U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2011–5167

Sources, Fate, and Transport of Nitrogen and Phosphorus 

in the Chesapeake Bay Watershed: An Empirical Model
Cover. Chesapeake Bay Bridge. Photograph by Jane Thomas, IAN Image Library (www.ian.umces.edu/imagelibrary/).
Sources, Fate, and Transport of Nitrogen 

and Phosphorus in the Chesapeake Bay 

Watershed: An Empirical Model

By Scott W. Ator, John W. Brakebill, and Joel D. Blomquist

Scientific Investigations Report 2011–5167

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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Suggested citation:

Ator, S.W., Brakebill, J.W., and Blomquist, J.D., 2011, Sources, fate, and transport of nitrogen and phosphorus in the 

Chesapeake Bay watershed: An empirical model: U.S. Geological Survey Scientific Investigations Report 2011–5167, 

27 p.

ISBN 978-1-4113-3262-1
iii

Contents

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

Introduction.....................................................................................................................................................2

Purpose and Scope ..............................................................................................................................5

Methods...........................................................................................................................................................5

Stream Network Development ...........................................................................................................5

Calibration Data.....................................................................................................................................6

Explanatory Data...................................................................................................................................7

SPARROW Model Calibration and Predictions................................................................................7

Model Limitations................................................................................................................................11

Nitrogen and Phosphorus in the Chesapeake Bay Watershed ...........................................................11

Watershed Sources............................................................................................................................11

Fate and Transport..............................................................................................................................17

Flux to Chesapeake Bay and Major Tributaries.............................................................................19

Summary and Implications.........................................................................................................................21

Acknowledgments.......................................................................................................................................22

References Cited..........................................................................................................................................22

Appendix. Reach-Scale Estimates of Mean-Annual Nitrogen and Phosphorus 

Fluxes in Streams of the Chesapeake Bay Watershed............................................................27

Reference Cited............................................................................................................................................27
iv

Figures

1–2. Maps showing—

1. Location of the Chesapeake Bay watershed and vicinity, including 

generalized land cover, point sources, and selected long-term 

stream monitoring stations for nutrient flux....................................................................3

2. Hydrogeologic settings within the Chesapeake Bay watershed ................................4

3. Location of stations for which mean annual flux estimates of 

total nitrogen and (or) total phosphorus were computed for 

use in SPARROW model calibration.................................................................................8

4. Graphs showing the distribution of stream order, streamflow, and watershed 

size among modeled stream reaches in the Chesapeake Bay watershed, 

and those with calibration stations ...........................................................................................9

5–10. Maps showing—

5. Mean annual maximum air temperature, 1971–2000, and streams 

with mean annual flow greater than 3.45 cubic meters per second.........................10

6. Estimated local yields of total nitrogen and phosphorus from 

agricultural sources ..........................................................................................................14

7. Estimated local (A) yields and (B) source shares of total nitrogen 

from atmospheric deposition...........................................................................................15

8. Share of local phosphorus yields attributable to siliciclastic or 

crystalline rocks.................................................................................................................16

9. Estimated (A) local and (B) delivered yields of total nitrogen (TN)...........................18

10. Estimated (A) local and (B) delivered yields of total phosphorus (TP) .....................19

11–12. Graphs showing—

11. Estimated shares of total nitrogen contributions from various 

watershed sources to Chesapeake Bay and to major tributaries 

at selected monitoring stations.......................................................................................20

12. Estimated shares of total phosphorus contributions from various 

watershed sources to Chesapeake Bay and to major tributaries 

at selected monitoring stations.......................................................................................21

Tables

1. Summary of nonlinear least-squares calibration results for CBTN_v4, 

the Chesapeake Bay watershed total nitrogen model .........................................................12

2. Summary of nonlinear least-squares calibration results for CBTP_v4, 

the Chesapeake Bay watershed total phosphorus model...................................................13

3. Estimated annual flux of total nitrogen and total phosphorus from 

watershed sources to Chesapeake Bay and at selected monitoring 

stations on major tributaries, in metric tons ..........................................................................20
v

Conversion Factors

Multiply By To obtain

Length

meter (m) 3.281 foot (ft)

kilometer (km) 0.6214 mile (mi)

Area

square kilometer (km2) 247 acre

hectare (ha) 0.003861 square mile (mi2)

square kilometer (km2) 0.3861 square mile (mi2)

Volume

cubic meter (m3) 35.3 cubic foot (ft3)

Mass

kilogram (kg) 2.205 pound, avoirdupois (lb)

megagram (Mg) 1.102 ton, short (2,000 lb)

kilogram per square kilometer 

(kg km-2)

0.00892 pound per acre (lb acre-1)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

 °F = (1.8 x °C) + 32

For units of measurement, this text uses negative exponents instead of the more common 

“per” symbol ( / ). As examples, m yr-1 herein is equivalent to m/yr (meters per year), and 

kg km-2 herein is equivalent to kg/km2 (kilograms per square kilometer).

Sources, Fate, and Transport of Nitrogen and 

Phosphorus in the Chesapeake Bay Watershed: 

An Empirical Model

By Scott W. Ator, John W. Brakebill, and Joel D. Blomquist

Abstract

Spatially Referenced Regression on Watershed Attributes 

(SPARROW) was used to provide empirical estimates of the 

sources, fate, and transport of total nitrogen (TN) and total 

phosphorus (TP) in the Chesapeake Bay watershed, and the 

mean annual TN and TP flux to the bay and in each of 80,579 

nontidal tributary stream reaches. Restoration efforts in recent 

decades have been insufficient to meet established standards 

for water quality and ecological conditions in Chesapeake 

Bay. The bay watershed includes 166,000 square kilometers of 

mixed land uses, multiple nutrient sources, and variable hydrogeologic, soil, and weather conditions, and bay restoration is 

complicated by the multitude of nutrient sources and complex 

interacting factors affecting the occurrence, fate, and transport 

of nitrogen and phosphorus from source areas to streams and 

the estuary. Effective and efficient nutrient management at 

the regional scale in support of Chesapeake Bay restoration 

requires a comprehensive understanding of the sources, fate, 

and transport of nitrogen and phosphorus in the watershed, 

which is only available through regional models. The current 

models, Chesapeake Bay nutrient SPARROW models, version 

4 (CBTN_v4 and CBTP_v4), were constructed at a finer 

spatial resolution than previous SPARROW models for the 

Chesapeake Bay watershed (versions 1, 2, and 3), and include 

an updated timeframe and modified sources and other explanatory terms.

Chesapeake Bay receives an estimated 1.32 x 108

kilograms (132,000 metric tons) of nitrogen and 9.74 x 106

kilograms (9,740 metric tons) of phosphorus annually from 

its watershed, mainly through its two largest tributaries, 

the Susquehanna and Potomac Rivers. Significant (α=0.10) 

sources of nutrients to streams in the watershed include 

fertilizer and manure applications in agricultural areas, undifferentiated urban activities, point sources, atmospheric deposition and direct fixation by crops (for nitrogen), and mineral 

sources (for phosphorus). Agriculture (primarily fertilizer 

applications and crop fixation) contributes more than half of 

the nitrogen delivered from the watershed to the bay; phosphorus contributions are more mixed, and fairly evenly distributed 

among agricultural (fertilizer and manure applications) and 

urban (including point) sources. Natural mineral dissolution 

contributes approximately 14 percent of the phosphorus flux 

from the watershed to the Chesapeake Bay. Empirical estimates of average yields from different source areas and of the 

portion of selected applications delivered to streams agree 

closely with previously reported values in the literature.

Nutrient fate and transport through the Chesapeake 

Bay watershed to the bay reflect the different physical and 

chemical properties of nitrogen and phosphorus compounds. 

Groundwater is an important pathway for nitrogen transport 

(as nitrate), and TN flux is greatest in areas with greater 

groundwater flow and in areas of the Piedmont underlain by 

carbonate rocks. TN flux decreases with increasing vegetative 

growth (likely indicative of plant uptake) and soil available 

water capacity (likely indicative of reducing conditions). 

Phosphorus transport to streams, conversely, is greatest in 

areas most likely to generate overland runoff and related erosion, including those with less permeable and more erodible 

soils and greater precipitation. Phosphorus transport also is 

greater in the Coastal Plain than in other areas, possibly due 

to saturation of soils with historical phosphorus applications. 

Both nitrogen and phosphorus are lost within watershed 

impoundments (lakes, ponds, or reservoirs), and nitrogen is 

also lost significantly along flowing reaches, particularly in 

small streams and in larger streams in warmer areas.
2 Sources, Fate, and Transport of Nitrogen and Phosphorus in the Chesapeake Bay Watershed: An Empirical Model

Introduction

Chesapeake Bay has been the focus of water-quality and 

ecological restoration efforts for several decades (Phillips, 

2007; U.S. Environmental Protection Agency, 2008). As the 

largest and most productive estuary in North America (U.S. 

Environmental Protection Agency, 2008), the bay is a vital 

ecological and economic resource. The bay and its tributaries 

have been degraded in recent decades, however, by excessive 

nutrients (nitrogen and phosphorus) and sediment from contributing watersheds. In 2000, the bay was listed as “impaired” 

under the Clean Water Act (Langland and others, 2003). 

Terrestrial and atmospheric inputs to Chesapeake Bay have 

increased by a factor of 6 to 8 for nitrogen and 13 to 24 for 

phosphorus since European colonization (Boynton and others, 

1995). Impacts of excessive nutrients and sediment include 

algal blooms, increased turbidity, decreased abundance of submerged aquatic vegetation and dissolved oxygen, and declining fisheries (Kemp and others, 2005; U.S. Environmental 

Protection Agency, 2008). Only 12 percent of Chesapeake 

tidal waters met ecological criteria for dissolved-oxygen levels 

during the summer months of 2005, 2006, and 2007, and only 

26 percent had acceptable chlorophyll-a levels in 2007 (U.S. 

Environmental Protection Agency, 2008). Although primary 

production in temperate estuaries is often nitrogen-limited 

(Vitousek and others, 1997), concentrations of nutrients and 

chlorophyll from 1985 through 2008 suggest that both nitrogen and phosphorus may limit production in Chesapeake Bay 

during different seasons and that phosphorus is the limiting 

nutrient in the spring (Prasad and others, 2010). Chesapeake 

Bay restoration efforts have been coordinated and managed 

since the 1980s by the U.S. Environmental Protection Agency 

(USEPA) in cooperation with other Federal, State, and local 

agencies through the Chesapeake Bay Program; current efforts 

are focused on pollution reduction, habitat restoration, fisheries management, watershed protection, and fostering public 

stewardship (U.S. Environmental Protection Agency, 2008).

Restoration efforts in the Chesapeake Bay watershed 

in recent decades have been insufficient to meet established 

standards. Concentrations of nitrogen and phosphorus in the 

estuary generally decreased between 1985 and 2008, and are 

controlled primarily by inputs from tributaries, which generally peaked in 1997 and have decreased since 2004 (Prasad 

and others, 2010). Natural variability in streamflow significantly affects fluvial nutrient fluxes, however. When adjusted 

for streamflow, trends from 1985 through 2008 are generally 

negative for nitrogen and phosphorus in most Chesapeake 

tributaries, although fluxes have increased in some streams 

(U.S. Geological Survey, 2009). Increasing nitrogen flux in 

the Choptank River, for example, likely reflects the importance of groundwater to nitrogen transport and increasing 

nitrate in groundwater in areas of the Delmarva Peninsula 

(Debrewer and others, 2008; Hirsch and others, 2010). In spite 

of generally decreasing nutrient fluxes in Chesapeake tributaries and concentrations in the estuary, concentrations are not 

decreasing quickly enough to meet established water-quality 

standards and the bay remains degraded (U.S. Environmental 

Protection Agency, 2008). Total maximum daily loads 

(TMDLs) have been established for nitrogen and phosphorus 

in the Chesapeake Bay to help manage nutrient reductions 

as mandated by the Clean Water Act (U.S. Environmental 

Protection Agency, 2011), and Presidential Executive Order 

13508 of 2009 directed multiple Federal agencies to develop 

and implement a new strategy for Chesapeake Bay protection and restoration (Federal Leadership Committee for 

Chesapeake Bay, 2010).

Chesapeake Bay restoration is complicated by the 

multitude of nutrient sources and complex interacting factors 

affecting the occurrence, fate, and transport of nitrogen and 

phosphorus from source areas to streams and the estuary. 

Chesapeake Bay drains 166,000 km2 (square kilometers) in six 

states and the District of Columbia (fig. 1). Most of the watershed is forested, but intensive agriculture and urban development occur in many areas. Major sources of nutrients to the 

bay and its tributaries include wastewater treatment plants, fertilizer and manure applications, and (for nitrogen) atmospheric 

deposition (Preston and Brakebill, 1999; Moore and others, 

2011). Natural hydrologic, geologic (fig. 2), and soil conditions relevant to the movement and persistence of nitrogen and 

phosphorus in the environment are also variable within the bay 

watershed. Nitrogen is readily transported as nitrate to groundwater and streams in areas underlain by carbonate bedrock 

(Ator and Ferrari, 1997; Miller and others, 1997; Ator and 

others, 1998; Lindsey and others, 1998; Greene and others, 

2005) and in areas of the Coastal Plain with well-drained permeable soils and sediments and oxic groundwater (Ator and 

others, 2005; Denver and others, 2010). Nitrate transported 

through groundwater contributes nearly half of the nitrogen 

flux in Chesapeake tributaries (Phillips and others, 1999). 

Multidecadal traveltimes typical of groundwater significantly 

complicate the understanding of restoration effectiveness, 

however, particularly when delays due to slow groundwater 

flow exceed the period of monitoring record. Phosphorus is 

less soluble than nitrate and is consequently transported most 

effectively in areas with steep slopes and (or) impermeable 

soils and sediments where overland runoff of precipitation is 

most likely. The design of restoration and management practices to mitigate nutrient transport is particularly complicated 

by the variety of these interacting natural factors (for example, 

Kaushal and others, 2008). 

Effective and efficient nutrient management at the 

regional scale in support of Chesapeake Bay restoration 

requires a comprehensive understanding of the sources, fate, 

and transport of nitrogen and phosphorus in the watershed 

that is available only through regional models. Targeting 

limited restoration and management resources most effectively 

requires an understanding of the spatial distribution and relative magnitude of nutrient sources (Castro and others, 2003), 

the natural conditions affecting nutrient fate and transport, 

and the most vulnerable or valuable resources to be protected. 
Introduction 3

Figure 1. Location of the Chesapeake Bay watershed and vicinity, including generalized land cover, point sources, and selected 

long-term stream monitoring stations for nutrient flux.
4 Sources, Fate, and Transport of Nitrogen and Phosphorus in the Chesapeake Bay Watershed: An Empirical Model

Figure 2. Hydrogeologic settings within the Chesapeake Bay watershed.
Methods 5

Available research on nutrients in the watershed supports conceptual models of these factors; however, consistent, comprehensive, and quantitative estimates require the use of numerical models. Spatially Referenced Regression On Watershed 

attributes (SPARROW) (Schwarz and others, 2006; Preston 

and others, 2009) has been used to estimate the total flux of 

nitrogen and phosphorus to Chesapeake Bay from the watershed and quantify nutrient sources and factors affecting the 

fate and transport for the late 1980s and early and late 1990s 

(Preston and Brakebill, 1999; Brakebill and others, 2001; 

Brakebill and Preston, 2004). Similar SPARROW models have 

also been calibrated for the wider northeastern United States 

(Moore and others, 2011), the upper Mississippi River watershed (Alexander and others, 2008), and the continental United 

States (Smith and others, 1997). Hydrological Simulation 

Program–FORTRAN (HSPF) (Bicknell and others, 1996) has 

also been used extensively to understand nutrient and sediment 

sources, fate, and transport in support of Chesapeake Bay restoration (U.S. Environmental Protection Agency, 1998). Other 

models that have been applied to evaluate nutrients in areas of 

the Chesapeake Bay watershed include MODFLOW (Sanford 

and Pope, 2011) and SWAT (Meng and others, 2010). 

Purpose and Scope

The sources, fate, transport, and flux of total nitrogen 

(TN) and total phosphorus (TP) in the Chesapeake Bay watershed are presented and discussed in this report. Interpretations 

are based on SPARROW models calibrated to mean annual 

conditions in 2002 in the Chesapeake Bay watershed for TN 

and TP. These models, CBTN_v4 and CBTP_v4, were constructed at a finer spatial resolution than previous SPARROW 

models for the Chesapeake Bay watershed (versions 1, 2, 

and 3; Preston and Brakebill, 1999; Brakebill and others, 

2001; Brakebill and Preston, 2004), and include an updated 

timeframe and modified sources and other explanatory terms. 

The development and calibration of the models are presented 

and discussed, along with the estimated flux of nitrogen and 

phosphorus in major tributaries and to the bay, the spatial 

distribution and significance of major sources, and significant 

factors affecting nitrogen and phosphorus delivery to stream 

channels and in-stream fate and transport. Specific estimates 

of nitrogen and phosphorus fluxes for each of 80,579 nontidal stream reaches within the watershed also are presented, 

including the total flux in each reach and the local (incremental) flux contributed by the local watershed and independent of 

any upstream contributions. This report is intended primarily 

for watershed managers and others needing a comprehensive, 

quantitative, and spatially distributed accounting and understanding of nitrogen and phosphorus in the Chesapeake Bay 

watershed; those seeking a detailed discussion of the theory, 

development, and application of SPARROW modeling are 

referred to Smith and others (1997) and Schwarz and others 

(2006).

Methods

The SPARROW modeling approach (Smith and others, 

1997; Schwarz and others, 2006) was used to estimate the 

mean annual flux of TN and TP to Chesapeake Bay and in 

each of 80,579 nontidal tributary reaches, and to identify and 

quantify significant factors affecting the occurrence, fate, and 

transport of nitrogen and phosphorus in streams of the bay 

watershed. SPARROW is a spatially explicit, mass-balance 

watershed model that uses nonlinear regression to quantify the 

spatial relation between observed constituent (such as nitrogen or phosphorus) fluxes in nontidal streams (the response 

or dependent variable) and constituent sources and factors 

affecting their overland and in-stream fate and transport 

(the explanatory or independent variables). Annual nutrient 

fluxes used as response variables to calibrate the models were 

estimated from observed streamflow and water chemistry 

on monitored streams. Response and explanatory variables 

were geographically referenced to a digital network of stream 

reaches and associated watershed catchments that facilitates 

the routing of water and associated constituents throughout 

the landscape. The SPARROW models predict the long-term 

mean-annual TN and TP flux for each network stream reach 

as a function of sources, factors influencing non-conservative 

delivery to the stream channel, and in-stream fate and transport. Mass-balance constraints ensure the in-stream nutrient 

flux at the end of each model reach equals the sum of flux 

generated within the reach subwatershed, any flux transported 

from upstream reaches, and any attenuation (losses) within 

the reach itself. Nutrient transport from uplands to stream 

channels and within the stream network was not assumed to 

be conservative, but rather was weighted by landscape factors 

affecting overland and in-stream fate and transport (Schwarz 

and others, 2006; Hoos and McMahon, 2009).

Stream Network Development

The digital network of streams and associated catchments 

used in SPARROW models for the Chesapeake Bay watershed 

was developed from the geospatial dataset, NHDPlus, a 

1:100,000-scale representation of stream hydrography built 

upon the National Hydrography Dataset (NHD) (Horizon 

Systems, 2010; Simley and Carswell, 2010). The development 

of network and stream characteristics (such as topology and 

mean annual streamflow) is described in Horizon Systems 

(2010). Reaches described as lakes, ponds, or reservoirs in 

NHDPlus were generally modeled as impounded reaches; 

the outlet reach for each impoundment was identified on the 

basis of the hydrologic sequence number. All other reaches 

were modeled as flowing streams. Terminal (target) reaches 

were generally assumed to be those identified as terminal 

flowlines in NHDPlus. Modifications to NHDPlus included 

corrections to stream connectivity and reach types (including 

flowing, impounded, and (or) terminal reaches) and the addition of stream and watershed attributes particularly relevant 
6 Sources, Fate, and Transport of Nitrogen and Phosphorus in the Chesapeake Bay Watershed: An Empirical Model

to SPARROW modeling (Brakebill and others, 2011). Surface 

areas of reservoirs on the lower Susquehanna River were 

compiled from Hainly and others (1995). The fraction of total 

streamflow delivered by braided reaches or other divergences 

in the NHDPlus network was compiled from a similar network 

developed for the wider northeastern United States (Moore 

and others, 2011). The NHDPlus-based model network used 

to support SPARROW calibration and predictions for the 

Chesapeake Bay watershed includes 80,579 reaches assumed 

to represent nontidal bay tributaries. Also included are an additional 1,329 reaches representing centerlines of tidal reaches 

of major Chesapeake tributaries; SPARROW predictions for 

these reaches were used only to estimate the total TN and TP 

fluxes to the bay.

The NHDPlus digital stream network represents a 

significant spatial refinement over that used by previous 

SPARROW models for the Chesapeake Bay watershed. The 

80,579 individual nontidal stream reaches in the model area 

drain local watershed catchments (independent of watersheds 

of any contributing upstream reaches) with a mean area of 2.1 

km2. Previous SPARROW models for the Chesapeake Bay 

watershed were constructed on a 1:500,000-scale hydrologic 

network with 2,734 stream reaches draining catchment areas 

averaging 75 km2 in size (Brakebill and others, 2010). 

Calibration Data

The SPARROW models were calibrated to independent 

estimates of mean annual contaminant flux at selected locations on the stream network where water-quality monitoring 

has been conducted. Annual in-stream TN and TP fluxes on 

nontidal Chesapeake tributaries used as dependent variables in 

SPARROW calibration were estimated using multiple regression modeling of available water chemistry and streamflow at 

monitored sites (Schwarz and others, 2006). 

Water-quality data for use in SPARROW calibration were 

compiled from available surface-water monitoring records collected between 1995 and 2009 by the U.S. Geological Survey 

(USGS), State agencies, and River Basin Commissions within 

the Chesapeake Bay watershed. A detailed description of 

data compilation methods is included in Langland and others 

(2007). Water-quality records for more than 600 stream sites 

(water-quality stations) with more than 50 TN and (or) TP 

observations between October 1970 and December 2009 were 

compiled and reviewed. In general, only water-quality stations 

for which a minimum of 5 years of record were available 

were retained. Stations with unavailable or uncertain location 

information or for which no water-quality data were available between January 2001 and December 2003 were omitted. 

In cases where multiple water-quality stations exist within 

the same local network catchment, only data from the station with the most complete water-quality data were retained. 

Water-quality observations at two stations within 0.32 km 

(kilometers) of one another on the Slate River were combined 

because the periods of record suggest sampling at one station 

is intended to replace sampling at the other. 

Streamflow data collected between 1980 and 2009 were 

compiled and associated with available water-quality data to 

support estimates of mean annual TN and TP flux at waterquality stations for use in SPARROW calibration. Streamflow 

data were compiled from USGS records (U.S. Geological 

Survey, 2011a) and associated with water-quality data collected at common locations. Water-quality data that were not 

collected at USGS stream gages were associated to flow data 

from nearby gages. Of the 205 water-quality stations used 

for flux estimation, water-quality to flow-station area ratios 

for 202 were between 0.5 and 1.5; the other three were 0.12 

(Chickahominy River), 0.26 (Licking Run), and 1.6 (South 

Fork, Potomac River).

 Water-quality data (observed TN and TP concentrations) 

and measured or estimated streamflow were used to estimate 

mean annual TN and TP flux at water-quality stations. 

Multiple-regression models calibrated to routine chemical 

observations and continuous streamflow (Cohn and others, 

1989; 1992) have been used extensively to estimate contaminant flux in monitored streams (for example, Johnson and 

Belval, 1998; Langland and others, 2006). For this application, 

TN and TP flux at water-quality stations in the Chesapeake 

Bay watershed were estimated using a nine-parameter model 

including terms for streamflow, time (decimal year), seasonality (sine and cosine of time), and squares of each using the 

USGS FLUXMASTER statistical routine (G.E. Schwarz, 

U.S. Geological Survey, written commun., 2008). Where 

trends in streamflow or water quality were evident, results 

were detrended to 2002 conditions. Flux estimates were also 

adjusted to reflect mass flux at the outlet of NHD catchments 

based on the ratio of the drainage area of the monitoring station to that of the catchment outlet. In cases where streamflow 

and water-quality measurements were collected on different 

reaches, flux estimates were similarly adjusted based on the 

ratio of the streamflow station area to NHD catchment area 

for the water-quality station. Diagnostics (including standard 

errors and residual distributions) were reviewed for each 

flux model, and TN or TP estimates from nine-parameter 

models that were considered unreliable were discarded and 

replaced with those from a simpler seven-parameter model 

lacking squared time and streamflow terms. Residual analysis 

suggested that the squared streamflow term can contribute 

substantial error in such flux models, particularly where data 

are sparse.

Flux estimates from across the Chesapeake Bay watershed were normalized and are therefore not subject to regional 

variations in hydrologic (for example, flood or drought) conditions. Mean annual TN and TP fluxes for use in SPARROW 

calibration were estimated using water-quality data available 

for a 15-year period centered on 2002 (1994 through 2009) 

and were adjusted (where possible) to reflect mean hydrologic conditions estimated from a 30-year flow record. Flux 

estimates for use in SPARROW calibration thus represent 

long-term mean conditions and generally eliminate potential 

effects of spatially variable hydrologic conditions within the 

watershed during the target year (2002). Available long-term 
Methods 7

flow data were used to calculate TN and TP flux estimates that 

represent the flux that would have occurred at each site during 

2002 had long-term mean hydrologic conditions occurred. 

Available calibration data for the SPARROW models 

reflect the spatial and temporal distributions of streamflow 

and surface-water-quality monitoring in the Chesapeake 

Bay watershed. The SPARROW models were calibrated to 

mean annual TN and TP flux estimates for 2002 at 181 and 

184 water-quality stations, respectively (fig. 3). In general, 

streamflow and water-quality monitoring (and therefore available TN and TP flux estimates for SPARROW calibration) are 

located disproportionately on larger Chesapeake tributaries, 

and lower-order streams are poorly represented (fig. 4). The 

80,579 nontidal stream reaches in the SPARROW network 

drain watersheds with a median total area of 5.0 km2; the 

smallest stream for which TN and TP flux estimates could be 

computed, however, drains a watershed more than twice that 

size (12.6 km2). SPARROW models calibrated with available 

flux estimates might be expected to reasonably represent TN 

and TP fluxes in larger Chesapeake tributaries, but improved 

understanding of TN and TP flux and processes in smaller 

watersheds might require more water-quality and streamflow 

data collected in particularly small streams.

Explanatory Data

Explanatory variables developed for use in SPARROW 

model calibration include spatially explicit and spatially 

comprehensive nutrient sources and watershed characteristics 

representative of processes significant to nutrient fate and 

transport (Schwarz and others, 2006). Explanatory variables 

representing TN and TP sources and transport factors were 

apportioned to stream reaches and associated watershed 

catchments and serve as independent variables in SPARROW 

calibration. 

Many of the explanatory variables considered for the 

model were extracted from those developed from geospatial 

data for similar models of large watersheds in the United 

States as part of the National Water-Quality Assessment 

(NAWQA) Program (Preston and others, 2011). Briefly, an 

inverse-distance weighting approach was used to interpolate 

data from the National Atmospheric Deposition Program/

National Trends Network (NADP/NTN) (U.S. Geological 

Survey, 2000; Alexander and others, 2001) to estimate wet 

atmospheric inorganic nitrogen deposition to model watersheds in 2002 (Wieczorek and LaMotte, 2010a). Available 

land-cover data for 2001 (Wieczorek and LaMotte, 2010b) 

and estimated inputs of nitrogen and phosphorus in fertilizer, 

fixation by crops, and manure in 2002 (Wieczorek and 

LaMotte, 2010c, d) were compiled and similarly apportioned 

to catchments within the model network, along with soil 

conditions and other watershed characteristics potentially 

relevant to nitrogen or phosphorus fluxes (Wieczorek and 

LaMotte, 2010e, f, g, h). Estimates of annual nitrogen and 

phosphorus discharges from (primarily municipal) point 

sources during 2002 to Chesapeake tributaries were compiled by the Chesapeake Bay Program (U.S. Environmental 

Protection Agency, 2009). Physiography and geology in the 

Chesapeake Bay watershed were compiled from Bachman and 

others (1998) and Brakebill and Kelley (2000). The enhanced 

vegetative index (EVI) for 2002, a globally consistent measure 

of vegetation conditions, was interpreted from data compiled 

from the Moderate Resolution Imaging Spectroradiometer 

(MODIS) instrument onboard the Earth Observing SystemTerra platform at 1-km resolution and 16-day compositing 

periods (Huete and others, 2002). 

SPARROW Model Calibration and Predictions

SPARROW models of TN and TP for the Chesapeake 

Bay watershed (CBTN_v4 and CBTP_v4) were calibrated 

from compiled data. A detailed discussion of the nonlinear 

regression and bootstrapping approach used to calibrate 

SPARROW models, estimate model coefficients, and predict contaminant flux in unmonitored streams is available in 

Schwarz and others (2006). Individual explanatory variables 

for potential inclusion in each Chesapeake SPARROW model 

were selected on the basis of current understanding of nutrient occurrence, fate, and transport in the watershed available 

through previous studies, including previous models for the 

Chesapeake Bay watershed (Preston and Brakebill, 1999; 

Brakebill and others, 2001; Brakebill and Preston, 2004) 

and the wider northeastern United States (Moore and others, 

2011). Models were generally constructed by including source 

terms, land-to-water variables, and aquatic (flowing and 

impounded) decay specification, in turn (Schwarz and others, 

2006). Nutrient source and aquatic decay variables were constrained to be non-negative in model calibration; land-to-water 

variables were not constrained. Nonlinear least-squares regression was used to calibrate exploratory models during model 

development; bootstrapping (which uses random resampling 

to infer the distribution of parameter estimators, Schwarz and 

others, 2006) was used to verify coefficient estimates in the 

final models and to estimate confidence intervals for predictions. Many different combinations of explanatory variables 

were included in preliminary model development. The final 

list of explanatory variables and the form of each model 

were determined through consideration of the overall model 

explanatory power and the geographic and statistical distribution of residuals, as well as the significance of each variable, 

its collinearity with other variables, and its contribution to the 

understanding of nutrient occurrence, fate, and transport.

Explanatory variable specifications in the SPARROW 

models were chosen to maximize the interpretability of model 

coefficients and comparability with literature values, as well 

as to support estimation of TN and TP fluxes in unmonitored 

areas (Schwarz and others, 2006). Source terms in the models are specified as either the estimated mass of nitrogen or 

phosphorus applied or deposited annually to each local catchment, or the area of a specific land cover or geologic setting. 
8 Sources, Fate, and Transport of Nitrogen and Phosphorus in the Chesapeake Bay Watershed: An Empirical Model

Figure 3. Location of stations for which mean annual flux estimates of total nitrogen and (or) total phosphorus were 

computed for use in SPARROW model calibration.
Methods 9

Estimated coefficients are thus interpreted as the proportion 

(fraction) of the applied or deposited nutrient mass transported 

to watershed streams, or the mean yield of TN or TP from 

the land cover or geologic setting, respectively. Generally, 

explanatory terms affecting nutrient transport from the land 

to streams (land-to-water terms) were specified in the models 

to interact with (potentially increase or decrease delivery 

of TN or TP to streams from) all sources except for point 

sources; terrestrial processes were assumed to be irrelevant for 

point sources discharging directly to streams. Soil erodibility 

(K-factor) in the TP model does not interact with the crystalline or siliciclastic rock sources, which are intended to represent natural sources of phosphorus to groundwater (Denver 

and others, 2010). The Coastal Plain term in the TP model 

similarly does not interact with these rock sources; there are 

no crystalline or siliciclastic rocks near the land surface in the 

Coastal Plain (Ator and others, 2005). Land-to-water terms 

were centered (mean-adjusted) and generally log-transformed; 

coefficients for log-transformed terms can be interpreted as the 

percent change in flux delivered to streams from each interacting source term for a 1-percent increase in each land-to-water 

variable (Schwarz and others, 2006). Instream nutrient losses 

(decay) in flowing streams were modeled as a first-order decay 

process and specified as a function of estimated time of travel 

(based on the stream reach length and estimated velocity, 

Horizon Systems, 2010), and coefficients can be interpreted 

as the mean annual rate of TN or TP removal within the 

stream reach. Decreasing rates of in-stream nitrogen decay 

with increasing stream size have been observed in previous 

SPARROW models in the Chesapeake Bay watershed (Preston 

and Brakebill, 1999) and elsewhere (Smith and others, 1997); 

denitrification and biotic nutrient uptake occur primarily in 

the benthic zone, and smaller streams typically support less 

streamflow per benthic area (Schwarz and others, 2006). Also, 

biological processes controlling nutrient uptake may increase 

with increasing temperature (Bothwell, 1988) and preliminary 

TN SPARROW models suggested a corresponding trend in TN 

residuals. In-stream losses were therefore modeled separately 

for classes of stream reaches defined by estimated mean 

annual flow (Horizon Systems, 2010) and mean annual maximum surface-air temperature from 1971 through 2000 (fig. 5); 

flow and temperature values defining different classes were 

selected based on results of preliminary models using various 

multiple arbitrary values (Preston and Brakebill, 1999). Losses 

in impoundments (lakes, ponds, and reservoirs) are specified 

as the inverse of the areal hydraulic load (the ratio of reservoir outflow to surface area) and estimated coefficients can 

be interpreted as an apparent settling velocity (Schwarz and 

others, 2006). In general, only terms significantly different 

from zero (α=0.10) were retained in the models. One term 

representing stream decay (aquatic decay in flowing streams) 

with a higher p-value was retained in the TN model, however; 

the estimated decay in this class of streams was more than 

ten times smaller than in other classes, as expected in light 

of mean annual flow (Preston and Brakebill, 1999) and air 

temperature (Bothwell, 1988). For the purpose of calibration, 

missing values for source or decay variables were assumed to 

be zero; missing values for land-to-water terms were set to the 

median of non-missing values.

SPARROW models were used to predict the spatial 

distribution of TN and TP fluxes within Chesapeake tributaries and the total flux of TN and TP to the bay (Schwarz and 

others, 2006). Estimated model coefficients were used along 

with values of explanatory terms in each catchment to estimate 

the total and local flux of TN and TP (overall, and from each 

source) for each stream in the model network (see Appendix). 

Predicted TN and TP fluxes at monitoring reaches (those with 

calibration data) were adjusted to match calibration data. Total 

TN and TP flux from the watershed to Chesapeake Bay was 

estimated as the sum of total estimated TN and TP flux at 

downstream terminal reaches in the model network. 

Although SPARROW is not designed for modeling 

tidal waters, 1,329 reaches representing centerlines of tidal 

parts of major Chesapeake tributaries are included in the 

Figure 4. The distribution of stream order, streamflow, and watershed size among modeled stream reaches in the Chesapeake Bay 

watershed, and those with calibration stations.
10 Sources, Fate, and Transport of Nitrogen and Phosphorus in the Chesapeake Bay Watershed: An Empirical Model

Figure 5. Mean annual maximum air temperature, 1971–2000, and streams with mean annual flow greater than 3.45 cubic meters 

per second.
Nitrogen and Phosphorus in the Chesapeake Bay Watershed 11

NHDPlus-based model network along with the 80,579 

nontidal tributary reaches, and TN and TP flux predictions 

were therefore also estimated for these reaches. Although 

predictions for these 1,329 centerline reaches are generally 

not presented in this report (on, for example, maps of TN or 

TP yields), they were included in estimating total TN and TP 

fluxes to Chesapeake Bay, which therefore include nutrient 

inputs (such as from point sources and atmospheric deposition) directly to major tidal tributaries. Predictions for these 

reaches also are included in the accompanying datafile for that 

purpose (see Appendix), although these predictions for tidal 

waters are not intended for other uses. Stream decay was not 

applied to centerline reaches for the purpose of these estimates; stream decay is calibrated in the SPARROW models 

to flowing reaches and is not intended to represent nutrient 

decay in tidal waters. Estimates of total TN and TP fluxes to 

Chesapeake Bay can therefore be interpreted to include all 

modeled terrestrial and atmospheric sources to tidal and nontidal tributaries and the effects of overland and fluvial transport, but not effects of losses or other processes in tidal waters.

Model Limitations

Predictions from the CBTN_v4 and CBTP_v4 

SPARROW models for the Chesapeake Bay, like those of all 

models, must be considered in light of the assumptions and 

simplifications inherent in the model specification and the 

limitations of available input data. Assumptions and simplifications inherent to SPARROW are discussed in Schwarz 

and others (2006). The models do not include all possible 

nutrient sources; minor sources or those for which spatially 

explicit estimates are not available may be incorporated by 

SPARROW into other source terms and (or) contribute to 

model uncertainty. The models reflect mean annual conditions 

over long periods, and the effects of processes or activities 

over seasons or other relatively short time periods are not 

represented. Estimation of TN and TP fluxes for use in 

SPARROW calibration and the development and allocation of 

much of the explanatory data were done with other statistical 

or geographic models that are limited by their own assumptions and simplifications. Water-quality data in the Chesapeake 

Bay watershed suitable for SPARROW calibration may be 

very representative of conditions in relatively large streams, 

but smaller streams are poorly represented. Headwater streams 

are typically most closely linked to adjacent uplands and 

associated contaminant sources, drain the majority of larger 

watersheds, and contribute directly to streams of all sizes 

(Alexander and others, 2007). Nearly half (45 percent) of the 

nitrogen delivered to streams in the northeastern United States 

is delivered to headwater streams (Alexander and others, 

2007).The increasing availability of stream hydrography at 

finer resolution (for example 1:100,000 scale for the current 

models) underscores the potential usefulness of increased 

water-quality and streamflow monitoring on small streams to 

support a better understanding of nutrient dynamics in those 

systems within regional models.

Nitrogen and Phosphorus in the 

Chesapeake Bay Watershed

The calibrated CBTN_v4 and CBTP_v4 SPARROW 

models identify and quantify significant sources of nitrogen 

and phosphorus, landscape characteristics affecting the 

delivery of nutrients to streams, losses within flowing and 

impounded streams, and estimated local (generated within 

each individual catchment) and delivered (to downstream 

estuaries) fluxes and yields for each of 80,579 streams in the 

Chesapeake Bay watershed. Explanatory terms in the TN 

model explain 98 percent of the spatial variability in mean 

annual TN flux estimates at the 181 calibration sites and 86 

percent of the variability in TN yields (table 1). Explanatory 

terms in the TP model similarly explain a significant part of 

the variability in the TP calibration data; flux-R2 and yield-R2

values for the TP model are 0.951 and 0.730, respectively 

(table 2). Relatively high flux-R2 values in SPARROW models 

are due in part to the natural correlation between watershed 

area and contaminant flux, and yield-R2 values are therefore 

likely more indicative of the explanatory value of model terms 

(Schwarz and others, 2006). 

Watershed Sources 

A variety of natural and human sources contribute 

nitrogen and phosphorus to the Chesapeake Bay watershed. 

Anthropogenic sources of nutrients that are significant (greater 

than zero, α=0.10) in the TN and TP SPARROW models 

include point sources, certain urban activities, and fertilizer 

and manure applications in agricultural areas (tables 1, 2). 

Significant sources of nitrogen also include direct fixation of 

atmospheric nitrogen by certain crops, and deposition from 

the atmosphere. Natural mineral sources in siliciclastic and 

crystalline rocks contribute significantly to the phosphorus 

flux in streams. 

Point sources input nutrients directly to streams in the 

Chesapeake Bay watershed (fig. 1; tables 1, 2). Point sources 

contribute both TN and TP to Chesapeake tributaries; the 

point source coefficient is near one in each model, as would be 

expected given that point sources discharge directly to streams 

with no opportunity for terrestrial losses. Most streams in the 

watershed receive no direct nitrogen or phosphorus inputs 

from point sources. Point sources can contribute substantially 

(more than 99 percent) to local TN or TP fluxes where they 

occur, however, and produce extremely high local yields. 

Agriculture contributes significantly to nonpoint nitrogen and phosphorus inputs in the Chesapeake Bay watershed. 

Approximately 24 percent of estimated nitrogen applications 

in fertilizers and direct fixation by crops reaches watershed 

streams (table 1). Howarth and others (1996) estimated that 

25 percent of nonpoint nitrogen applications (including from 

fertilizers and fixation by leguminous crops) from temperate 

regions is transported to streams draining to the North Atlantic 
12 Sources, Fate, and Transport of Nitrogen and Phosphorus in the Chesapeake Bay Watershed: An Empirical Model

Ocean, and Preston and Brakebill (1999) estimated that 28 

percent of nitrogen from fertilizer applications was transported 

to Chesapeake tributaries in 1987. Conversely, less than 6 

percent of TN from manure and TP from both fertilizers 

and manure is transported to watershed streams (tables 1, 

2). Organic nitrogen in manure and phosphorus compounds 

generally are less soluble and therefore, mobile in the environment than inorganic nitrogen compounds commonly applied as 

fertilizers (Hem, 1985). Also, nitrogen and phosphorus in animal wastes may be largely recycled from other local sources 

(such as locally grown feed), and relatively little nitrogen or 

phosphorus in manure may represent a net influx of nutrients 

to local watersheds such as that in chemical fertilizers and fixation from the atmosphere (Howarth and others, 1996). Moore 

and others (2011) similarly reported substantially lower export 

coefficients for TN and TP from manure than from fertilizers 

for a wider area of the northeastern United States, although 

Preston and Brakebill (1999) reported similar export coefficients for TN from fertilizers and manure in the Chesapeake 

Bay watershed in 1987. 

Unlike point sources, agriculture is widespread within the 

Chesapeake Bay watershed, and fertilizer and manure applications represent significant sources of TN and TP to streams 

in many areas. Agriculture in the Chesapeake Bay watershed 

occurs primarily in the northern Piedmont, the Eastern Shore 

of the Coastal Plain (the Delmarva Peninsula), and in isolated 

valleys in the mountainous areas, particularly the Great Valley 

from Virginia through Pennsylvania (figs. 1, 2). Predicted 

local yields of TN and TP from agricultural sources (fertilizers, manure, and crop fixation) are accordingly highest in 

these areas (fig. 6). Local yields of nutrients from manure are 

particularly high in the southern Shenandoah Valley, the lower 

Table 1. Summary of nonlinear least-squares calibration results for CBTN_v4, the Chesapeake Bay watershed total nitrogen model.

[MSE, mean squared error; RMSE, root mean squared error; kg, kilogram; yr, year; km2, square kilometer; EVI, enhanced vegetative index; AWC, available 

water capacity; m, meter; mm, millimeter; d, days; WY02, water year 2002 (October 2001 through September 2002); MAQ, mean annual flow; m3 s-1, cubic 

meters per second; T30, mean annual maximum temperature from 1971 through 2000; °C, degrees Celsius; <, less than; >, greater than; ≤, less than or equal 

to]

Total Nitrogen, 2002 

(n = 181, MSE = 0.0836, RMSE = 0.289, flux R2 = 0.978, yield R2 = 0.858)

Explanatory variables Estimate Units 90-percent 

confidence interval Standard error p1

Sources

 Point sources (kg yr-1) 0.774 0.375 – 1.17 0.242 0.0008

 Crop fertilizer and fixation (kg yr-1) 0.237 0.177 – 0.297 0.0363 < 0.0001

 Manure (kg yr-1) 0.0582 0.0138 – 0.103 0.0269 0.0157

 Atmospheric deposition (kg yr-1) 0.267 0.179 – 0.355 0.0533 < 0.0001

 Urban2 (km2) 1,090 kg km-2 yr-1 707 – 1,480 234 < 0.0001

Land-to-water delivery

 ln[Mean EVI for WY02 (dimensionless)] -1.70 -2.65 – -0.737 0.580 0.0039

 ln[Mean soil AWC (fraction)] -0.829 -1.26 – -0.401 0.260 0.0016

 ln[Groundwater recharge (mm)] 0.707 mm-1 0.499 – 0.916 0.126 < 0.0001

 ln[Piedmont carbonate (percent of area)] 0.158 0.0755 – 0.241 0.0500 0.0018

Aquatic decay

 Impoundments, inverse hydraulic load (yr m-1) 5.93 m yr-1 0.271 – 11.6 3.42 0.0424

 Streams, time of travel (d) in: 

 Small (MAQ ≤ 3.45 m3 s-1) 0.339 d-1 0.0936 – 0.585 0.148 0.0118

 Large (MAQ > 3.45 m3 s-1), T30 > 18.5°C 0.153 d-1 0.0622 – 0.245 0.0551 0.0030

 Large (MAQ > 3.45 m3 s-1), T30 ≤ 15°C 0.0131 d-1 -0.111 – 0.137 0.0751 0.431

1

 p-values are one-sided for sources and aquatic-decay coefficients (which were constrained to be non-negative) and two-sided for land-to-water delivery 

coefficients.

2

 Urban land includes all developed land, as defined by Wieczorek and LaMotte, 2010b.
Nitrogen and Phosphorus in the Chesapeake Bay Watershed 13

Delmarva Peninsula, and southeastern Pennsylvania, where 

livestock (primarily poultry and cattle) production is greatest, 

and manure represents the majority of local TP sources and 

nearly half of local TN sources to these areas. Local yields 

from fertilizer applications and crop fixation are more evenly 

distributed throughout agricultural areas of the watershed, 

and represent the majority of local TN and TP yields from all 

sources in many areas. 

Urban areas yield, on average, 1,090 kg km-2 yr-1 (kilograms per square kilometer per year) of TN and 49 kg km-2 yr-1

of TP to streams in the Chesapeake Bay watershed. Individual 

urban sources of TN and TP are generalized and not distinguished by the SPARROW models, but may include fertilizer 

applications to turf grasses, septic systems, leaking sewer 

lines, domestic animals, local deposition from automobiles, 

or spills in commercial or industrial areas. Like point sources, 

urban areas are limited spatially within the watershed, but 

may contribute substantially to in-stream TN and TP fluxes in 

isolated urban areas.

Atmospheric deposition contributes significantly to TN 

export in streams throughout the Chesapeake Bay watershed. 

Although nitrogen gas is naturally abundant in the atmosphere, 

atmospheric wet deposition of inorganic nitrogen is derived 

primarily from emissions generated by the combustion of 

fossil fuels and from certain agricultural activities (Driscoll 

and others, 2003). An estimated 27 percent of atmospheric 

nitrogen deposition reaches streams of the watershed (table 1), 

which is similar to previous estimates for nonpoint nitrogen 

applications from temperate areas draining to the North 

Atlantic Ocean (Howarth and others, 1996) and for streams 

of the northeastern United States (Moore and others, 2011). 

Unlike other sources, atmospheric deposition occurs within 

Table 2. Summary of nonlinear least-squares calibration results for CBTP_v4, the Chesapeake Bay watershed total phosphorus 

model.

[MSE, mean squared error; RMSE, root mean squared error; kg, kilogram; yr, year; km2, square kilometer; mm, millimeter; m, meter; <, less than]

Total Phosphorus, 2002 

(n = 184, MSE = 0.225, RMSE = 0.474, flux R2 = 0.951, yield R2 = 0.730)

Explanatory variables Estimate Units 90-percent 

confidence Interval Standard error p1

Sources

 Point sources (kg yr-1) 0.877 0.573 – 1.18 0.183 < 0.0001

 Crop fertilizer (kg yr-1) 0.0377 0.0171 – 0.0583 0.0125 0.0014

 Manure (kg yr-1) 0.0253 0.0144 – 0.0362 0.00658 0.0002

 Siliciclastic rocks (km2) 8.52 kg km-2 yr-1 6.10 – 10.9 1.46 < 0.0001

 Crystalline rocks (km2) 6.75 kg km-2 yr-1 3.25 – 10.2 2.12 0.0009

 Urban2 (km2) 49.0 kg km-2 yr-1 30.4 – 67.7 11.3 < 0.0001

Land-to-water delivery

 Soil erodibility (K factor) 6.25 3.55 – 8.95 1.63 0.0002

 ln[Well-drained soils (percent)] -0.100 -0.153 – -0.0478 0.0317 0.0019

 Coastal Plain (percent of area) 1.02 0.681 – 1.35 0.204 < 0.0001

 ln[Precipitation3 (mm)] 2.06 mm-1 0.567 – 3.55 0.903 0.0237

Aquatic decay

 Impoundments, inverse hydraulic load (yr m-1) 54.3 m yr-1 12.1 – 96.5 25.5 0.0174

1

 p-values are one-sided for sources and aquatic-decay coefficients (which were constrained to be non-negative) and two-sided for land-to-water delivery 

coefficients.

2

 Urban land includes all developed land, as defined by Wieczorek and LaMotte, 2010b.

3

 Mean annual precipitation, 1971 through 2000.
14 Sources, Fate, and Transport of Nitrogen and Phosphorus in the Chesapeake Bay Watershed: An Empirical Model

Figure 6. Estimated local yields of total nitrogen and phosphorus from agricultural sources.
Nitrogen and Phosphorus in the Chesapeake Bay Watershed 15

each individual catchment within the Chesapeake Bay watershed (fig. 7a), and represents the majority of TN sources in 

northern and western forested areas (particularly in western 

Pennsylvania and Virginia), where other nitrogen sources are 

limited (fig. 7b). 

Minerals in crystalline and siliciclastic rocks represent 

natural sources of TP export in some areas of the Chesapeake 

Bay watershed. Forested areas have been noted as significant 

TP sources in previous SPARROW models (for example, 

Alexander and others, 2008; Moore and others, 2011), and 

likely represent a proxy for any background phosphorus 

sources not accounted for by other source terms. Crystalline 

and siliciclastic rocks in the eastern Piedmont, Blue Ridge, and 

Valley and Ridge Physiographic Provinces have been identified as likely sources of dissolved phosphorus to groundwater 

and—by extension—to receiving streams (Denver and others, 

2010), however, and may be the source of TP exports noted 

from forested areas in previous models. The estimated mean 

yields of 6.8 and 8.5 kg km-2 yr-1 of phosphorus from areas of 

the Chesapeake Bay watershed underlain by crystalline and 

siliciclastic rocks (respectively) (table 2) are similar to mean 

exports reported by Dillon and Kirchner (1975) for natural 

forested areas underlain by similar rocks in southern Ontario 

(4.8 kg km-2 yr-1 and 10.7 kg km-2 yr-1 for granitic igneous 

and sedimentary rocks, respectively), and to phosphorus 

exports from natural forested watersheds in other temperate 

areas (Dillon and Kirchner, 1975; Likens and others, 1977). 

Phosphorus yields from mineral sources are generally much 

smaller than from other sources where they exist, but represent 

the majority of the small TP flux from relatively natural areas, 

particularly in the northern and western mountainous areas of 

the Chesapeake Bay watershed (fig. 8).

Figure 7. Estimated local (A) yields and (B) source shares of total nitrogen from atmospheric deposition.
16 Sources, Fate, and Transport of Nitrogen and Phosphorus in the Chesapeake Bay Watershed: An Empirical Model

Figure 8. Share of local phosphorus yields attributable to siliciclastic or crystalline rocks.
Nitrogen and Phosphorus in the Chesapeake Bay Watershed 17

Fate and Transport 

Nitrogen and phosphorus are typically not transported 

conservatively through the environment, but are subject to a 

variety of mostly biologically mediated losses and transformations in both terrestrial and aquatic settings. Fate and transport 

processes relevant to nitrogen and phosphorus are represented 

in the SPARROW models by land-to-water and aquatic decay 

terms selected to represent known factors contributing to 

the spatial distribution of these nutrients in groundwater and 

streams of the watershed. Land-to-water terms selected for the 

TN model reflect major factors controlling the fate, transport, 

and (therefore) occurrence of nitrogen in the Chesapeake 

Bay watershed and vicinity, including plant uptake, redox 

conditions, and hydrogeologic conditions important to nitrate 

transport through groundwater. Conversely, phosphorus compounds are relatively insoluble, and land-to-water terms in the 

TP model generally reflect the importance of transport through 

overland runoff.

Land-to-water terms in the TN model reflect the importance of plant uptake, redox conditions, and groundwater 

to the fate and transport of nitrogen in the Chesapeake Bay 

watershed. Decreasing TN delivery to streams in areas of 

greater EVI (greener) (table 1) likely reflects healthier plant 

growth and the incorporation of nitrogen in plant biomass 

rather than groundwater or streams. TN delivery to streams 

increases with increasing groundwater recharge and is greater 

in areas underlain by carbonate rocks in the Piedmont than 

in other areas (table 1). Assuming no net change in aquifer 

storage (and neglecting withdrawals), areas with greater 

groundwater recharge will similarly yield greater groundwater 

discharge to streams. Nitrate in groundwater discharge 

contributes nearly half of nitrogen flux to streams in the 

Chesapeake Bay watershed (Phillips and others, 1999), and 

significantly greater nitrate concentrations in groundwater 

and concentrations and yields in streams in areas underlain by 

carbonate bedrock than in areas underlain by other rock types 

are well documented (for example, Ator and Denis, 1997; 

Lizarraga, 1997; Miller and others, 1997; Ator and Ferrari, 

1998; Greene and others, 2005). The importance of carbonate 

rocks to nitrogen transport is apparent in particularly high 

predicted yields of TN from fertilizers in parts of the northern Piedmont (fig. 6a). The existence of carbonate rocks in 

the Valley and Ridge or Appalachian Plateau (or overall in 

the watershed) do not constitute significant positive land-towater terms in the TN model, perhaps due to different types 

or intensity of sources than in areas of the Piedmont carbonate. Although the Piedmont carbonate area is predominantly 

agricultural, for example, areas of the Appalachian Plateau and 

Valley and Ridge underlain by carbonate rocks support more 

of a mixture of land uses (Phillips and others, 1999). Nitrogen 

losses through denitrification are common in reducing 

(generally anoxic or suboxic) waters of the Chesapeake Bay 

watershed (Miller and others, 1997; Ator, 2008; Denver and 

others, 2010), and soil denitrification causes the single greatest nitrogen losses in the Susquehanna, Potomac, James, and 

Rappahannock watersheds (Van Breemen and others, 2002). 

The importance of redox conditions to TN flux is represented 

in the SPARROW model by available water capacity (AWC) 

of soils (table 1). AWC is generally greater in soils with 

greater organic matter and finer texture (U.S. Department of 

Agriculture, 1998), and increasing AWC may be indicative of 

relatively poorly drained reducing areas.

Phosphorus compounds are generally much less soluble 

than nitrate, and phosphorus delivery from the land surface to 

streams generally occurs predominantly in suspended form, 

often attached to sediment (Hem, 1985). Land-to-water terms 

in the phosphorus model therefore generally represent the 

likelihood of overland runoff and soil erosion; TP delivery is 

greater in areas with greater average precipitation and where 

soils are more erodible and less well-drained and therefore 

more likely to promote runoff rather than infiltration of precipitation (table 2). The significance of the Coastal Plain as a 

land-to-water term may reflect increasing phosphorus saturation of soils in that area and resulting decreasing soil retention of applied phosphorus compounds. Phosphorus inputs to 

cropland on the Delmarva Peninsula are approximately double 

that removed at harvest, and phosphorus has consequently 

accumulated in soils at an average annual rate of approximately 10 to 15 kg ha-1 (kilograms per hectare) (Staver and 

Brinsfield, 2001). 

Impoundments significantly decrease in-stream fluxes of 

both TN and TP (tables 1, 2). The estimated mean settlement 

velocity of 5.9 m yr-1 (meters per year) in the TN model (table 

1) suggests that denitrification is the main cause of nitrogen 

loss in watershed impoundments; algal uptake is typically 

more efficient and has been observed at higher rates, generally 

greater than 25 m yr-1 (Alexander and others, 2002; Schwarz 

and others, 2006). The mean loss rate of TP in impoundments 

is considerably higher (54.3 m yr-1, table 2) than that of TN, as 

might be expected if settling of particulates is the main cause 

for lost TP from the water column. Mean settlement rates for 

suspended sediment in reservoirs are generally much higher 

than those of TN or TP (Schwarz and others, 2006; Brakebill 

and others, 2010). The implications of these estimated coefficients may be important for future management of the 

Chesapeake Bay watershed, as the TN estimate suggests most 

of the nitrogen is lost permanently to the atmosphere, whereas 

most of the TP is merely stored in impoundments and may be 

remobilized in the future.

Significant nitrogen losses occur within flowing streams 

as well as impoundments in the Chesapeake Bay watershed. 

Although aquatic decay in flowing streams was not significant in the TP model (table 2), significant decay terms were 

included in the TN model (table 1). Mean estimated decay 

is greatest in the smallest 90 percent of streams [with mean 

annual flow less than 3.45 m3 s-1(cubic meters per second) 

(122 cubic feet per second)] in the Chesapeake Bay watershed (table 1), and the mean estimate of 0.34 m yr-1 is consistent with previous estimates for similar streams (Preston 

and Brakebill, 1999; Schwarz and others, 2006). The mean 

estimated rate of TN decay in larger streams (with mean 
18 Sources, Fate, and Transport of Nitrogen and Phosphorus in the Chesapeake Bay Watershed: An Empirical Model

annual flow greater than or equal to 3.45 m3 s-1) is more than 

an order of magnitude greater where the mean-maximum air 

temperature is greater than 18.5°C (degrees Celsius) than in 

cooler areas less than or equal to 15°C (table 1). A similar 

geographic pattern in nitrogen fate and transport has been 

observed previously; Boyer and others (2002) estimated 

that the Susquehanna and Potomac Rivers export 23 and 19 

percent of anthropogenic nitrogen inputs to their watersheds 

(respectively), whereas the Rappahannock and James Rivers 

export only 11 percent of these inputs.

Decay processes in flowing and impounded streams significantly limit the transport of nutrients from the Chesapeake 

Bay watershed to tidal waters. Comparison of local and 

delivered yields (fig. 9) illustrates that delivery of nitrogen 

from much of the Susquehanna watershed is relatively efficient (near 100 percent); more significant aquatic nitrogen 

losses in the Potomac watershed and further south reflect 

the importance of temperature to aquatic decay of nitrogen 

in large rivers (table 1). The greatest local nitrogen yields 

in the Chesapeake Bay watershed (outside of catchments 

affected by large point sources) occur in the predominantly 

agricultural areas of the Shenandoah Valley, the Great Valley, 

and Piedmont in Pennsylvania and central Maryland, and on 

the Delmarva Peninsula (fig. 9a). Much of this nitrogen is 

lost along streams, particularly in the upper Potomac watershed, however. The greatest yields of nitrogen delivered to 

Chesapeake Bay are contributed from agricultural areas of the 

northern Piedmont and Valley and Ridge, areas from which 

cooler temperatures and (or) close proximity limit nitrogen 

losses during fluvial transport to the bay (fig. 9b). Unlike 

nitrogen, however, local and delivered yields of phosphorus 

are very similar for much of the Chesapeake Bay watershed 

(fig. 10). Aquatic decay in the TP model is limited to impoundments, and predicted phosphorus delivery through the stream 

network is close to 100 percent in many areas, even from the 

Susquehanna watershed. Reservoirs behind the Safe Harbor 

and Holtwood Dams on the lower Susquehanna River have 

reached their capacity for retaining sediment and attached 

phosphorus (Hainly and others, 1995), and the SPARROW 

model suggests minimal phosphorus retention even in the 

downstream reservoir behind Conowingo Dam. 

Figure 9. Estimated (A) local and (B) delivered yields of total nitrogen (TN). Local yields represent TN flux delivered to streams from 

individual local catchments; delivered yields represent TN flux delivered to downstream terminal reaches (generally tidal waters).
Nitrogen and Phosphorus in the Chesapeake Bay Watershed 19

Flux to Chesapeake Bay and Major Tributaries

Watershed sources contribute an estimated 132,000 Mg 

(metric tons) (1.32 x 108 kg) of nitrogen and 9,740 Mg (9.74 x 

106 kg) of phosphorus to the Chesapeake Bay and tidal tributaries annually (table 3). Because these estimates are based on 

SPARROW models calibrated to TN and TP flux during 2002 

under long-term mean hydrologic conditions (see above), they 

represent the typical flux of nitrogen and phosphorus under 

such conditions. Actual nutrient fluxes vary considerably from 

year to year due to normal variability in weather (particularly 

precipitation) and streamflow (Langland and others, 2006). 

Nearly two-thirds (62 percent) of the nitrogen flux and nearly 

half (44 percent) of the phosphorus flux from the watershed to 

the bay during mean weather conditions is contributed by the 

combined flow of the Susquehanna and Potomac Rivers; 45 

percent of the nitrogen flux and 28 percent of the phosphorus 

flux is contributed by the Susquehanna River alone (table 3). 

Nitrogen contributions to Chesapeake Bay from the 

watershed are attributable primarily to agriculture. The 

combination of manure and fertilizer applications and fixation 

by crops provides more than half (54 percent) of the estimated 

nitrogen contributions to the bay and the largest source of 

nitrogen in most major tributaries (fig. 11). In a wider study 

of nitrogen contributions to 34 estuaries in the eastern United 

States, Castro and others (2003) similarly estimated that 

53 percent of nitrogen contributed to Chesapeake Bay is 

attributable to agricultural runoff. Boyer and others (2002) 

similarly estimated that agricultural fertilizer use and fixation by crops, alone, contributed between 38 and 58 percent 

of nitrogen inputs to the Susquehanna, Potomac, James, and 

Rappahannock watersheds in the early 1990s. Agriculture is 

common in many areas of the Chesapeake Bay watershed, particularly near tidal waters (such as on the Delmarva Peninsula) 

and along major tributaries (such as the Susquehanna River) 

where opportunities for nitrogen losses along the stream 

network are limited (fig. 1). Contributions of point sources and 

atmospheric deposition are much smaller (approximately 16 

percent each) and undifferentiated urban sources contribute an 

additional 12 percent of total estimated nitrogen flux from the 

watershed to the bay (fig. 11). 

Figure 10. Estimated (A) local and (B) delivered yields of total phosphorus (TP). Local yields represent TP flux delivered to streams 

from individual local catchments; delivered yields represent TP flux delivered to downstream terminal reaches (generally tidal waters).
20 Sources, Fate, and Transport of Nitrogen and Phosphorus in the Chesapeake Bay Watershed: An Empirical Model

Table 3. Estimated annual flux of total nitrogen and total phosphorus from watershed sources to Chesapeake Bay and at selected 

monitoring stations on major tributaries, in metric tons.

[Mg, metric tons; Md., Maryland; Va., Virginia]

Chesapeake Bay or 

nontidal tributary1 (station number)

Total Nitrogen (Mg) Total Phosphorus (Mg)

CBTN_v4 

model

Mean,

1990–20102

CBTP_v4 

model

Mean,

1990–20102

Chesapeake Bay3 132,000 9,740

Nontidal tributary (station number):

 1. Susquehanna River at Conowingo, Md. (01578310) 59,900 60,000 2,680 2,090

 2. Potomac River at Washington, D.C. (01646580) 21,600 25,800 1,620 1,800

 3. James River at Cartersville, Va. (02035000) 4,720 5,000 963 1,060

 4. Rappahannock River near Federalsburg, Va. (01668000) 2,010 2,030 321 364

 5. Appomattox River at Matoaca, Va. (02041650) 613 677 54.1 63.6

 6. Pamunkey River near Hanover, Va. (01673000) 614 668 80.4 75.0

 7. Mattaponi River near Beulahville, Va. (01674500) 259 284 22.9 25.9

 8. Patuxent River near Bowie, Md. (01594440) 669 727 49.7 54.5

 9. Choptank River near Greensboro, Md. (01491000) 219 222 15.3 13.6

1

 See figure 1 for locations.

2

 From U.S. Geological Survey, 2011b.

3

 Estimates include inputs to tidal tributaries, such as as from point sources and atmospheric deposition.

Figure 11. Estimated shares of total nitrogen contributions from various watershed sources to Chesapeake Bay and to 

major tributaries at selected monitoring stations.
Summary and Implications 21

The flux of phosphorus from the Chesapeake Bay 

watershed to the bay is contributed primarily from a mixture 

of urban and agricultural sources. Nearly half (43 percent) of 

the phosphorus reaching the bay is contributed from upstream 

agricultural fertilizer and manure applications; a nearly equal 

flux is contributed from point sources and other indistinguishable urban sources (fig. 12). The remainder (14 percent) of 

phosphorus contributed to the bay is from natural sources, 

including minerals in siliciclastic and crystalline rocks.

Summary and Implications

Spatially Referenced Regression On Watershed Attributes 

(SPARROW) modeling was used to provide quantitative 

empirical estimates of the sources, fate, and transport of 

nitrogen and phosphorus within the Chesapeake Bay watershed and to estimate mean annual total nitrogen (TN) and 

total phosphorus (TP) flux to the bay and in each of more than 

80,000 tributary stream reaches represented in the NHDPlus 

(1:100,000-scale) geospatial dataset. The models were calibrated to mean annual TN and TP fluxes during 2002 in 181 

and 184 watershed streams (respectively) that were estimated 

on the basis of available long-term nutrient and streamflow 

monitoring. Because the models were calibrated to estimated 

TN and TP flux during 2002 under long-term mean hydrologic 

conditions, they represent such long-term average conditions, 

rather than weather and resulting hydrologic conditions in any 

particular year. 

Human sources contribute substantially to the nitrogen 

and phosphorus flux to Chesapeake Bay and major tributaries. Significant (α=0.10) sources of nutrients in the watershed 

include (primarily municipal) point sources, undifferentiated 

urban activities, and fertilizer and manure applications in 

agricultural areas. Additional significant sources of nitrogen 

include atmospheric deposition and direct fixation by crops; 

significant natural sources of phosphorus in Chesapeake tributaries include minerals in siliciclastic and crystalline rocks. 

Empirical estimates of average yields from source areas and 

proportions of selected applications transported to streams 

agree closely with previous estimates reported in the literature.

The fate and transport of nitrogen and phosphorus from 

source areas to streams and within the stream network are 

affected by natural hydrogeologic and soil conditions and by 

the distribution of impoundments (lakes, ponds, and reservoirs) in the watershed. Greater TN flux in areas of greater 

groundwater recharge (and presumably, discharge) and in 

areas underlain by selected carbonate rocks reflects the 

importance of groundwater to nitrogen transport (as nitrate) 

in the watershed, and the previously documented greater 

nitrate concentrations in streams and groundwater of carbonate 

areas. The importance of plant uptake and redox conditions to 

nitrate stability and fate in groundwater and streams is likely 

reflected in the significance of enhanced vegetative index 

(EVI) and soil available water capacity (AWC) (respectively) 

as land-to-water terms in the TN model. Nitrogen losses 

within impounded streams are likely due primarily to denitrification; losses within flowing streams are greatest in streams 

with mean annual flow less than 3.45 m3 s-1 (cubic meters per 

Figure 12. Estimated shares of total phosphorus contributions from various watershed sources to Chesapeake Bay and to 

major tributaries at selected monitoring stations.
22 Sources, Fate, and Transport of Nitrogen and Phosphorus in the Chesapeake Bay Watershed: An Empirical Model

second) (122 cubic feet per second), and in larger streams 

in warmer areas. Phosphorus transport from source areas to 

streams is greatest in areas where increased runoff and erosion 

are likely; the significance of the Coastal Plain to phosphorus 

transport may reflect soil saturation of phosphorus from 

previous applications in that setting. Phosphorus losses occur 

within impounded streams and rivers, but losses in flowing 

reaches are on average statistically insignificant. 

Results from the TN and TP SPARROW models provide 

regional insight on nutrient sources and movement within the 

Chesapeake Bay watershed that can be particularly useful for 

management and restoration efforts. Along with estimated 

local and delivered mean annual TN and TP fluxes for each 

of more than 80,000 streams, the models provide empirically 

derived source shares and transport factors that provide insight 

into the most important processes in different areas and the 

most effective management strategies for different restoration 

goals.

Reducing nutrients from human sources could be particularly effective at limiting nitrogen and phosphorus flux from 

the watershed to the bay. Natural sources of nutrients occur in 

the watershed and provide the majority of relatively low nutrient fluxes from certain areas; more than 10 percent of total 

phosphorus flux to the bay is attributable to mineral sources. 

Human activities constitute the major sources of nutrients 

from the watershed to the bay, however, and the greatest 

potential for nutrient reductions. Agriculture, for example, 

contributes more than half of the nitrogen reaching the bay. 

Most of the agricultural nitrogen is derived from fertilizer 

applications and fixation by crops, and 24 percent of nitrogen from these sources does not contribute to crop growth, 

but rather is lost to streams. Precision applications or other 

techniques designed to limit fertilizer applications while maintaining crop yields may be particularly effective at limiting 

nitrogen flux to the Chesapeake Bay. Phosphorus is generally 

less mobile in the environment than nitrogen compounds and 

applied phosphorus is likely to be sequestered in terrestrial 

environments such as soils. Point sources discharging directly 

to streams provide approximately one-third of the phosphorus 

reaching the bay, and nearly half of the flux in some major 

tributaries. Reducing point sources may be more effective 

at limiting the overall flux of phosphorus than of nitrogen to 

Chesapeake Bay. 

A review of regionally significant factors affecting nutrient fate and transport in the bay watershed could be useful, 

along with source descriptions for targeting management 

resources to specific areas. Regardless of sources, phosphorus 

transport is more efficient in areas where surface runoff is 

more likely, including areas with more erodible soils, relatively poor drainage, and greater precipitation. Similarly, 

nitrogen transport is most efficient in areas with greater 

groundwater recharge, certain carbonate rocks, and less reducing conditions that may contribute to denitrification. Targeting 

restoration activities to areas most likely to deliver nitrogen or 

phosphorus to streams may be useful alternatives if limiting 

applications or other sources is overly costly or otherwise 

difficult. Nutrient losses also occur within the aquatic system. 

Nitrogen loss rates are generally greater in smaller streams, 

and in larger streams in warmer areas of the watershed. Both 

nitrogen and phosphorus fluxes are decreased in impounded 

streams; nitrogen loss is likely due mainly to denitrification, 

whereas phosphorus attached to sediment particles may be lost 

to settling. These different loss processes may have important 

implications for restoration efforts, as nitrogen is lost permanently to the atmosphere through denitrification, whereas 

much of the phosphorus is merely stored in impoundments 

and may be remobilized in the future. Consideration of these 

aquatic losses is also important when balancing restoration 

goals for local streams with those of downstream receiving 

waters such as Chesapeake Bay.

Acknowledgments

This work is a product of the Priority Ecosystems Studies 

(PES) and National Water-Quality Assessment (NAWQA) 

Programs of the U.S. Geological Survey (USGS), and benefited from previous model development for the northeastern 

United States by Moore and others (2011). Assistance with 

network development and other geographic data compilation 

was provided by Andrew LaMotte of USGS. Technical suggestions on this report were provided by Jeff Chanat and 

Daniel Wise of USGS; Valerie Gaine and Timothy Auer of 

USGS provided editorial suggestions and graphics and layout 

assistance, respectively. We also thank Anne W. Nolin and 

Eric Sproles of the Department of Geosciences, Oregon State 

University, for their contributions in developing the enhanced 

vegetative index. The water-quality monitoring data on which 

this analysis is based reflects the commitment of State and 

Federal partnerships to collect such data to track the condition 

of water resources in the Chesapeake region.
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Appendix 27

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Appendix. Reach-Scale Estimates 

of Mean-Annual Nitrogen and 

Phosphorus Fluxes in Streams of the 

Chesapeake Bay Watershed

Mean annual total nitrogen (TN) and total phosphorus (TP) fluxes predicted by version 4 of the Chesapeake 

Bay SPARROW TN model (CBTN_v4) and TP model 

(CBTP_v4) are available online in a tab-delimited ASCII file 

at http://pubs.usgs.gov/sir/2011/5167/CBTNTP_v4_predict.

txt. Variables in the online file are described in the header 

(denoted by lines starting with “#”), and include selected characteristics of the NHDPlus-based model network, as well as 

estimates of total and local (incremental) flux for each model 

reach and the fraction of local flux from each catchment that 

is delivered to downstream terminal reaches, which generally represent tidal waters. The file includes predictions for 

81,908 individual stream reaches within the Chesapeake Bay 

watershed as defined by the National Hydrography Dataset 

Plus [NHDPlus, mid-Atlantic region (02)] medium resolution 

(1:100,000-scale) geospatial dataset (Horizon Systems, 2010), 

including 80,579 reaches representing nontidal tributaries and 

1,329 reaches representing centerlines of tidal parts of major 

Chesapeake tributaries. These reaches can be identified by the 

variable, TIDAL_CHANNEL. Although SPARROW is not 

designed for modeling tidal waters, predictions for these 1,329 

reaches can be used to estimate the total flux of TN or TP to 

Chesapeake Bay or tidal tributaries (including from sources 

contributing directly to tidal waters), but are not intended for 

other purposes. Stream decay was not applied to centerline 

tidal reaches for the purpose of these estimates; stream decay 

is calibrated in the SPARROW models to flowing reaches and 

is not intended to represent nutrient losses in tidal waters. 

Reference Cited

Horizon Systems, 2010, NHDPlus documentation, version 

1, available online at http://www.horizon-systems.com/

nhdplus/documentation.php.

Prepared by USGS West Trenton Publishing Service Center.

Edited by Valerie M. Gaine.

Graphics and layout by Timothy W. Auer.

For additional information, contact:

Director, MD-DE-DC Water Science Center

U.S. Geological Survey

5522 Research Park Drive

Baltimore, MD 21228

or visit our Web site at:

http://md.water.usgs.gov
Ator, S.W., Brakebill, J.W., and Blomquist, J.D.—Sources, Fate, and Transport of Nitrogen and Phosphorus in the Chesapeake Bay Watershed: An Empirical Model—Scientific Investigations Report 2011–5167

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