U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2006-3110

January 2007

Submarine Ground-Water Discharge: Nutrient Loading and Nitrogen 

Transformations

Printed on recycled paper

Eutrophication of coastal waters due 

to nonpoint source land-derived nitrogen (N) loads is a worldwide phenomenon and perhaps the greatest agent of 

change altering coastal ecology (National 

Research Council, 2000; Howarth and 

others, 2000). Within the United States, 

a majority of estuaries have been determined to be moderately to severely 

impaired by eutrophication associated 

with increasing nutrient loads (Bricker 

and others, 1999).

In coastal watersheds with soils of 

high hydraulic conductivity and permeable coastal sediments, ground water is 

a major route of transport of freshwater 

and its solutes from land to sea. Freshwater flowing downgradient from aquifers 

may either discharge from a seepage face 

near the intertidal zone, or flow directly 

into the sea as submarine ground-water 

discharge (SGD) (fig. 1). In the coastal 

aquifer, entrainment of saline pore water 

occurs prior to discharge, producing a 

gradient in ground-water salinity from 

land to sea, referred to as a subterranean 

estuary (Moore, 1999). In addition, 

processes including density-driven flow 

and tidal pumping create brackish and 

saline ground-water circulation. Hence, 

submarine ground-water discharge 

often consists of a substantial amount of 

recirculating seawater. Mixing of fresh 

and saline ground waters in the context of 

coastal sediments may alter the chemical composition of the discharging fluid. 

Depending on the biogeochemical setting, removal of fixed N due to processes 

leading to N2 (dinitrogen gas) production 

in the nearshore aquifer and subterranean 

estuary may significantly attenuate landderived N loads; or, processes such as ion 

exchange and tidal pumping in the subterranean estuary may substantially accelerate the transport of both land-derived and 

sediment re-mineralized N to estuarine 

water columns.

As emphasized by Burnett and others (2001, 2002), a fundamental problem 

in evaluating the importance of groundwater discharge in marine geochemical 

budgets is the difficulty of collecting 

samples across the salinity gradients of 

coastal aquifers. In addition, locating and 

quantifying rates of submarine groundwater discharge remains a challenge due 

to the diffuse and spatially and temporally heterogeneous nature of discharge. 

As a result, with regard to the study of 

biogeochemical cycles and chemical 

loads to coastal waters, the seepage face 

and subterranean estuary are relatively 

new and under-studied zones in the 

aquatic cascade from watershed to sea. 

Processes occurring in those zones must 

be understood and considered for proper 

modeling and management of coastal 

water resources.

Approaches to Investigating 

Transformations

To investigate controls on nutrient 

loads carried by submarine ground-water 

discharge, the U.S. Geological Survey 

(USGS) and Woods Hole Oceanographic 

Institution are examining ground-water 

flow, nutrient transport, and biogeochemistry in nearshore portions of coastal 

aquifers in a range of settings that contrast in terms of hydrogeology, land uses, 

and climate. This fact sheet describes 

research at sites in Waquoit Bay, Massachusetts, and in Tampa Bay, Florida. The 

biogeochemical investigations of nitroFigure 1.  Crosssection of a submarine ground-water

discharge zone (from

Swarzenski, Bratton,

and others, 2004).

SGD = 3 (meteoric waters + connate waters + recirculated seawater)

Seawater

Submarine Spring

Brackish Pore Water

Recirculation Cell

Land Surface

Sea Floor

Freshwater Discharge

Fresh Pore Water

Seepage at

Shore Face

Fresh Water-Salt Water Mixing Zone

Fresh Pore Water

Freshwater Discharge

Fresh Water/Salt Water

Mixing Zone

Saline Pore Water

Water Table

Saline Pore Water

Confining Unit
gen are being carried out in concert with 

examinations of radiochemical groundwater discharge tracers, seepage meter 

studies, and streaming resistivity surveys 

to identify locations and sources of 

submarine ground-water discharge and to 

quantify fluxes (Swarzenski and others, 

2001; Talbot and others, 2003; Abraham 

and others, 2003; Swarzenski, Burnett 

and others, 2004; Swarzenski, Charette, 

and Langevin, 2004; Swarzenski, Bratton, and Crusius, 2004; and Crusius and 

others, 2005).

Our three primary areas of research 

with regard to N biogeochemistry in submarine ground-water discharge zones are:

Using naturally occurring N stable 

isotope ratios to trace fixed N loss.

Application of isotope pairing experiments to develop new understanding 

of the N cycle in coastal aquifers.

Using noble (inert) gases as tracers 

of N2 production.

Nitrogen Stable Isotopic Ratios

At the Waquoit Bay site the research 

team is using a stainless-steel drive point 

piezometer system to collect pore water 

samples in high-resolution vertical profiles. The samples are analyzed for a suite 

1.

2.

3.

of biogeochemically cycled elements and 

tracers (Charette and Sholkovitz, 2006; 

Kroeger and Charette, unpublished data). 

The piezometer system allows profiles 

to be collected to a depth of 9 meters 

(m) or more with a sampling interval as 

small as 0.15 m. The study is examining 

three major subsurface water masses with 

distinct biogeochemical characteristics: 

the nearshore freshwater aquifer, and 

two fresh and saline water mixing zones 

(referred to as shallow and deep subterranean estuaries).

The dominant pattern in nitrogen 

concentrations in the nearshore freshwater aquifer at the head of Waquoit 

Bay is the occurrence of both nitrate 

and ammonium plumes (fig. 2A) with 

concentrations exceeding 200 micromolar (μM) in some locations. The nitrate 

and ammonium plumes were constant 

features during 3 years of sampling, but 

concentrations do vary over time.

Ammonium is the dominant form 

of nitrogen within the deep subterranean 

estuary, with maximum concentrations 

in individual profiles (40 to 70 μM) 

occurring at salinities of 26 to 28, and 

at 5- to 8-m depths within the sediment 

(fig. 2A and 2C). Brackish to saline pore 

waters are generally devoid of nitrate, 

have dissolved oxygen concentration 

from 0 to 3 milligrams per liter, and a 

low oxidation/reduction potential. During 

transport through the subterranean estuary, ammonium concentration generally 

suggests conservative behavior. The 

greatest concentrations of ammonium 

are at the highest salinity. The apparent conservative behavior of ammonium 

along the salinity gradient suggests that 

the preponderance of ammonification 

occurs at highest salinity, and that mixing 

and dilution are the dominant processes 

controlling ammonium concentration in 

the deep subterranean estuary. Based on 

radiochemical and hydrological estimates of fresh and saline ground-water 

discharge and on nitrogen concentrations 

in those zones, regenerated ammonium 

transport to the bay by advection of 

brackish to saline pore water is estimated 

to be in the range of 25 percent of the 

land-derived dissolved inorganic nitrogen 

load (Talbot and others, 2003; Abraham 

and others, 2003).

The co-occurrence of nitrate and 

ammonium is uncommon throughout 

the nearshore aquifer and subterranean 

estuary. The largely mutually exclusive 

distributions of nitrate and ammonium 

may be in part due to the loss of both 

N species in locations where advection 

brings nitrate-bearing waters with a low 

Figure 2.  Graph showing (A) nitrate and ammonium concentrations; (B) nitrogen stable isotopic ratios; (C) salinity

and dissolved oxygen concentration, in a depth profile through a freshwater aquifer and into a subterranean estuary.

Blue shaded areas indicate regions of co-occurrence of nitrate and ammonium. Abbreviations and symbols are as

follows: δ15N (per mil), the stable isotope ratio calculated as [(15N/14N sample)/(15N/14N atmospheric nitrogen) – 1] x

1000; m, meters; μM, micromoles per liter; D.O., dissolved oxygen; mg/L, milligrams per liter.

0

2

4

6

8

0 10 20 30

0

2

4

6

8

0 20 40 60 80 100

0

2

4

6

8

0 6 12 18 24

CONCENTRATION (μM) D CONCENTRATION 15N (per mil)

DEPTH (m)

A B C

Nitrate

Ammonium

Nitrate

Ammonium

Salinity

D.O. (mg/L)
dissolved-oxygen concentration into contact with relatively reducing ammoniumrich waters (fig. 2, blue shaded areas). In 

those mixing zones, a decrease in concentration and an increase in the nitrogen 

stable isotopic ratio in both nitrate and 

ammonium suggests concurrent loss of 

ammonium and nitrate, perhaps due to 

coupled nitrification/denitrification, or to 

other N2-producing microbial processes 

(fig. 2A and 2B).

The pattern of nitrogen loss shown 

in figure 2 is a consistent one, observed 

in a number of locations in both fresh and 

saline portions of the nearshore aquifer. 

Mixing of the nitrate and ammonium 

plumes in the freshwater zone may be 

related in part to compression of groundwater flow lines associated with thinning 

of the freshwater aquifer near the seepage 

face. Denitrification of land-derived 

nitrate at low salinity within the subterranean estuary (fig. 2, blue shaded area at 

5.5-m depth) may (1) provide an explanation for the absence of nitrate in brackish 

and saline subterranean waters and (2) 

suggest that transformations occurring 

within subterranean estuaries do have the 

potential to modify land-derived nitrogen 

loads prior to discharge to the sea.

Isotope Pairing

There has been a dramatic increase 

in recent years in the number of microbial N transformation pathways that 

have been shown or proposed to occur in 

marine environments (Luther and others, 

1997; Hulth and others, 1999; Zehr and 

Ward, 2002). Of particular importance 

among the “new” N transformations is 

anaerobic ammonium oxidation (anammox) (fig. 3), a microbial process that 

in some settings occurs at significant 

rates at the ecosystem scale (Dalsgaard 

and others, 2003; Kuypers and others, 

2003). Anammox has not been previously 

investigated in submarine ground-water 

discharge zones, and yet preliminary evidence from isotope pairing experiments 

at Waquoit Bay suggests that it may be 

an important pathway for N2 formation in 

those environments.

With academic collaborators at the 

Woods Hole Oceanographic Institution, 

the study team is developing methods to 

investigate the consequences of advection through permeable sediments on N 

transport and transformations via a series 

of batch incubation experiments and 

flow-through experiments designed to 

simulate water transport through permeable marine sediments. The study is particularly focused on loss of fixed nitrogen 

due to production of N2, and will involve 

a combined approach of isotope pairing 

and membrane inlet mass spectrometry 

with molecular biology to quantify and 

identify pathways of N2 production.

Noble Gases as Tracers

With collaborators at the Marine 

Biological Laboratory, Woods Hole, and 

the Woods Hole Oceanographic Institution, the USGS study team is estimating 

the magnitude of N2-producing processes 

within the range of biogeochemical zones 

occurring within freshwater, brackish, 

and saline aquifers. Membrane inlet mass 

spectrometry (MIMS) is used for rapid 

analysis of N2 and argon concentrations 

in ground water. Measured N2 concentrations will be compared to concentrations 

expected in the absence of in-aquifer N2

production to calculate concentration of 

excess N2. Complications in the interpretation of dissolved gas concentrations in 

ground water are (1) uncertainty regarding water temperature at the time of 

recharge to the aquifer, which will determine the inherited N2

/argon (Ar) ratio 

and (2) the presence of excess air due to 

entrapment of air bubbles at the time of 

recharge (Heaton and Vogel, 1981), followed by partial or complete dissolution 

of the trapped gases (Peeters and others, 

2002). After recharge, hydrostatic pressure and bubble surface tension tend to 

cause bubble dissolution and oversaturation of gases. Since N2

 concentration/Ar 

concentration in air is greater than in 

water at saturation, bubble entrapment 

would tend to increase measured N2/Ar in 

ground water and may result in overestimation of denitrification. To estimate 

concentrations of dissolved gases due to 

bubble entrapment and to constrain estimates of temperature at recharge, a subset 

of samples will be analyzed in the laboratory at the Woods Hole Oceanographic 

Institution for the full suite of noble gas 

concentrations by peak-height manometry using combined magnetic sector 

and quadrupole mass spectrometry. For 

those analyses, a set of samples will be 

obtained in stainless steel transfer vessels, 

and vacuum extracted in the laboratory 

for storage in glass ampoules. The gas 

samples will be chemically purified and 

cryogenically separated for mass spectrometric analysis. Based on the results 

of those analyses, recharge temperature, 

bubble entrapment, and the extent of 

bubble dissolution can be modeled.

Estimates of N2 production in freshwater aquifers are being compared to 

estimates of land-derived, ground-water 

transported nitrogen loads to coastal 

waters. Those comparisons will provide 

an important test of hypotheses regardFigure 3.  A simplified nitrogen (N) cycle highlighting the role of anammox.

Anammox short circuits the pathway to nitrogen gas (N2) production by circumventing the coupling of aerobic nitrification to denitrification. Note the depiction

of nitrite (NO2

-

) as an intermediate in nitrification, denitrification, or dissimilatory

nitrate reduction to ammonium (DNRA). (Modified from Trimmer and others, 2003).

Abbreviations are as follows: NO2, nitrite; NO3, nitrate; NH4, ammonium; -NH3,

reduced nitrogen in organic form.

N2

NO2

NO3

NO2

NH4

N - fixation 

Aerobic

nitrification

denitrification

Anaerobic

Ammonification

Assimilation

NH Anammox Organic - 3

DNRA
ing the behavior of N during transport 

through watersheds and of N loading 

models used to manage coastal watersheds and coastal waters. In addition, 

the study will test for N2 production in 

mixing zones between fresh and saline 

ground water.

References Cited

Abraham, D.M., Charette, M.A., Allen, 

M.C., Rago, A., and Kroeger, K.D., 

2003, Radiochemical estimates of 

submarine groundwater discharge to 

Waquoit Bay, Massachusetts: The Biological Bulletin, v. 205, p. 246–247.

Bricker, S.B., Clement, C.G., Pirhalla, 

D.E., Orlando, S.P., and Farrow, 

D.R.G., 1999, National estuarine 

eutrophication assessment—Effects 

of nutrient enrichment in the nation’s 

estuaries: National Oceanic and 

Atmospheric Administration, National 

Ocean Service, Special Projects Office 

and the National Centers for Coastal 

Ocean Science, Silver Spring, Md.

Burnett W.C., Taniguchi, M., and 

Oberdorfer, J., 2001, Measurement 

and significance of the direct discharge 

of groundwater into the coastal zone: 

Journal of Sea Research, v. 46, 

p. 109–116.

Burnett W., Chanton J., Christoff, J., 

Kontar, E., and others, 2002, Assessing 

methodologies for measuring groundwater discharge to the ocean: EOS, 

v. 83, no. 11, p. 117, 122, 123.

Charette, M.A., and Sholkovitz, E.R., 

2006, Trace element cycling in a subterranean estuary—Part 2. Geochemistry of the pore water: Geochimica et 

Cosmochimica Acta, v. 70, p. 811–826.

Crusius, J., Koopmans, D., Bratton, J., 

Charette, M.A., Kroeger, K.D., Ryckman, L., Halloran, K., and Colman, 

J., 2005, Submarine groundwater 

discharge to a small estuary estimated 

from radon and salinity measurements 

and a box model: Biogeosciences 

Discussions, v. 2, p. 1–35.

Dalsgaard, T., Canfield, D.E., Petersen, 

J., Thamdrup, B., and Acuna-Gonzalez, J., 2003, N2

 production by the 

anammox reaction in the anoxic water 

column of Golfo Dulce, Costa Rica: 

Nature, v. 422, p. 606–608.

Heaton, T.H.E., and Vogel, J.C., 1981, 

“Excess air” in groundwater: Journal 

of Hydrology, v. 50, p. 201–216.

Howarth, R.W., and others, 2000, Nutrient pollution of coastal rivers, bays, 

and seas: Issues in Ecology, v. 7, 

p. 1–15.

Hulth, S., Aller, R.C., and Gilbert, F., 

1999, Coupled anoxic nitrification/

manganese reduction in marine sediments: Geochimica et Cosmochimica 

Acta, v. 63, p. 49–66.

Kuypers, M.M.M., Sliekers, A.O., 

Lavik, G., Schmid, M., Jorgensen, 

B.B., Kuenen, J.G., Damste, J.S.S., 

Strous, M., and Jetten, M.S.M., 2003, 

Anaerobic ammonium oxidation by 

anammox bacteria in the Black Sea: 

Nature, v. 422, p. 608–611.

Luther, G.W., Sundgy, B., Lewis, G.L., 

Brendel, P.G., and Silverberg, N., 

1997, Interactions of manganese 

with the nitrogen cycle—Alternative 

pathways to dinitrogen: Biochimica et 

Biophysica Acta, v. 61, p. 4043–4053.

Moore, W.S., 1999, The subterranean 

estuary—A reaction zone of ground 

water and sea water: Marine Chemistry, v. 65, p. 111–125.

National Research Council, 2000, Clean 

coastal waters—Understanding and 

reducing the effects of nutrient pollution: National Academy Press, 

Washington, D.C.

Peeters, F., Beyerle, U., Aeschbach-Hertig, W., Holocher, J., Brennwald, M.S., 

and Kipfer, R., 2002, Improving noble 

gas based paleoclimate reconstruction and groundwater dating using 

20Ne/22Ne ratios: Geochimica et Cosmochimica Acta: v. 67, p. 587–600.

Swarzenski, P.W., Reich, C.D., Spechler, 

R.M., Kindinger, J.L., and Moore, 

W.S., 2001, Using multiple geochemical tracers to characterize the hydrogeology of the submarine spring off 

Crescent Beach, Florida: Chemical 

Geology, v. 179, p. 187–202.

Swarzenski, P.W., Burnett, B., 

Reich, C., Dulaiova, H., Martin R., 

and Meunier, J., 2004, Novel geophysical and geochemical techniques to 

study submarine groundwater discharge in Biscayne Bay, Florida: 

U.S. Geological Survey Fact Sheet 

2004-3117, 1 folded sheet (4 p.).

Swarzenski, P.W., Charette, M., and 

Langevin, C., 2004, An autonomous, 

electromagnetic seepage meter to study 

coastal groundwater/surface water 

exchange: U.S. Geological Survey 

Open-File Report 2004–1369, 1 folded 

sheet (4 p.).

Swarzenski, P.W., Bratton, J., and 

Crusius, J., 2004, Submarine groundwater discharge and its role in coastal 

processes and ecosystems: U.S. 

Geological Survey Open-File Report 

2004–1226, [4] p.

Talbot, J.M., Kroeger, K.D., Rago, A., 

Allen, M.C., and Charette, M.A., 2003, 

Nitrogen flux and speciation through 

the subterranean estuary of Waquoit 

Bay, Massachusetts: The Biological 

Bulletin, v. 205, p. 244–245.

Trimmer, M., Nicholls, J.C., and Deflandre, B., 2003, Anaerobic ammonium 

oxidation measured in sediments along 

the Thames Estuary, United Kingdom: 

Applied and Environmental Microbiology, v. 69, p. 6447–6454.

Zehr, J.P., and Ward, B.B., 2002, Nitrogen cycling in the ocean–New perspectives on processes and paradigms: 

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Acknowledgments

We thank our collaborators on 

these projects: Edward Sholkovitz, 

William Jenkins, Karen Casciotti, Katrina 

Edwards (Woods Hole Oceanographic 

Institution), Anne Giblin and Jane 

Tucker (Marine Biological Laboratory), 

Dirk Koopmans, Christopher Reich, 

Brian Blake-Collins, Jason Greenwood 

(USGS). Laurinda Travers, Betsy Boynton, Debra Foster, and Iris Collies aided 

with document preparation.

Related Links

USGS Submarine Groundwater Discharge 

Program: http://coastal.er.usgs.gov/sgd/

Coastal Groundwater Geochemistry 

(WHOI): http://www.whoi.edu/science/

MCG/groundwater/

Novel geophysical and geochemical techniques used to study submarine groundwater discharge in Biscayne Bay, Florida: 

http://sofia.usgs.gov/publications/fs/2004-

3117/

An autonomous, electromagnetic seepage 

meter to study coastal groundwater/surface-water exchange: http://sofia.usgs.

gov/publications/ofr/2004-1369/

Submarine Ground-Water Discharge and Its 

Influence on Coastal Processes and Ecosystems: http://soundwaves.usgs.gov/2004/06/

research4.html

Oceanus magazine article “Water Flowing 

Underground”: http://www.whoi.edu/oceanus/viewArticle.do?id=2485

By Kevin D. Kroeger1, Peter W. Swarzenski2,

John Crusius1, John F. Bratton1 and

Matthew A. Charette3

1

U.S. Geological Survey, Woods Hole, Mass.

2

U.S. Geological Survey, St. Petersburg, Fla.

3

Woods Hole Oceanographic Institution, Woods 

Hole, Mass.

Contact Information:

Kevin D. Kroeger

U.S. Geological Survey

Woods Hole Science Center

384 Woods Hole Rd.

Woods Hole, MA 02543

508-457-2270

kkroeger@usgs.gov