98 99.5

1,000

100

10

1

0.5 2 5 10 20 30 50 70 80 90 95 98 99.5

10,000

1,000

100

10

0.5 2 5 10 20 30 50 70 80 90 95 98 99.5

10,000

1,000

100

10

0.5 2 5 10 20 30 50 70 80 90 95 98 99.5

Streamflow, in cubic feet per second

EXPLANATION

Observed

Simulated

Figure 5. Flow-duration curves simulated by the 2003 and 2008 versions of the Onondaga Lake Basin model, Onondaga 

County, New York, at the mouths of major tributaries to the lake: A, Onondaga Creek (reach 137), B, Harbor Brook (reach 206), 

C, Ley Creek (reach 312), and D, Ninemile Creek (reach 443).
Model Revisions 15

Table 4. Model-performance statistics for 1997–2003 streamflows simulated by the 2008 version of the Onondaga Lake Basin model, 

Onondaga County, New York, at the mouths of major tributaries to the lake.

[Site locations are shown in figure 1. Bold values indicate statistics that are equal to or better than those computed for streamflows simulated by the 2003 version of the Onondaga Lake Basin model (Coon and Reddy, 2008). ft3

/s, cubic feet per second]

Site name and identification number

Mean 

observed 

flow 

(ft3

/s)

Mean 

simulated 

flow 

(ft3

/s)

Correlation 

coefficient

Mean error 

(bias) 

(ft3

/s)

Mean 

error 

(percent)

Coefficient 

of model-fit 

efficiency

Daily mean streamflow

Onondaga Creek at Spencer Street (04240010) 161 160 0.90 -1.06 -0.66 0.80

Harbor Brook at Hiawatha Boulevard (04240105) 9.72 10.0 .79 .32 3.14 .61

Ley Creek at Park Street (04240120) 39.7 39.5 .84 -.20 -.51 .68

Ninemile Creek at Lakeland (04240300) 141 151 .91 10.1 6.70 .74

Monthly mean streamflow

Onondaga Creek at Spencer Street (04240010) 161 160 0.95 -1.01 -0.63 0.90

Harbor Brook at Hiawatha Boulevard (04240105) 9.74 10.1 .86 .33 3.30 .74

Ley Creek at Park Street (04240120) 39.9 39.7 .87 -.13 -.32 .74

Ninemile Creek at Lakeland (04240300) 141 152 .98 10.3 6.77 .92

0

30

60

90

120

150

180

210

0 30 60 90 120 150 180 210

Concentration of total suspended solids,

in milligrams per liter 

Concentration of suspended sediment, in milligrams per liter

Line of equality

Figure 6. Paired concentrations of total suspended solids and suspended sediment in water samples 

collected in Onondaga Lake Basin, Onondaga County, New York, 2005–08.
16 Improvement in Precipitation-Runoff Model Simulations by Recalibration and Model Applications, Onondaga Basin, N.Y.

Observed concentration

B

C D

E

A

Suspended-sediment concentration, in milligrams per liter

Suspended-sediment concentration, in milligrams per liter

EXPLANATION

2003 model

2008 model

1

10

100

1,000

10,000

100,000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

1

10

100

1,000

10,000

100,000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

1

10

100

1,000

10,000

100,000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

1

10

100

1,000

10,000

100,000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

1

10

100

1,000

10,000

100,000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

Figure 7. Suspended-sediment concentrations simulated by the 2003 and 2008 versions of the Onondaga Lake Basin model, Onondaga 

County, New York, for selected headwater subbasins, 2005–08: A, Onondaga Creek (reach 102), B, Rattlesnake Gulf (reach 109), C, North 

Branch Ley Creek (reach 302), D, South Branch Ley Creek (reach 304), and E, Willow Brook (reach 405). 
Model Revisions 17

section “Creation of New Landslide PERLND”) was required 

to simulate the large storm-related sediment loads that were 

derived from erosion of landslide materials in and adjacent to 

the channel. 

In a second subbasin, South Branch Ley Creek (fig. 7D), 

observed base-flow SS concentrations were also high compared to other sites. This subbasin is highly developed, and 

sediment could be derived from any exposed soil; however, no 

plausible source of sediment was identified that could justify 

modifications to the model, as was done for Rattlesnake Gulf. 

An additional modeling difficulty arose because the magnitude 

of base-flow SS concentrations varied during the simulation 

period from more than 100 milligrams per liter (mg/L) during 

late 2006 through early 2007 to as low as 50 mg/L during the 

last year of the NPS study (2007–08). Coincidentally, some 

stormflow concentrations were in this same low range; these 

results indicated that the source of sediment from storm to 

storm was variable and that either sediment was not always 

available to be washed off or the precipitation intensity was 

not great enough to remove large loads of sediment. These 

inconsistent patterns in SS concentrations made calibration of 

this site difficult, especially because consistent results were 

obtained for other calibration sites with similar land uses.

The large discrepancies between the 2003 and 2008 

simulations of SS that were noted in flows for the selected 

headwater subbasins (fig. 7) also were evident at all four 

calibration sites near the mouths of the major tributaries 

(fig. 8). Observed SS concentrations were limited to the sites 

near the mouths of Onondaga Creek (fig. 8A) and Ninemile 

Creek (fig. 8D). In general, simulations of base-flow SS 

concentrations by the 2008 model increased, and in most 

cases, peak concentrations decreased, compared to the results 

simulated by the 2003 model.

Changes to the Water-Quality Components of the 

Model

Concentrations of OP and organic phosphorus (OrgP) 

were calibrated to the 2005–08 NPS study data. Revisions to 

parameter values associated with OrgP, which is the major 

component of P in surface water, were made to minimize the 

differences between observed and simulated P concentrations. 

The accuracies of simulations of nutrient concentrations are 

subject to the accuracies of simulations of streamflow and 

sediment concentrations, especially for storm periods. Errors 

in precipitation records, which affect the magnitude and timing 

of peak flows, will consequently introduce errors in simulated 

nutrient concentrations.

Orthophosphate Concentrations

Revisions to parameter values that were made to calibrate 

OP concentrations in the 2008 model were applied consistently 

to each land type in all of the five major subdivisions of 

the Onondaga Lake Basin (fig. 2), except for the following 

parameters and land types. The rate at which OP accumulated 

(ACQOP) and the maximum storage of OP on the land surface 

(SQOLIM) varied by subdivision for row-crop, farmstead, 

and developed land. The concentration of OP in interflow 

outflow (IOQC) for row-crop and farmstead land in the Otisco 

Lake subbasin (area D in fig. 2) differed from IOQC values 

applied to the same land uses elsewhere in the Onondaga 

Lake Basin. Similarly, the concentration of OP in groundwater 

outflow (AOQC) for developed land types in the Harbor 

Brook subbasin (area C in fig. 2), wetlands in the Otisco Lake 

subbasin and most land types in the middle Ninemile Creek 

subbasin (area E in fig. 2) differed from AOQC values applied 

to the same land types elsewhere in the Onondaga Lake Basin.

OP concentrations simulated in base and peak flows 

by the 2003 model generally were too low and too high, 

respectively, when compared with observed data from 

selected headwater subbasins (figs. 9A, B, and E). Simulated 

concentrations at the mouths of the major tributaries by both 

versions of the model were relatively close (fig. 10), except 

for Harbor Brook (fig. 10B). On this stream, at Hiawatha 

Boulevard (site 04240105; fig. 1), the observed data displayed 

an unexplainable upward trend in OP concentrations, and 

2008-model revisions attempted to mimic this pattern by 

using the HSPF special-actions module to periodically 

change the concentration of OP in groundwater outflows from 

PERLNDs in the Harbor Brook subbasin. At the mouth of 

Ninemile Creek (fig. 10D), both model versions generated 

OP concentrations that were high compared to observed 

values. This discrepancy was unresolvable given that properly 

calibrated OP concentrations from upstream sites resulted 

in at-the-mouth concentrations that could not be lowered 

to the range indicated by the observed values. No plausible 

explanation for a decrease in observed OP concentrations at 

the mouth of Ninemile Creek around the beginning of 2007 

could be offered. 

Phosphorus Concentrations

Phosphorus concentrations were affected by the 

combined calibrations of OP and OrgP concentrations to 

observed values. Because OP typically is a much smaller 

component of P than OrgP, revisions to parameter values 

that control OrgP concentrations were made to improve the 

fit between observed and simulated P concentrations. These 

revisions were applied consistently to each land type in all 

of the five major subdivisions of the Onondaga Lake Basin 

(fig. 2). Phosphorus concentrations simulated by both versions 

of the model were relatively close to observed concentrations. 

Noticeable differences between model simulations were 

evident for North Branch Ley Creek (fig. 11C) and South 

Branch Ley Creek (fig. 11D), where base-flow concentrations 

from the 2008 model were lower than those from the 2003 

model, and for Willow Brook (fig. 11E), where 2008-model 

concentrations were greater than those from the 2003 model. 

These changes reflected revisions to model parameter values 

for subbasins dominated respectively by wetlands (North 

Branch Ley Creek), developed areas (South Branch Ley 
18 Improvement in Precipitation-Runoff Model Simulations by Recalibration and Model Applications, Onondaga Basin, N.Y.

Observed concentration

B

C D

A

Suspended-sediment concentration, in milligrams per literSuspended-sediment concentration, in milligrams per liter

EXPLANATION

2003 model

2008 model

10

100

1,000

10,000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008 10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008 10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

10

100

1,000

10,000

10

100

1,000

10,000

1

10

100

1,000

10,000

1

Figure 8. Suspended-sediment concentrations simulated by the 2003 and 2008 versions of the Onondaga Lake Basin model, Onondaga 

County, New York, at the mouths of major tributaries to the lake, 2005–08: A, Onondaga Creek (reach 137), B, Harbor Brook (reach 206), 

C, Ley Creek (reach 312), and D, Ninemile Creek (reach 443).
Model Revisions 19

Observed concentration

EXPLANATION

2003 model

2008 model

B

C D

E

A

0.001

0.010

0.100

1.000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008 10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008 10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

0.001

0.010

0.100

1.000

0.001

0.010

0.100

1.000

0.001

0.010

0.100

1.000

0.001

0.010

0.100

1.000

Concentration of orthophosphate, as P, in milligrams per liter

Concentration of orthophosphate, as P, in milligrams per liter

Figure 9. Concentrations of orthophosphate, as phosphorus (P), simulated by the 2003 and 2008 versions of the Onondaga Lake Basin 

model, Onondaga County, New York, for selected headwater subbasins, 2005–08: A, Onondaga Creek (reach 102), B, Rattlesnake Gulf 

(reach 109), C, North Branch Ley Creek (reach 302), D, South Branch Ley Creek (reach 304), and E, Willow Brook (reach 405).
20 Improvement in Precipitation-Runoff Model Simulations by Recalibration and Model Applications, Onondaga Basin, N.Y.

Observed concentration

EXPLANATION

2003 model

2008 model

B

C D

A

0.001

0.010

0.100

1.000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008 10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008 10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

0.001

0.010

0.100

1.000

0.001

0.010

0.100

1.000

0.001

0.010

0.100

1.000

Concentration of orthophosphate, as P, in milligrams per liter

Concentration of orthophosphate, as P, in milligrams per liter

Figure 10. Concentrations of orthophosphate, as phosphorus (P), simulated by the 2003 and 2008 versions of the Onondaga Lake Basin 

model, Onondaga County, New York, at the mouths of major tributaries to the lake, 2005–08: A, Onondaga Creek (reach 137), B, Harbor 

Brook (reach 206), C, Ley Creek (reach 312), and D, Ninemile Creek (reach 443).
Model Revisions 21

Phosphorus concentration, in milligrams per liter

Phosphorus concentration, in milligrams per liter

Observed concentration

EXPLANATION

2003 model

2008 model

B

C D

E

A

0.001

0.100

1.000

10.000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008 10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008 10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

0.010

0.001

0.100

1.000

10.000

0.010

0.001

0.100

1.000

10.000

0.010

0.001

0.100

1.000

10.000

0.010

0.01

0.10

1.00

Figure 11. Phosphorus concentrations simulated by the 2003 and 2008 versions of the Onondaga Lake Basin model, Onondaga County, 

New York, for selected headwater subbasins, 2005–08: A, Onondaga Creek (reach 102), B, Rattlesnake Gulf (reach 109), C, North Branch 

Ley Creek (reach 302), D, South Branch Ley Creek (reach 304), and E, Willow Brook (reach 405). 
22 Improvement in Precipitation-Runoff Model Simulations by Recalibration and Model Applications, Onondaga Basin, N.Y.

Creek), and agricultural uses (Willow Brook). The effects of 

the 2008-model revisions associated with developed areas 

were also evident in the P concentrations simulated for the 

sites at the mouths of the major tributaries, where lower P 

concentrations were simulated compared to the 2003 model 

(fig. 12). The exception was Harbor Brook (fig. 12B) where, as 

for OP concentrations at Hiawatha Boulevard (site 04240105; 

fig. 1), an unexplainable, albeit less pronounced, upward 

trend in observed P concentrations necessitated the simulation 

of higher concentrations by the 2008 model than had been 

required for calibration of the 2003 model. 

Chloride Concentrations in Onondaga Creek

Chloride (Cl) concentrations, which were not simulated 

by the 2003 model, were simulated by the 2008 model to 

address questions regarding the magnitude of salt contributions to Onondaga Lake from Onondaga Creek during 2010. 

The existence of brine springs along Onondaga Creek has 

been known since the mid-1700s, and commercial production of salt was a main industry in the Syracuse area during 

the 18th and 19th centuries (Kappel, 2000). The average of 

measured Cl concentrations ranged from less than 30 mg/L in 

the headwaters area of the basin (McKenna and others, 1999) 

to 300–400 mg/L near Cardiff (site 04237962; fig. 1) and 

600–700 mg/L near the mouth of Onondaga Creek (from data 

provided by Antonio Deskins, Onondaga County Department 

of Water Environment Protection, written commun., 2008). 

The 2008 model was modified to include simulation of 

chloride concentrations in the Onondaga Creek Basin only. 

The model was calibrated to Cl concentrations measured by 

OCWEP at monitoring sites near Cardiff (site 04237962), 

at Dorwin Avenue (site 04239000), at Spencer Street 

(site 04240010), and at Kirkpatrick Street (site 04240011, 

fig. 1; table 1). The simulated concentrations matched the 

range and seasonal pattern of observed concentrations 

(fig. 13). Concentrations were inversely related to flow; 

that is, Cl concentrations decreased with increasing flow. 

Concentrations increased substantially between Dorwin 

Avenue at the southern boundary of Syracuse and Spencer 

Street about 5 miles (mi) downstream and within 1 mi of 

the creek’s mouth. The source of this salt has not been 

determined, but the increase in Cl concentrations along this 

reach of Onondaga Creek has been documented previously 

(Effler and Whitehead, 1996) and might be attributed to 

groundwater brine discharges. Cl concentrations almost 

double in magnitude between Spencer Street and Kirkpatrick 

Street, 0.15 mi downstream, where springs discharge brine 

directly into the creek. The largest of these springs has 

a Cl concentration of about 60,000 mg/L and is a large 

contributor of salt to Onondaga Lake (Yager and others, 

2007). As a result of the high background concentrations 

from these continuous groundwater discharges, the expected 

wintertime increase in concentrations that often results from 

the application of road-deicing salt in urban areas (Hayhurst 

and others, 2010) was obscured. Adjustments were made to 

the simulated concentrations by inputting time series of Cl 

loads that varied by time and input location on the basis of 

intermittent discharges of brackish and saline groundwater to 

Onondaga Creek from 2006 to 2009 during Onondaga County 

sewer-construction projects (Janaki Suryadevara, Onondaga 

County Department of Water Environment Protection, written 

commun., 2010).

Model Applications

Following recalibration, the 2008 model was used to 

compute sediment and phosphorus loading rates from the 

various land types in the basin, compute the loads of sediment 

and phosphorus that were generated within each subbasin, 

and estimate the probable contributions of phosphorus from 

each subbasin to Onondaga Lake. Chloride concentrations 

in Onondaga Creek were simulated to assess the relative 

contributions of salt from different sources in the basin and 

to estimate the loads of Cl that were entering Onondaga 

Lake from this tributary. Scenarios of land-use changes and 

best-management practices can be developed, and model 

output can be used, to evaluate the effects that these changes 

or practices are likely to have on sediment and phosphorus 

loads entering Onondaga Lake. As an example, the model 

was revised to reflect basin conditions prior to European 

colonization (forested instead of agricultural or developed 

land) to estimate the probable minimum phosphorus loading to 

Onondaga Lake.

Sediment and Phosphorus Loading Rates

Average annual loading rates for sediment and 

phosphorus (both OP and OrgP) were computed by the 

2008 model of the Onondaga Lake Basin for the water years 

1998–2008. The basin was divided into five major hydrologic 

areas for modeling purposes (fig. 2), and loading rates for each 

of the pervious and impervious land types within each area 

were compiled (table 5). Differences among the rates from 

the different areas were not unexpected. Variable precipitation 

inputs used in the model, the failure of a single precipitation 

record to adequately represent nonuniform precipitation 

patterns across the basin, and localized differences in 

topography and land-management practices not accounted for 

in the creation of the PERLNDs and IMPLNDs necessitated 

the use of different parameter values to simulate and calibrate 

surface runoff, sediment washoff, and nutrient processes. 

These factors and the different resultant sets of parameter 

values produced different loading rates, a common and 

predictable outcome of watershed modeling. 

The average of the five area loading rates for each land 

type (table 5) can be used as estimates of basinwide loading rates. (Total phosphorus loading rates can be estimated 

from the sum of the OP and OrgP values.) Loading rates were 

largest for farmstead and row-crop land uses for all three 
Model Applications 23

Observed concentration

EXPLANATION

2003 model

2008 model

B

C D

A

Phosphorus concentration, in milligrams per literPhosphorus concentration, in milligrams per liter

0.001

0.100

1.000

10.000

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008 10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008 10/1/2005 4/1/2006 10/1/2006 4/1/2007 10/1/2007 4/1/2008 9/30/2008

0.010

0.001

0.100

1.000

10.000

0.010

0.10

1.00

10.00

0.01 0.01

0.10

1.00

Figure 12. Phosphorus concentrations simulated by the 2003 and 2008 versions of the Onondaga Lake Basin model, Onondaga County, 

New York, at the mouths of major tributaries to the lake, 2005–08: A, Onondaga Creek (reach 137), B, Harbor Brook (reach 206), C, Ley 

Creek (reach 312), and D, Ninemile Creek (reach 443).
24 Improvement in Precipitation-Runoff Model Simulations by Recalibration and Model Applications, Onondaga Basin, N.Y.

0

800

1,600

2,400

3,200

4,000

1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

0

200

400

600

800

1,000

1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

0

800

1,600

2,400

3,200

4,000

1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

0

800

1,600

2,400

3,200

4,000

1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

EXPLANATION

Observed

Simulated

Chloride concentration, in milligrams per literChloride concentration, in milligrams per liter

B

C D

A

Figure 13. Observed and simulated chloride concentrations along Onondaga Creek, Onondaga County, New York: A, near 

Cardiff (site 04237962), B, at Dorwin Avenue (site 04239000), C, at Spencer Street (site 04240010), and D, at Kirkpatrick Street 

(site 04240011).

constituents—SS, OP, and OrgP. The lowest sediment loading 

rates were for wetlands, followed by forested land with high 

infiltration rates and low runoff potentials. Forests had the 

lowest loading rates of both OP and OrgP. The average annual 

precipitation during the simulation period, 39.2 inches (in.), 

approximated the 30-year normal precipitation, 40.0 in., as 

recorded by the NWS at the Syracuse Hancock International 

Airport (National Weather Service, 2011). This similarity suggests that the climatic conditions that existed during the model 

simulation period were representative of long-term conditions, 

and thus that the computed loading rates can be considered 

representative of long-term rates in Onondaga County.

The average annual loading rates for water years 1998–

2008 for the five major subdivisions in the Onondaga Lake 

Basin that were estimated by the two versions of the model are 

compared in table 6. Sediment loading rates for all land types, 

except wetlands, were higher in the results from the 2008 

model than from the 2003 model. (As explained previously, 

this increase resulted from calibration of the model to SS, 

rather than TSS, concentrations.) Relative to the 2003 model, 

the 2008-model loading rates of OP increased, and those of 

OrgP decreased, for row-crop, farmstead, and wetland land 

types; loading rates of OrgP increased for forested, pasturehay, and developed land types.

Subbasin Loads of Sediment and Phosphorus

Average annual yields of SS (fig. 14), OP, and P 

(figs. 15A and B) from each modeled subbasin were computed 

by subtracting the subbasin input load (that is, the load from 

upstream subbasins that entered a given subbasin reach) from 

the output load (the total load that exited a given subbasin 

reach) and dividing by the subbasin area. These values 

reflected the constituent contributions from the land segments 

and the gains or losses from instream processes within 

each subbasin. 
Model Applications 25

Table 5. Average annual sediment and phosphorus loading rates for water years 1998–2008 from pervious and impervious land types 

in five major subdivisions of the Onondaga Lake Basin simulated by the 2008 version of the precipitation-runoff model of the Onondaga 

Lake Basin, Onondaga County, New York.

[Specified areas are identified in figure 2. A, Upper and middle Onondaga Creek Basins; B, Ley Creek and lower Onondaga and Ninemile Creek Basins; 

C, Harbor Brook Basin; D, Otisco Lake Basin; and E, Middle Ninemile Creek and West Branch Onondaga Creek Basins. CSO, combined sewer overflow; 

--, no data]

Land type Sediment loading rates (short tons per acre per year)

Area A Area B Area C Area D Area E Average

Forest with low runoff potential 0.05 0.002 0.001 0.07 0.06 0.04

Forest with high runoff potential .19 .11 .10 .26 .19 .17

Pasture-hay with low runoff potential .12 .008 .002 .21 .18 .10

Pasture-hay with high runoff potential .77 .46 .42 1.02 .80 .69

Row crops 2.06 .36 .36 3.10 2.77 1.73

Farmstead 3.22 -- 1.17 4.12 3.94 3.11

Wetland 0.00 0.00 0.00 0.00 0.00 0.00

Landslide 30.3 -- -- -- -- 30.3

Low-intensity residential .26 .17 .16 .32 .30 .24

High-intensity residential .42 .23 .21 .56 .32 .35

Commercial/industrial/transportation .51 .27 .24 .74 .64 .48

CSO low-intensity residential -- .17 .16 -- -- .17

CSO high-intensity residential -- .23 .21 -- -- .22

CSO commercial/industrial/transportation -- .27 .24 -- -- .26

Orthophosphate, as phosphorus, loading rates (pounds per acre per year)

Area A Area B Area C Area D Area E Average

Forest with low runoff potential .017 .016 .010 .021 .017 .02

Forest with high runoff potential .018 .018 .012 .021 .018 .02

Pasture-hay with low runoff potential .020 .018 .010 .024 .020 .02

Pasture-hay with high runoff potential .021 .020 .015 .025 .022 .02

Row crops .145 .076 .061 .775 .260 .26

Farmstead .254 -- .172 1.61 .910 .74

Wetland .139 .142 .088 .254 .234 .17

Low-intensity residential .085 .065 .052 .097 .089 .08

High-intensity residential .101 .065 .054 .121 .111 .09

Commercial/industrial/transportation .113 .073 .060 .142 .127 .10

CSO low-intensity residential -- .11 .12 -- -- .12

CSO high-intensity residential -- .14 .32 -- -- .23

CSO commercial/industrial/transportation -- .07 .29 -- -- .18

Organic phosphorus loading rates (pounds per acre per year)

Area A Area B Area C Area D Area E Average

Forest with low runoff potential .06 .009 .006 .09 .08 .05

Forest with high runoff potential .14 .08 .08 .18 .16 .13

Pasture-hay with low runoff potential .10 .014 .009 .14 .13 .08

Pasture-hay with high runoff potential .30 .18 .16 .38 .33 .27

Row crops 1.18 .31 .30 1.56 1.45 .96

Farmstead 8.91 -- 3.30 11.3 10.9 8.60

Wetland .08 .06 .02 .11 .11 .08

Low-intensity residential .49 .43 .42 .53 .52 .48

High-intensity residential .77 .70 .63 .86 .33 .66

Commercial/industrial/transportation .96 .85 .78 1.11 1.07 .95

CSO low-intensity residential -- .45 .42 -- -- .44

CSO high-intensity residential -- .54 .71 -- -- .63

CSO commercial/industrial/transportation -- .67 .86 -- -- .77
26 Improvement in Precipitation-Runoff Model Simulations by Recalibration and Model Applications, Onondaga Basin, N.Y.

Table 6. Average annual sediment and phosphorus loading rates for water years 1998–2008 from pervious land types in five major 

subdivisions of the Onondaga Lake Basin simulated by the 2003 and 2008 versions of the precipitation-runoff model of the Onondaga 

Lake Basin, Onondaga County, New York.

[Values are averages of loading rates from the five simulated areas shown in figure 2. Values in bold type are the higher of the two associated values]

Land type

Sediment 

(short tons per acre per year)

Orthophosphate, as P 

(pounds per acre per year)

Organic phosphorus 

(pounds per acre per year)

2003 model 2008 model 2003 model 2008 model 2003 model 2008 model

Forest with low runoff potential 0.01 0.04 0.02 0.02 0.03 0.05

Forest with high runoff potential .10 .17 .02 .02 .07 .13

Pasture-hay with low runoff potential .04 .10 .02 .02 .06 .08

Pasture-hay with high runoff potential .32 .69 .02 .02 .18 .27

Row crops .45 1.73 .04 .26 1.12 .96

Farmstead 1.28 3.11 .25 .74 9.58 8.60

Wetland 0.00 0.00 .04 .17 .10 .08

Low-intensity residential .10 .24 .08 .08 .08 .48

High-intensity residential .13 .35 .13 .09 .11 .66

Commercial/industrial/transportation .18 .48 .13 .10 .29 .95

Negative yields of SS, OP, and P that are associated with 

subbasin 121 reflect the mitigative effects of the Onondaga 

Reservoir at the confluence of Onondaga Creek and West 

Branch Onondaga Creek on these constituents. The negative 

yields of these constituents in subbasin 409 are attributed to 

the mitigative effects of Otisco Lake. The negative yield of SS 

in subbasin 138 is a result of the backwater effect of Onondaga 

Lake on the harbor at the mouth of Onondaga Creek. The 

high SS yields from subbasins 105 and 109 were generated 

from the erosion of landslide materials in Rainbow Creek and 

Rattlesnake Gulf Basins, respectively. High OP and P yields in 

subbasin 423 are a result of the estimated nutrient discharges 

from the wastewater-treatment plant in Marcellus (fig. 1). 

Other subbasins with high yields of OP and P generally had 

large areas of agricultural or developed land.

Watershed-Management Analysis

Once OP and P loads and yields had been computed for 

individual subbasins (fig. 15), the model was used to estimate 

the portion of each load that was likely to contribute to the 

total loads entering Onondaga Lake. The objective of this 

analysis was to enable targeting of proposed remediation 

projects in areas of the basin that would result in the greatest 

load decrease for a given financial and manpower investment. 

The model was repeatedly modified by removing each 

subbasin, in turn, from the simulation. The total loads at 

the mouth of each major tributary to Onondaga Lake were 

output for each run and compared to the loads simulated by 

the calibrated 2008 model. The difference in loads entering 

the lake was assumed to be the incremental contribution 

from the removed subbasin. Output from these model runs 

are presented in paired figures that show the average annual 

yields (in pounds per acre) generated within a subbasin for 

orthophosphate (fig. 16A) and phosphorus (fig. 17A) and the 

subbasin yields of orthophosphate (fig. 16B) and phosphorus 

(fig. 17B) that are transported through the watershed to 

Onondaga Lake.

The general conclusion that can be drawn from these 

comparative figures is that subbasins with large yields in the 

headwater areas of the Onondaga Lake Basin are less likely to 

be major contributors of P and OP to the lake than subbasins 

proximal to the lake. This is particularly applicable to the 

subbasins upstream from the Onondaga Reservoir (subbasin 

121) and Otisco Lake (subbasin 409), each of which has a 

mitigative effect on input loads. Conversely, large loads that 

are generated in subbasins proximal to Onondaga Lake—

that is, the urban subbasins in Syracuse—are less likely to 

be naturally mitigated, and the contributions of P and OP to 

the lake are high. Remediation of loads derived from these 

subbasins would produce the greatest load-reduction benefits 

to Onondaga Lake. 
Model Applications 27

-1-2-3

3210

001

201

401

601

801

011

211

411

611

811

121

321

521

721

921

131

331

531

731

102

302

502

702

203

403

603

803

013

213

004

204

404

604

804

014

214

414

614

814

024

224

424

624

824

034

234

434

634

834

044

244

444

105

Yield, in tons per acre per year 994 Subbasin number

Figure 14. Average annual yields of suspended sediment from subbasins simulated by the precipitation-runoff model of Onondaga Lake Basin, Onondaga County, New York.
28 Improvement in Precipitation-Runoff Model Simulations by Recalibration and Model Applications, Onondaga Basin, N.Y.

-0.3-0.2-0.1

0.00.10.20.30.4

001

201

401

601

801

011

211

411

611

811

121

321

521

721

921

131

331

531

731

102

302

502

702

203

403

603

803

013

213

004

204

404

604

804

014

214

414

614

814

024

224

424

624

824

034

234

434

634

834

044

244

444

105

r aeyr ep er car ep sdnuop ni , dl ei Y

994

Subbasin number

A

Figure 15.

Average annual yields of A, orthophosphate, as phosphorus (P), and B, phosphorus from subbasins simulated by the precipitation-runoff model 

of Onondaga Lake Basin, Onondaga County, New York.
Model Applications 29 -1.5

-1.0-0.5

0.00.51.01.52.0

001

201

401

601

801

011

211

411

611

811

121

321

521

721

921

131

331

531

731

102

302

502

702

203

403

603

803

013

213

004

204

404

604

804

014

214

414

614

814

024

224

424

624

824

034

234

434

634

834

044

244

444

105

raeyrepercarepsdnuopni,dleiY

994

Subbasin number

B

Figure 15. Average annual yields of A, orthophosphate, as phosphorus (P), and B, phosphorus from subbasins simulated by the precipitation-runoff model of Onondaga Lake Basin, Onondaga County, New York.—Continued
30 Improvement in Precipitation-Runoff Model Simulations by Recalibration and Model Applications, Onondaga Basin, N.Y.

100 Subbasin boundary and number

409

503

417

121

127

111

137

108

303

112

434

130

501

401

304

405

406

116

306

125

104

439

115

422

436

123

118

428

310

113

402

400

129

408

442

204

117

502

301

410

407

302

102

427

110

418

423

107

429

100

433

435

119

101

404

103

106

438

440

202

105

441

124

305

122

126

132

136

120

205

308

114

403

206

437

133

425

109

415

430

419

128

201

432

414

416

424

421

412

413

312

311

411

203 131

135

207

134

134

420

307 313

138

309

443

499

444

426

431

76°20' 76°10' 76°

43°

42°50'

EXPLANATION

-0.09 - 0.00

>0.00 - 0.03

>0.03 - 0.05

>0.05 - 0.09

>0.09 - 0.15

>0.15 - 0.20

>0.20 - 0.25

>0.25 - 0.30

0 5 MILES

0 5 KILOMETERS

Base from U.S. Geological Survey, Seamless Data Distribution System,

accessed in 2006 at URL http://seamless.usgs.gov

Universal Transverse Mercator projection, Zone 18, scale 1:250,000

Orthophosphate yield,

in pounds per acre per year

Lake

Onondaga

Lake

Otisco

A

Figure 16. Orthophosphate, as phosphorus (P), A, average annual subbasin yields and B, estimated subbasin yields that enter 

Onondaga Lake, Onondaga County, New York.
Model Applications 31

100 Subbasin boundary and number

409

503

417

121

127

111

137

108

303

112

434

130

501

401

304

405

406

116

306

125

104

439

115

422

436

123

118

428

310

113

402

400

129

408

442

204

117

502

301

410

407

302

102

427

110

418

423

107

429

100

433

435

119

101

404

103

106

438

440

202

105

441

124

305

122

126

132

136

120

205

308

114

403

206

437

133

425

109

415

430

419

128

201

432

414

416

424

421

412

413

312

311

411

203 131

135

207

134

134

420

307 313

138

309

443

499

444

426

431

76°20' 76°10' 76°

43°

42°50'

EXPLANATION

-0.09 - 0.00

>0.00 - 0.03

>0.03 - 0.05

>0.05 - 0.09

>0.09 - 0.15

>0.15 - 0.20

>0.20 - 0.25

>0.25 - 0.30

0 5 MILES

0 5 KILOMETERS

Base from U.S. Geological Survey, Seamless Data Distribution System,

accessed in 2006 at URL http://seamless.usgs.gov

Universal Transverse Mercator projection, Zone 18, scale 1:250,000

Orthophosphate yield,

in pounds per acre per year

Lake

Onondaga

Lake

Otisco

B

Figure 16. Orthophosphate, as phosphorus (P), A, average annual subbasin yields and B, estimated subbasin yields that enter 

Onondaga Lake, Onondaga County, New York.—Continued
32 Improvement in Precipitation-Runoff Model Simulations by Recalibration and Model Applications, Onondaga Basin, N.Y.

100 Subbasin boundary and number

409

503

417

121

127

111

137

108

303

112

434

130

501

401

304

405

406

116

306

125

104

439

115

422

436

123

118

428

310

113

402

400

129

408

442

204

117

502

301

410

407

302

102

427

110

418

423

107

429

100

433

435

119

101

404

103

106

438

440

202

105

441

124

305

122

126

132

136

120

205

308

114

403

206

437

133

425

109

415

430

419

128

201

432

414

416

424

421

412

413

312

311

411

203 131

135

207

134

134

420

307 313

138

309

443

499

444

426

431

76°20' 76°10' 76°

43°

42°50'

EXPLANATION

-0.74 - 0.0

>0.0 - 0.1

>0.1 - 0.2

>0.2 - 0.4

>0.4 - 0.6

>0.6 - 0.8

>0.8 - 1.0

>1.0 - 1.6

Base from U.S. Geological Survey, Seamless Data Distribution System,

accessed in 2006 at URL http://seamless.usgs.gov

Universal Transverse Mercator projection, Zone 18, scale 1:250,000

Phosphorus yield,

in pounds per acre per year

A

0 5 MILES

0 5 KILOMETERS

Lake

Onondaga

Lake

Otisco

Figure 17. Phosphorus A, average annual subbasin yields and B, estimated subbasin yields that enter Onondaga Lake, Onondaga 

County, New York.
Model Applications 33

100 Subbasin boundary and number

409

503

417

121

127

111

137

108

303

112

434

130

501

401

304

405

406

116

306

125

104

439

115

422

436

123

118

428

310

113

402

400

129

408

442

204

117

502

301

410

407

302

102

427

110

418

423

107

429

100

433

435

119

101

404

103

106

438

440

202

105

441

124

305

122

126

132

136

120

205

308

114

403

206

437

133

425

109

415

430

419

128

201

432

414

416

424

421

412

413

312

311

411

203 131

135

207

134

134

420

307 313

138

309

443

499

444

426

431

76°20' 76°10' 76°

43°

42°50'

0 5 MILES

0 5 KILOMETERS

EXPLANATION

-1.15 - 0.0

>0.0 - 0.1

>0.1 - 0.2

>0.2 - 0.4

>0.4 - 0.6

>0.6 - 0.8

>0.8 - 1.0

>1.0 - 1.5

Phosphorus yield,

in pounds per acre per year

B

Base from U.S. Geological Survey, Seamless Data Distribution System,

accessed in 2006 at URL http://seamless.usgs.gov

Universal Transverse Mercator projection, Zone 18, scale 1:250,000

Lake

Onondaga

Lake

Otisco

Figure 17. Phosphorus A, average annual subbasin yields and B, estimated subbasin yields that enter Onondaga Lake, Onondaga 

County, New York.—Continued
34 Improvement in Precipitation-Runoff Model Simulations by Recalibration and Model Applications, Onondaga Basin, N.Y.

Chloride Loads in Onondaga Creek

During the simulation period, 1998–2008, the simulated annual loads of Cl in Onondaga Creek near Cardiff 

(site 04237962; fig. 1; table 1) and at Dorwin Avenue 

(04239000; fig. 1; table 1) were stable (fig. 18). The annual 

loads near Cardiff ranged from 8,600 to 9,400 short tons and 

the average annual load was 9,000 tons, whereas the annual 

loads at Dorwin Avenue ranged from 8,100 to 8,600 tons and 

the average annual load was 8,400 tons. Chloride loads more 

than quadrupled between Dorwin Avenue and Spencer Street 

(site 04240010; fig. 1; table 1) and increased again downstream from Spencer Street (fig. 18). As discussed previously, 

these increases are likely caused by springs that discharge 

brine to the creek; the spring downstream from Spencer Street 

flows at about 1 cubic foot per second and discharges almost 

100,000 tons of sodium chloride annually (Yager and others, 

2007). During 1998–2004, the simulated loads in Onondaga 

Creek at Spencer Street and at the mouth (reach 138; fig. 2) 

were also fairly stable; average annual loads were 41,000 and 

72,000 tons, respectively. Starting in 2005, the loads at 

Spencer Street and at the mouth increased (fig. 18), presumably as a result of briny groundwater that was pumped to 

dewater sewer-construction sites in Syracuse and discharged 

to Onondaga Creek. By 2008, the simulated annual load 

of Cl had increased to 124,000 tons at Spencer Street and 

155,000 tons at the mouth.

Precolonization (Forested) Scenario

To define the bounding condition that presumably would 

reflect no effects of human activities in the basin and therefore the lowest practicable limit of P loads to Onondaga Lake 

that could be attained by mitigation measures, the model was 

modified to create a scenario of precolonization (mostly forested) conditions. First, all agricultural, developed, and impervious land types were converted to forested land except in 

areas adjacent to Onondaga Lake; these areas were changed to 

wetlands as indicated on historical maps (on file in the Ithaca, 

N.Y., office of the U.S. Geological Survey). Second, the 

Onondaga Reservoir and its associated mitigative effects on 

sediment and particulate loads were removed. Third, the dam 

at the north end of Otisco Lake, as well as the withdrawals by 

Onondaga County Water Authority, were removed from the 

model; a new stage-discharge relation to reflect these changes 

was created. Fourth, all instructions pertaining to the simulation of the tunnel through which Harbor Brook flows for 

about half of its length in subbasin 206 (fig. 2) were removed. 

Finally, the nutrient inputs from the Marcellus wastewatertreatment plant were removed.

Under precolonization conditions, the probable 

combined average annual loads of OP and P from the four 

major tributaries to the lake would be 2.00 and 11.91 tons, 

respectively (table 7). These loads reflect overall decreases 

of 46 and 56 percent from present-day OP and P loads, 

respectively. For a given tributary, a completely forested basin 

presumably would generate 38 to 79 percent less OP and 47 to 

81 percent less P on an average annual basis than is generated 

and transported to Onondaga Lake currently (1998–2008). 

0

20,000

40,000

60,000

80,000

100,000

120,000

140,000

160,000

180,000

1997 1999 2001 2003 2005 2007 2009

Annual chloride load, in tons

Near Cardiff—site 04237962

Dorwin Avenue—site 04239000

Spencer Street—site 04240010

Atmouth

EXPLANATION

Year

Figure 18. Annual chloride 

loads simulated at four sites 

along Onondaga Creek by the 

precipitation-runoff model of 

Onondaga Lake Basin, Onondaga 

County, New York.
Summary 35

Table 7. Average annual orthophosphate, as phosphorus (P), and phosphorus loads simulated in tributaries to Onondaga 

Lake by the precipitation-runoff model of Onondaga Lake Basin, Onondaga County, New York, under current (1998–2008) and 

precolonization (forested) conditions.

Tributary Drainage area, 

in square miles

Orthophosphate, as P, load, short tons Total phosphorus load, tons

Current Forested Percent

difference Current Forested Percentdifference

Onondaga Creek 111 1.29 0.81 -38 11.06 5.91 -47

Harbor Brook 12.1 .24 .05 -79 1.11 .26 -77

Ley Creek 30.0 .63 .29 -55 4.62 .86 -81

Ninemile Creek 115 1.55 .85 -45 10.03 4.88 -51

Sum 3.71 2.00 -46 26.82 11.91 -56

Summary

During 2003–07, the U.S. Geological Survey (USGS), 

in cooperation with the Onondaga Lake Partnership (OLP), 

developed a basin-scale precipitation-runoff model of the 

285-square-mile Onondaga Lake Basin with the computer 

program, Hydrological Simulation Program–Fortran (HSPF), 

which simulated streamflows and loads of sediment, phosphorus, and nitrogen in the major tributaries of Onondaga Lake. 

The model was intended to provide water-resource managers with a tool to better understand the processes responsible 

for the generation of loads of sediment and nutrients that 

were transported to Onondaga Lake. This objective was only 

partly attained because data for calibration of the model were 

available from monitoring sites only at or near the mouths 

of the major tributaries to Onondaga Lake; no calibration 

data from headwater subbasins where loads originated were 

available. To address this limitation and thereby decrease the 

uncertainty in the simulation results that were associated with 

headwater processes, the USGS undertook a 3-year (2005–08) 

basinwide study to assess the quality of surface water in the 

Onondaga Lake Basin. Streamflow and water-quality data that 

were collected at 25 sites in the basin enabled assessment of 

the relative contributions of nonpoint sources associated with 

the major land uses in the basin, as well as known sources 

and presumed sinks of sediment and nutrient loads, which 

previously had not been evaluated. The newly acquired data 

from the nonpoint-source study were used to recalibrate the 

components of the model that simulated streamflow, water 

temperature, and suspended-sediment, orthophosphate, and 

phosphorus concentrations.

Prior to recalibration, all input datasets were extended 

5 years from the end of the original model’s simulation 

period, from October 1, 2003, through September 30, 2008. 

An existing subbasin was divided to permit direct calibration 

of the effects of a farmstead that dominated the water-quality 

characteristics of a small part of the original subbasin; the 

new subbasin was monitored during the nonpoint-source 

study. Land-use and land-cover acreages for 1992 (used in the 

original model) and 2001 were compared, and acreages in 13 

urbanized subbasins were converted from forest and wetland 

to developed land uses as necessary for the recalibrated 

model. The hydrologic response units (HRUs) included in 

the model were revised by the removal of a high-sedimentyield agricultural HRU and the additions of an HRU that 

represented landslides in the Rattlesnake Gulf subbasin and 

a set of developed HRUs in the Harbor Brook subbasin. 

The mitigative effects of Onondaga Reservoir and Otisco 

Lake were assessed, and the effects related to the Onondaga 

Reservoir were incorporated into the model. 

Model parameter values in the original 2003 model were 

revised as necessary to minimize the differences between 

simulated data and the newly acquired observed data from 

the nonpoint-source study. The resultant 2008 version of the 

model improved the simulation of processes in the headwater subbasins, including overland and groundwater flow, and 

the generation and transport of suspended-sediment, orthophosphate, and phosphorus. The fit between simulated and 

observed streamflows in small subbasins was improved by 

matching base flows, storm peaks, and storm recessions more 

precisely than had been possible with the original model. 

Simulated recessional and low flows were either increased or 

decreased as appropriate for a given stream, and peak flows 

generally were decreased in the 2008 model. The use of suspended-sediment (SS) data in the 2008 model rather than the 

surrogate constituent, total suspended solids (TSS), resulted in 

increases in simulated sediment concentrations in low flows 

and, in most cases, decreases in peak-flow concentrations. 

Simulated orthophosphate (OP) concentrations in base flows 

generally increased, and those for peak flows decreased, for 

selected headwater subbasins in the 2008 model. Phosphorus 

(P) concentrations simulated by the 2008 model for forested 
36 Improvement in Precipitation-Runoff Model Simulations by Recalibration and Model Applications, Onondaga Basin, N.Y.

subbasins were relatively close to those simulated by the 2003 

model. Phosphorus concentrations generally decreased in 

developed and wetland-dominated subbasins but increased in 

agricultural subbasins. In addition to the changes mentioned 

above, the 2008 model also included the simulation of chloride 

concentrations in the Onondaga Creek Basin only. 

The recalibrated 2008 model generated output that was 

used to (1) compute loading rates for the land types that were 

simulated in the model, (2) conduct a watershed-management 

analysis that estimated the portion of the total subbasin load 

that was likely to be transported to Onondaga Lake, and 

(3) compute and assess chloride (salt) loads to Onondaga Lake 

from the Onondaga Creek Basin. Additionally, the use of the 

model for scenario development and subsequent comparison 

of before-and-after model outputs was demonstrated by the 

simulation of precolonization (forested) conditions in the 

basin to estimate the probable minimum phosphorus loads to 

the lake. 

Farmstead and row-crop land uses produced the highest 

simulated loading rates of SS, OP, and organic phosphorus 

(OrgP). The lowest sediment loading rates were from wetlands, followed by forested land with high infiltration rates 

and low runoff potentials. Forests had the lowest loading rates 

of both OP and OrgP. 

Yields of OP and P generally were high in subbasins 

with large areas of agricultural or developed land. The largest 

sediment yields were associated with basins in which landslides and erosional problems had been identified. Negative 

yields were computed for Onondaga Reservoir and Otisco 

Lake. Subbasins that generated large yields of OP or P, but 

were distant from Onondaga Lake, were less likely to make 

substantial contributions to the total load entering the lake than 

subbasins proximal to the lake. Conversely, most of the yields 

from urbanized subbasins close to the lake made relatively 

large contributions to the lake’s total input loads.

Simulated loads of chloride in Onondaga Creek increased 

dramatically in Syracuse between Dorwin Avenue at the southern boundary of the city and Spencer Street, about 5 miles 

downstream. Another large increase occurred downstream 

from Spencer Street and was evident in simulated results for 

the next reach downstream at the mouth of the creek. The 

presumed or documented sources of these loads are springs 

that discharge groundwater brine to the creek. On the basis of 

simulated loads for the period 1998–2004, the average annual 

load of Cl in Onondaga Creek increased from 9,000 tons near 

Cardiff to 72,000 tons at the creek’s mouth. A time-trend 

analysis of chloride loads indicated a large increase in chloride 

inputs to Onondaga Lake starting in 2005.

A simulation scenario was developed wherein all humanrelated activities (agriculture and development) were removed 

from the Onondaga Lake Basin and the land was returned to 

precolonization conditions of forests and wetlands. Under this 

scenario, the probable combined average annual loads of OP 

and P from the four major tributaries to the lake would be 2.00 

and 11.91 tons, respectively, or an overall decrease of 46 and 

56 percent from present-day OP and P loads, respectively.

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Prepared by the Pembroke Publishing Service Center.

For additional information write to:

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U.S. Geological Survey

30 Brown Rd.

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Coon—Improvement in Precipitation-Runoff Model Simulations, Onondaga Lake Basin, Onondaga County, New York—Scientific Investigations Report 2011–5203