Biogeochemistry of
Estuaries


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Biogeochemistry of
Estuaries

Thomas S. Bianchi
Department of Oceanography, Texas A&M University

2007


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Library of Congress Cataloging-in-Publication Data
Bianchi, Thomas S.
Biogeochemistry of estuaries / Thomas S. Bianchi.
p. cm.
Includes bibliographical references and index.
ISBN: 0-19-516082-7
ISBN-13: 978-0-19-5160826
1. Biogeochemical cycles. 2. Estuarine ecology.
QH344.B53 2006
577.7 86—dc22
2005033998

9 8 7 6 5 4 3 2 1
Printed in the United States of America
on acid-free paper

I. Title.


To Jo Ann and Christopher
for their unending support and patience



As we progress further into truly coupled analyses of ecosystems, it is
becoming essential for a greater percentage of us to pool our expertise.
This professional altruism is increasingly critical to our discipline.
Robert G. Wetzel


Preface

Over the past decade there has been a rapid increase in human population growth along
coastal regions of the world. Consequently, many estuarine systems have been affected
by the serious environmental impacts of this encroachment. A greater knowledge of the
biogeochemical cycling in estuaries, which involves the transformation, fate, and transport of chemical substances, is critical in understanding the effects of these environmental
alterations—from a regional and global context. For example, the impact of eutrophication, which is widespread in many estuaries around the world, can only be fully understood
in the context of the physical dynamics of each system. Approaching estuarine science
from a biogeochemical perspective requires a fundamental background in the subdisciplines of chemistry, biology, geology, and in many cases atmospheric science. My
motivation for writing this book is that many, if not all, of the books on estuarine biogeochemistry to date are edited volumes too diffuse and difficult to use as textbooks for
advanced undergraduate and graduate courses. This book is focused on biogeochemical
cycles and attempts to comprehensively examine the physical, geochemical, and ecosystem properties of estuaries in the context of global and environmental issues. Following an
introductory chapter, Estuarine Science and Biogeochemical Cycles, the book is divided
into the following parts: I. Physical Dynamics of Estuaries; II. Chemistry of Estuarine
Waters; III. Properties of Estuarine Sediments; IV. Organic Matter Sources and Transformation; V. Nutrient and Trace Metal Cycling; VI. Anthropogenic Inputs to Estuaries;
VII. Global Impact of Estuaries.
In chapter 1, the reader is provided with a general background on the historical importance of estuaries during the advance of human civilizations (via trade, transportation,
food resources, etc.); it is no coincidence that most of the largest cities in the world are
situated on estuaries. This chapter also introduces the general concepts of biogeochemical cycling as they relate to estuaries. Part I of the book begins with the description
of how and when different estuaries were formed and how they are currently classified
from a geomorphological/physical mixing perspective; this part is critical as it sets the
framework from which biogeochemical cycling will be controlled across different systems.



viii PREFACE
Part II examines the molecular properties of estuarine waters and the effects of mixing
freshwater and seawater, as well as dissolved gases. Many estuaries and rivers have been
shown to be net sources of carbon dioxide to the atmosphere; this part includes a discussion on the controls of carbon dioxide cycling in estuaries and the ramifications that
estuarine carbon dioxide fluxes (and other greenhouse gases) may have in global warming
issues. In part III, I begin my discussion on estuarine sediments, the repository for historical changes in estuarine watershed and water column processes. Interactions between
sediments and the water column in estuaries are particularly important due to shallow
water columns commonly found in these systems. Primary production and decomposition
will be discussed in the context of system level dynamics in part IV; this part will cover
the dynamics of such processes as they relate to the previously described parts on element
cycling. I will also introduce many of the important bulk and chemical biomarker techniques used to “trace” organic matter inputs to these highly dynamic systems. In part V, an
overview is provided on nutrient and trace metal cycling in estuaries with a focus on the
major natural and anthropogenic sources of nutrients. General cycles are first discussed,
followed by more detailed case studies for specific nutrients and metals. Part VI covers
the dominant organic and inorganic contaminants in estuaries with an emphasis on the
role of partitioning and binding coefficients in controlling the availability of contaminants
to estuarine organisms. The natural cycling of dissolved organic carbon as well as the
mineralogical properties of suspended particles in a system will have significant effects
on these exchange processes. This part also provides some classic case studies on contaminant cycling as well as some new insights on the management of these systems. Finally,
part VII provides an introduction to river-dominated margins, the zones where the major
rivers/estuaries of the world meet the sea. These zones are different from the traditional
estuarine/coastal zones in that the processing and residence times of dissolved and particulate materials is usually shorter, with a greater potential for the transport of terrigenous
materials to the deep ocean. Recent work has also shown that fluvial inputs from rivers
and estuaries are not the only important inputs from the continents to the coastal ocean.
Groundwater inputs may serve as another transport route for materials processed on the
continents to make it to the ocean; this part discusses the recent work on groundwater
inputs as well as the ramifications of these inputs to estuarine flux models.
This book is designed for graduate level classes in estuarine biogeochemistry and/or
ecosystem dynamics. Prerequisites for such a course may include introductory courses
in inorganic and organic chemistry, environmental and/or ecosystem ecology, and some

basic knowledge of calculus. This book should also prove to be a valuable resource for
researchers in marine and environmental sciences because of the diversity of illustrations
and tabular data used in the examples of estuarine case studies, as well as the exhaustive
bibliographic sources. The basic organization of the book is derived from classes in global
and estuarine biogeochemistry that I have taught for several years.


Acknowledgments

Over the 4 years it has taken to write this book, other people have helped along the
way, and I am eternally grateful for their input. I want to especially thank Rebecca
Green (Tulane University) and Jo Ann Bianchi for carefully reading all the chapters
and providing helpful comments. One or more chapters were reviewed by the following
scientists: Mark Baskaran (Wayne State University); Elizabeth Canuel (Virginia Institute of Marine Science [VIMS]—College of William and Mary); Daniel. L. Childers
(Florida International University); Dan Conley (National Environmental Research Institute, Denmark); John M. Jaeger (University of Florida); Ronald Kiene (Dauphin Island Sea
Lab [DISL]—University of Southern Alabama); Rodney Powell (Louisiana Universities
Marine Consortium [LUMCON]); Peter A. Raymond (Yale University); Sybil P. Seitzinger
(Rutgers University); Christopher K. Sommerfield (University of Delaware); and William
J. Wiseman (National Science Foundation—Polar Programs). While all these people have
helped greatly to improve the book, I am responsible for any errors that remain. I also thank
my colleagues in the department of Earth and Environmental Sciences at Tulane University
for the many discussions we have had in recent years on coastal environments, particularly Mead Allison, Brent McKee, George Flowers, and Franco Marcantonio, as well as
Mike Dagg (LUMCON) for stimulating conversations in our many car trips to LUMCON.
Michel Meybeck (Université de Pierre et Marie Curie), Sid Mitra (S.U.N.Y., Binghamton),
Scott Nixon (University of Rhode Island), and Hans Paerl (University of North Carolina)
provided useful references for certain chapters. Jeffrey S. Levinton and Robert G. Wetzel,
with their extensive experience in book writing, provided invaluable advice and wisdom
on how to cope with all the stresses of such an endeavor.
I owe special thanks to Charlsie Dillon for typing all the tables in the book and
coordinating all the correspondence involved with getting permission rights for select

illustrations—Jeremy Williams also assisted in the early stage of this as well. Cathy B.
Smith did a superb job of redrawing all the illustrations, of which there were many, in the
book. All the library research was conducted at LUMCON, where I am especially grateful


x

ACKNOWLEDGMENTS

to librarians John Conover and Shanna Duhon for their tireless assistance and hospitality.
Special thanks to Michael Guiffre who helped design the book cover.
I would like to thank my family, Jo Ann, Christopher, and Grandmaster Chester, for
their support and patience, and my parents for their continued inspiration over the years.
Finally, I would like to thank Lyle More for taking the time to inspire a young fledgling
in need of guidance at a very critical age.


Contents

1 Estuarine Science and Biogeochemical Cycles

3

Importance of Estuaries
3
Description of Estuarine Science
3
Human Impact on Estuaries and Management Issues
Biogeochemical Cycles in Estuaries
9

Summary 10

I Physical Dynamics of Estuaries
2 Origin and Geomorphology

6

11
13

Age, Formation, and Classification
13
Distribution and Sedimentary Processes within Estuarine Types
Summary 32

3 Hydrodynamics

34

Hydrologic Cycle 34
General Circulation, Mixing Patterns, and Salt Balance
Residence Times
50
Summary 53

II Chemistry of Estuarine Waters
4 Physical Properties and Gradients

55
57


Thermodynamic Equilibrium Models and Kinetics
Physical Properties of Water and Solubility of Salts

57
60

41

19


xii

CONTENTS

Sources and Mixing of Dissolved Salts in Estuaries 65
Concepts and Measurement of Salinity
72
Reactivity of Dissolved Constituents
74
Ion Activity, Speciation, and Equilibrium Models 75
Effects of Suspended Particulates and Chemical Interactions
Summary 81

5 Dissolved Gases in Water

80

84


Composition of the Atmosphere
85
Atmosphere–Water Exchange
87
Water-to-Air Fluxes of Carbon Dioxide and Other Dissolved Gases
in Estuaries 90
Summary 99

III Properties of Estuarine Sediments 101
6 Sources and Distribution of Sediments

103

Weathering Processes 103
Erosion, Transport, and Sedimentation 106
Estuarine Turbidity Maximum, Benthic Boundary Layer, and
Fluid Muds 111
Summary 117

7 Isotope Geochemistry

119

Basic Principles of Radioactivity 119
Radionuclides in Estuarine Research 122
Stable Isotopes 159
Summary 171

IV Organic Matter Sources and Transformation 175

8 Organic Matter Cycling

177

Production of Organic Matter 177
Particulate and Dissolved Organic Matter in Estuaries 181
Decomposition of Organic Detritus 200
Early Diagenesis 204
Animal-Sediment Relations and Organic Matter Cycling 214
Controls on the Preservation of Organic Matter in Estuarine Sediments
Summary 221

217


CONTENTS

9 Characterization of Organic Matter
Bulk Organic Matter Techniques
Molecular Biomarkers 235
Summary 294

224

224

V Nutrient and Trace Metal Cycling 297
10 Nitrogen Cycle

299


Sources of Nitrogen to Estuaries 299
Transformations and Cycling of Inorganic and Organic Nitrogen
Sediment-Water Exchange of Dissolved Nitrogen 326
Nitrogen Budgets for Selected Estuaries 336
Summary 343

11 Phosphorus and Silica Cycles

346

Sources of Phosphorus to Estuaries 346
Phosphorus Fluxes Across the Sediment-Water Interface
Cycling of Inorganic and Organic Phosphorus 357
Phosphorus Budgets from Selected Estuaries 362
Sources of Silica to Estuaries 365
Silica Cycling 368
Summary 373

12 Sulfur Cycle

311

351

373

Sources of Sulfur to Estuaries 373
Cycling of Inorganic and Organic Sulfur in Estuarine Sediments 375
Cycling of Inorganic and Organic Sulfur in Estuarine Waters 388

Summary 393

13 Carbon Cycle

395

The Global Carbon Cycle 395
Transformations and Cycling of Dissolved Inorganic Carbon 396
Carbon Dioxide and Methane Emissions in Estuaries 402
Transformations and Cycling of Dissolved and Particulate Organic
Carbon 413
The Ecological Transfer of Carbon 422
Carbon Budgets for Selected Estuaries 423
Summary 434

xiii


xiv CONTENTS

14 Trace Metal Cycling

436

Sources and Abundance of Trace Metals 436
Background on Metal Ion Chemistry 438
Trace Metal Cycling in the Water Column 444
Trace Metal Cycling and Fluxes in Sediments 456
Summary 461


VI Anthropogenic Inputs to Estuaries 463
15 Anthropogenic Stressors in Estuaries

465

Anthropogenic Change in Estuaries 465
Partitioning and Toxicity of Trace Metals 470
Partitioning and Toxicity of Hydrophobic Organic Contaminants
Nutrient Loading and Eutrophication 481
Historical Reconstruction of Environmental Change 486
Summary 491

VII Global Impact of Estuaries 493
16 Estuarine–Coastal Interactions

495

Rivers, Estuaries, and the Coastal Ocean 495
River-Dominated Ocean Margins 498
Groundwater Inputs to the Coastal Ocean 502
Summary 504

Appendices 506
1
2
3
4

Atomic Weights of Elements 506
SI Units and Conversion Factors 509

Physical and Chemical Constants 511
Geologic Timetable 511

Glossary

512

References
Index

689

535

472


Biogeochemistry of
Estuaries


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Chapter 1
Estuarine Science and
Biogeochemical Cycles

Importance of Estuaries
Estuaries are commonly described as semi-enclosed bodies of water, situated at the interface between land and ocean, where seawater is measurably diluted by the inflow of

freshwater (Hobbie, 2000). The term “estuary,” derived from the Latin word aestuarium,
means marsh or channel (Merriam-Webster, 1979). These dynamic ecosystems have some
of the highest biotic diversity and production in the world. Not only do they provide a
direct resource for commercially important estuarine species of fishes and shellfish, but
they also provide shelter and food resources for commercially important shelf species that
spend some of their juvenile stages in estuarine marshes. For example, high fish and shellfish production in the northern Gulf of Mexico is strongly linked with discharge from the
Mississippi and Atchafalaya rivers and their associated estuarine wetlands (Chesney and
Baltz, 2001). Commercial fishing in this region typically brings in 769 million kg of
seafood with a value of $575 million. Fisheries production and coastal nutrient enrichment, via rivers and estuaries, are positively correlated within many coastal systems around
the world (Nixon et al., 1986; Caddy, 1993; Houde and Rutherford, 1993). The coupling
of physics and biogeochemistry occurs at many spatial scales in estuaries (figure 1.1;
Geyer et al., 2000). Estuarine circulation, river and groundwater discharge, tidal flooding, resuspension events, and exchange flow with adjacent marsh systems (Leonard and
Luther, 1995) all constitute important physical variables that exert some level of control
on estuarine biogeochemical cycles.

Description of Estuarine Science
There has been considerable debate about the definition of an estuary because of the
divergent properties found within and among estuaries from different regions of the world.
3


Figure 1.1 Schematic showing important linkages between physical (e.g., tidal currents, river discharge, and groundwater) and biological
(e.g., fish migrations, larval transport) processes in estuaries. (Modified from Geyer et al., 2000.)


ESTUARINE SCIENCE AND BIOGEOCHEMICAL CYCLES

5

Consequently, there have been numerous attempts to develop a comprehensive and universally accepted definition. Pritchard (1967, p. 1) first defined estuaries based on salinity as

“semi-enclosed coastal bodies of water that have a free connection with the open sea and
within which sea water is measurably diluted with fresh water derived from land drainage.”
A general schematic representation of an estuary, as defined by Pritchard (1967), and further modified by Dalrymple et al. (1992) to include more physical and geomorphological
processes, is shown in figure 1.2. In this diagram, we see a wide range of salinities
(0.1–32), wave processes that dominate at the mouth of the estuary, tidal processes that
occur in the middle region, and river or fluvial processes at the head of the estuary. The
relative importance of physical forcing from each of these regions can vary seasonally
(e.g., coastal wave energy versus river discharge), and ultimately determine the mixing
dynamics of both water and sediments in estuaries. More recently, Perillo (1995, p. 4)
provided an even more comprehensive definition of an estuary as “a semi-enclosed coastal
body of water that extends to the effective limit of tidal influence, within which sea water
entering from one or more free connections with the open sea, or any other saline coastal
body of water, is significantly diluted with fresh water derived from land drainage, and can
sustain euryhaline biological species from either, part or the whole of their life cycle.” This
definition provides the basis from which to work from in this book. Others studies have
also shown the utility of using a geomorphological classification in determining characteristic “signatures” of estuaries in distinct regions in North America, such as the west coast

Figure 1.2 Classic estuarine zonation depicted from the head region, where fluvial processes dominate, to the mid- and mouth regions where tidal and wave processes are the
dominant controlling physical forces, respectively. Differences in the intensity and sources
of physical forcing throughout the estuary also result in the formation of distinct sediment
facies. (Modified from Dalrymple et al., 1992, with permission.)


6

BIOGEOCHEMISTRY OF ESTUARIES

(Emmett et al., 2000) and northeastern (Roman et al., 2000) and southeastern (Dame
et al., 2000) Atlantic coasts. Further details on the origin and complexity of estuarine
geomorphology are provided in chapter 2.

The field of estuarine science has in essence, suffered from an identity crisis from
its early inception (1950s and 1960s) to the present—as reflected in the extensive list of
ambiguous definitions of an estuary found in the literature (Elliot and McLusky, 2002).
Some of this perceived “identity crisis” has resulted from the diversity of vernacular terms
(e.g., bay, sound, harbor, bight) commonly used in place of “estuary.” The inconspicuous
usage of the term “estuary” has in part, impeded the development of “Estuarine Science”
as a discipline distinct from that described as unique boundary environments in the fields
of “Oceanography” and “Limnology.” In fact, due to the unique complexity and dynamic
nature of estuaries there has been a recent call for a “synthesis approach” in defining estuaries on a broader categorical scale (Hobbie, 2000). The proposed synthesis would allow
for a greater ability to describe changes in estuarine ecosystems as they relate to physical
changes and to provide more statistical and mathematical correlations between biological
and environmental parameters. Moreover, it was suggested that mathematical simulation
models could serve to combine process descriptions with correlation determinations, along
with a number of other interrelated processes in a single system or region. There is clearly
a need for improved classification of estuaries if we are to effectively contend with the
growing legislative, administrative, and socio-economic demands in coastal management
which requires more unambiguous terminology than currently exists in estuarine science
(Elliot and McLusky, 2002). Fortunately, these changes have already begun in places such
as Australia and Europe with classification schemes like “The Australian-Environmental
Indicators: Estuaries and Sea” (Ward et al., 1998); and “The European Union Water
Framework Directive” (European Union, 2000), respectively.

Human Impact on Estuaries and Management Issues
Recent estimates indicate that 61% of the world population lives along the coastal margin (Alongi, 1998). These impacts of demographic changes in human populations have
clearly had detrimental effects on the overall biogeochemical cycling in estuaries. Nutrient enrichment is perhaps the most widespread problem in estuaries around the world
(Howarth et al., 2000, 2002). For example, 44 estuaries along the entire U.S. coastline
have been diagnosed as having nutrient overenrichment (figure 1.3; Bricker et al., 1999).
From a broader perspective, Hobbie (2000) recently summarized the findings of an earlier
U.S. National Research Council report focused on the major effects of human population growth on estuaries. A slightly modified version of this summary is as follows: (1)
nutrients, especially nitrogen, have increased in rivers and estuaries resulting in harmful

algal blooms and a reduction in water column oxygen levels; (2) coastal marshes and
other intertidal habitats have been severely modified by dredging and filling operations;
(3) changes in watershed hydrology, water diversions, and damming of rivers have altered
the magnitude and temporal patterns of freshwater flow and sediment discharge to estuaries; (4) many of the commercially important species of fishes and shellfish have been
overexploited; (5) extensive growth and industrialization has resulted in high concentrations of both organic [polycyclic aromatic hydrocarbon (PAHs) and polychlorinated


Nutrient Sources to Coastal Waters

St. Croix River/Cobscook Bay

Hood Canal

Englishman Bay

South Puget
Sound

Narraguagus Bay

Sheepscot Bay
Casco Bay
Boston Harbor

Tomales Bay
San Francisco Bay
Elkhorn Slough
Choctawhatchee
Bay
Calcasieu

Lake

Newport Bay

Pamlico River
Neuse River
New River

Tijuana Estuary
Galveston Bay
San Antonio Bay

St. Johns Bay
Perdido Bay

Corpus Christi Bay
Upper Laguna Madre
Baffin Bay
Lower Laguna Madre

Mississippi
River Plume

Lake
Pontchartrain

Tampa Bay
Sarasota Bay
Charlotte Harbor
Calcoosahatchee R.


South Ten
Thousand Islands
Florida Bay

7

Figure 1.3 Forty-four estuaries along the U.S. coastline that have been diagnosed as having nutrient overenrichment. (From Bricker et al., 1999,
with permission.)

ESTUARINE SCIENCE AND BIOGEOCHEMICAL CYCLES

Long Island Sound
Gardiners Bay
Great South Bay
Barnegat Bay
Delaware Inland Bays
Chesapeake Bay
Patuxent River
Potomac River
York River
Tangier/Pocomoke


8

BIOGEOCHEMISTRY OF ESTUARIES

biphenyls (PCBs)] and inorganic contaminants (heavy metals) in estuarine sediments and
waters; and (6) introduced species have resulted in alterations in habitats, loss of native

species, and a reduction in commercially important species. Model predictions indicate
that, by 2050, an estimated 8.5 billion people will be living in exoreic watersheds (e.g.,
watersheds draining the ocean); this increase is greater than 70% based on numbers from
1990 (Kroeze and Seitzinger, 1998).
An understanding of the role that biogeochemical and physical processes play in regulating the chemistry and biology of estuaries is fundamental to evaluating complex
management issues (Bianchi et al., 1999a; Hobbie, 2000). Biogeochemistry links processes that control the fate of sediments, nutrients, and organic matter, as well as trace
metal and organic contaminants. Thus, the discipline requires an integrated perspective
on estuarine dynamics associated with the input, transport, and either accumulation or
export of materials that largely control primary productivity. The metabolism of in situ
primary production and the utilization of allochthonous organic matter are also linked
to patterns of secondary productivity and fishery yields in estuaries. As humans alter
regional watersheds and local landscapes of estuaries, our ability to detect abiotic and
biotic signals reflective of biogeochemical change in these systems will be critical in determining how we manage these unique coastal ecosystems. While there remain opposing
views concerning how to effectively manage these diverse systems, a synthetic perspective [as described earlier (Hobbie, 2000)] will clearly lead to a more comprehensive
approach.
Fortunately, we are beginning to actually detect measurable improvements in the water
quality of some estuaries due to scientifically based nutrient reductions and extensive longterm monitoring studies. For example, the Patuxent River in Maryland (USA), a tributary
of the Chesapeake Bay, experienced extensive eutrophication from sewage inputs and
non-point sources over four decades (1960–2000; D’Elia et al., 2003).
During the late 1970s, scientists began to develop a dialogue with policy makers
in this region, as well as local and national funding agencies, which resulted in stable
funding for well-structured monitoring programs. In fact, the results from these studies
led to some of the first documented nutrient control standards for an estuarine basin
in the United States. Furthermore, based on preliminary indications it appears that the
proposed nitrogen (N) removal strategy has succeeded in improving water quality in the
Patuxent River estuary (D’Elia et al., 2003). This further corroborates that long-term and
scientifically based monitoring programs can result in effective remediation strategies for
environmental problems in estuaries (D’Elia et al., 1992). However, it should be noted
that gaining general acceptance of nutrient overenrichment in the larger Chesapeake Bay
system, along with consensus for nutrient controls, was a long and arduous task for

scientists in the region (Malone et al., 1993). Nevertheless, similar reductions in nutrient
loading have also resulted in significant water quality improvement in other regions of
the world, such as the Baltic Sea (Elmgren and Larsson, 2001). Factors leading to the
general success of estuarine management programs have recently been summarized as:
having key individuals, a lead agency, an institutional structure, long-term scientific data,
widespread public perception of the problem, and an ecosystem-level perspective (Boesch
et al., 2000; Boesch, 2002).
New approaches using integrated ecological and economic modeling are providing new
tools for adaptive management of estuaries (Constanza and Voinov, 2000). For example,


ESTUARINE SCIENCE AND BIOGEOCHEMICAL CYCLES

9

a Patuxent Landscape Model (PLM) was developed to serve as a tool for the analysis of physical and biological variables, based on socioeconomic changes in the region.
This adaptive approach allows for optimizing models, based on changes in the resolution
of the model over time, along with “consensus building” where scientists and policy makers are frequently involved in continuously changing stages of model development. The
PLM has been very effective in addressing land-use changes in the basin and how these
changes control hydrologic flow and ultimately nutrient delivery into the Patuxent River
estuary (Costanza and Voinov, 2000). The use of General Ecosystem Models (GEMs)
in estuaries, like the PLM, has grown from prior applications in the Coastal Ecosystem
Landscape Spatial Simulation (CELSS) model (Costanza et al., 1990) and wetland systems
like the Florida Everglades.

Biogeochemical Cycles in Estuaries
Some of the first applications of the integrative field of “Biogeochemistry” are derived from
organic geochemical studies where organisms and their molecular biochemistry were used
as an initial framework for interpreting sources of sedimentary organic matter (Abelson and
Hoering, 1960; Eglinton and Calvin, 1967). Biogeochemical cycles involve the interaction

of biological, chemical, and geological processes that determine sources, sinks, and fluxes
of elements through different reservoirs within ecosystems. Much of this book will use
this basic box-model approach to understand the cycling of elements in estuarine systems.
Therefore, we need to first define some of the basic terms before we can understand
how fluxes and reservoirs interact to determine chemical budgets in a biogeochemical box
model (figure 1.4). For example, a reservoir is the amount of material (M), as defined by
its chemical, physical, and/or biological properties. The units used to quantify material in
a reservoir, in the box or compartment of a box model, are typically of mass or moles. Flux
(F) is defined as the amount of material that is transported from one reservoir to another
over a particular time period (mass/time or mass/area/time). A source (Si ) is defined as the
flux of material into a reservoir, while a sink (So ) is the flux of material out of the reservoir
(many times proportional to the size of the reservoir). The turnover time is required to
remove all the materials in a reservoir, or the average time spent by elements in a reservoir.
Finally, a budget is essentially a “checks and balances” of all the sources and sinks as they
relate to the material turnover in reservoirs. For example, if the sources and sinks are the
same, and do not change over time, the reservoir is considered to be in a steady state. The
term cycle refers to when there are two or more connecting reservoirs, whereby materials
are cycled through the system—generally with a predictable pattern of cyclic flow.

Source
(S i )

Reservoir
(M)

Sink
(So)

Figure 1.4 Schematic of box model commonly used in
biogeochemical cycling work, showing reservoirs (M), sinks

(So ), and sources (Si ).


10 BIOGEOCHEMISTRY OF ESTUARIES
The spatial and temporal scales of biogeochemical cycles vary considerably depending
on the reservoirs considered. In the case of estuaries, most biogeochemical cycles are
based on regional rather than global scales. However, with an increasing awareness of
the importance of atmospheric fluxes of biogases (e.g., CO2 , CH4 , N2 O) in estuaries and
their impact on global budgets (Seitzinger, 2000; Frankignoulle and Middelburg, 2002),
some budgets will involve both regional and global scales.

Summary
1. The coupling of physics and biogeochemistry occurs at many spatial scales in
estuaries. Some of the dominant physical forcing variables that impact biogeochemical cycles are estuarine circulation, river and groundwater discharge, tidal
flooding, exchange flow with adjacent marsh systems, and resuspension events.
2. According to Perillo (1995, p. 4), an estuary is defined as “a semi-enclosed
coastal body of water that extends to the effective limit of tidal influence, within
which sea water entering from one or more free connections with the open sea,
or any other saline coastal body of water, is significantly diluted with fresh water
derived from land drainage, and can sustain euryhaline biological species from
either part or the whole of their life cycle.”
3. An improved classification scheme for estuaries is needed if we are to effectively contend with the growing legislative, administrative, and socioeconomic
demands in coastal management which requires more unambiguous terminology
than currently exists.
4. Approximately 61% of the world population lives within and around the estuarine watersheds (Alongi, 1998). Demographic changes in human populations
have clearly had detrimental effects on the overall biogeochemical cycling in
estuaries, with nutrient enrichment being the most widespread global problem.
5. There have recently been successful nutrient abatement programs in estuarine
systems around the world. Factors leading to the overall success of these management programs are having key individuals, a lead agency, an institutional
structure, long-term scientific data, widespread public perception of the problem,

and an ecosystem-level perspective.
6. New approaches using GEMs in estuarine management have allowed for optimization of models based on changes in the resolution of the model over
time, along with “consensus building”—where scientists and policy makers are
frequently involved in continuously changing stages of model development.
7. Box models are commonly used biogeochemical studies that involve the interaction of biological, chemical, and geological processes that determine sources,
sinks, and fluxes of elements through different reservoirs within ecosystems.