&EPA
United States
Environmental Protection
Agency
ENVIRONMENTAL
RESEARCH BRIEF
Green Island and the Hyporheic Zone
Why Restoration Matters
Laura A. Hockenbury1, Barton R. Faulkner2,
Kenneth J. Forshay2, J. Renee Brooks3
Photo courtesy of Philip Bayles, RaptorViews Aerial Imagit
Abstract:
Large river floodpiains present diverse benefits to communities, yet manage-
ment strategies often fail to consider the broad suite of ecosystem services
they provide. The U.S. Environmental Protection Agency (EPA) is evaluating
the benefits associated with restoring large river floodpiains, with emphasis on
the benefits of levee setbacks and revetment removals. This effort will provide
scientific support for community-based environmental decision making within
our study area on the McKenzie River, a tributary to the Willamette River in
Oregon, and support emerging restoration efforts along the Yakima River in
Yakima, Washington, and across the nation. The ERA is working with the
McKenzie River Trust, the City of Yakima, and the Washington Department
of Transportation to bring a more holistic approach to enhance sustainability,
with consideration of the ecosystem services offered by dynamic river sys-
tems. Restoring hydrologic connectivity in fioodplains can enhance the overall
ecological condition of riparian systems. We have examined groundwater flow
patterns, denitrification rates, and water isotopic signatures for identifying
water sources at Green Island, a 1,100 acre restoration effort located at the
1 U.S. Environmental Protection Agency, Region 10, Seattle, WA 98101, United States
# U.S. Environmental Protection Agency, National Risk Management Research Laboratory,
Ada, OK 74820, United States
3 U.S. Environmental Protection Agency, National Health and Environmental Effects
Research Laboratory, Corvallis, OR 97333 United States

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confluence of the McKenzie and Willamette Rivers
in order to identify specific benefits of increased
hydrologic connectivity. The Yakima River, which
winds through a highly productive agricultural val-
ley, has been identified as having high potential for
successful restoration and increased floodplain
connectivity. The EPA is undergoing research to
assess groundwater flow and denitrification rates
occurring within the Yakima River floodplain. With
these two case studies, the EPA will present a sci-
entific review of the issues and benefits associated
with restoring large river floodplains through levee
setback and the influence of hydrologic connectivity.
Introduction
The Willamette River is the 13th largest river in the
conterminous U.S. and produces more runoff per
unit of land area than any of the larger rivers (Hulse
et al2002). Dams and other human modifications
of the river network have contributed to the decline
of native fish populations, in particular salmon (Rath-
ert et al., 1999). Green Island is at the confluence
of the McKenzie River and Willamette River north
of Eugene, Oregon (McKenzie River Trust, 2013).
The Green Island section along the Willamette is
unique in that it closely resembles natural stream
conditions and natural riparian forest development
in the central valley. At 1,100 acres, Green Island
is the largest protected property managed by the
McKenzie River Trust and presents one of the best
remaining opportunities within the Willamette Valley
for preserving and restoring adynamic and ecologi-
cally diverse river system. Since 2007, more than
5,600 feet of levees have been removed from the
Island, over 100,000 native trees and shrubs have
been planted on the property, and 475 acres have
been converted from agriculture fields to floodplain
forest (McKenzie RiverTrust, 2013). In July-August
of 2008, the EPA installed 50 shallow (-30 feet
deep) groundwater monitoring wells on the Green
Island site in locations ranging from young to old
riparian systems, to agricultural areas of the island
still protected by levees.
The goal of installing groundwater monitoring wells
was to examine the sustainability and efficacy of
the extensive restoration efforts occurring on Green
Island. The McKenzie River Trust's goal for Green
Island is to create a robust ecosystem composed
of a rich mosaic of historic floodplain habitat types,
through cooperative partnerships dedicated to in-
novative, flexible and adaptive management (McK-
enzie RiverTrust, 2013). Through a combination of
field and lab studies measuring biogeochemistry,
we are evaluating effects of floodplain restoration
on nitrogen retention, hydraulic connectivity, and
water quality, as well as quantifying the benefits of
ecosystem services created by best management
practices (BMP's). There are few to no evaluations
of the suite of ecosystem services or effects of
best management practices on nitrogen in litera-
ture (Forshay and Dodson, 2011). Our Willamette
Ecosystem Services Project at Green Island will
help identify floodplain habitats and processes that
enhance denitrification; assess biogeochemical
benefits of restoring floodplains; develop sustain-
able practices to retain nitrogen; and estimate the
nitrogen-removing ecosystem services provided
by floodplains in large river corridors of the Pacific
Northwest.
Our Research
At Green Island, the EPA has focused on three
components of water quality: identifying source
water, modeling near channel (hyporheic) connec-
tivity. and assessing rates and drivers of nitrogen
processing. This combination details an overall
story of where the water is coming from, where it
is going, how it changes in the floodplain, and the
potential benefits provided. Here, we review each
approach and the current results.
Source water
By looking at variation in stable isotope composition
of river water, we can determine the source water
for the Willamette and McKenzie Rivers. Due to the
rainout effect or Rayieigh fractionation, as weather
systems move inland, heavier water isotopes,
expressed as relative concentration of deuterium
(52H) in water, will preferentially form water droplets
and become precipitation (Brooks et. al, 2012).
By the time the system reaches higher elevations
and mountain ranges, the remaining precipitation
occurs as much lighter water isotopes. Thus, we
are able to track the mean elevation of the source
water based on the isotopic signature.
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Source water for the Willamette has a distinct sea-
sonal pattern in regards to elevation. There are three
major hydrologic zones in the Willamette separated
by elevation: valley floor (<200 m), low mountains
of the Western Cascades (200-1200 m), and the
snow zone (>1200 m). River isotope values are
lowest/lighter during the dry summer months and
highest/heavier during February to March. During
the dry summer, source water is primarily from a
higher elevation, principally snow melt. During
the wet season, source water is also influenced
by valley floor or low mountain precipitation. While
the snow zone only accounts for 12% of the land
area and receives 15% of the overall precipitation,
it makes up 60-80% of the Willamette flow during
the summer. These findings highlight the vulner-
ability of flow in the Willamette to the influence of a
warming climate on snowpack (Brooks et al., 2012).
The elevation difference between source water for
the river and locai precipitation means that we can
use water isotopes to detect the proportion of river
water versus local precipitation contributions to the
groundwater on Green Island.
Groundwater
But where does this water go? How does it interact
with the surrounding floodplain? Green Island is
a river system with a greater amount of naturally
influenced landscape as compared to rivers with
river bank armoring. Because of this, Green Island
hydrology is considered to be well connected—i.e.,
the river and the floodplain have a greater rate of
interaction. Well connected floodplains may offer
significant benefits to river water quality. Specifically,
the hyporheic zone may play a substantial role in
denitrification enhancement, water temperature
buffering, and riverbank filtration (Faulkner et al.,
2012). The hyporheic zone is defined broadly as
the zone of exchange between surface water (i.e.
CP
CO
May 2009
July 2009
Isoscapes for hyporheic zone 52H ratios for May and for July 2009
3

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the river) and subsurface flow (i.e., groundwater)
(Faulkner et al., 2012). In these zones, water flows
under and adjacent to river channels where stream-
water and groundwater meet. Hyporheic zones are
ecotones and create a rich ecological interface.
We found that in May, 2009 at the tail end of the
wet season, S2H is higher and relatively well-mixed
due to increase hyporheic flow, while in July it was
lighter, with the isolines bunched, indicating greater
heterogeneity and influence from surrounding lower
valley groundwater areas.
If we could see hyporheicflow in thefloodplain
landscape. This image shows the subsurface
pathlines from a groundwater flow model based on
hydraulic measurements in wells. Flow originates
at the black cells along the Willamette River's edge
as well as the edges of its tributaries and alcoves,
and then moves laterally into and beneath the
riverbanks. The green cells show areas where
hyporheic water and other groundwater emerge
in connected cutoffs and alcoves for the naturally
meandering river system.
Our model indicates that during the dry season,
hyporheic flow along the Willamette River moves
primarily parallel to the main river channel (Faulkner
et al., 2012). During the wet season, water moves
laterally away from the river through the hyporheic
zone, with deeper infiltration into the underlying
aquifer of groundwater. This groundwater-surface
water interaction indicates connectivity and river dy-
namism, traits associated with increased ecological
functional hyporheic zones. Since the levees were
removed at Green Island, this reach ofthe river can
be a cross-connecting more complex network of
channels with greater interaction of surface water
with hyporheic zones through subsurface pathlines.
These results, along with our stable isotope results,
imply that in the warm summer months, hyporheic
flow plays an important role in regulating the near-
river groundwater environment. It allows us to lay
out a framework for evaluating the potential water
quality benefits, such as nitrogen reduction due to
denitrification and water cooling due to heat dissi-
pation along these subsurface pathlines. Although
not discussed further here, this latter component of
our research is also important and ongoing, since
many river ecosystems in the Pacific Northwest are
sensitive to temperature increase, which may be
m itigated by hyporheic flows (Faulkner et al., 2012).
Ecosystems and Denitrification
The main focus of our research is on the potential
benefits provided by the hyporheic zone, with a
specific lens on the hyporheic zone's potential to be
a nitrate sink. Nitrate is a naturally occurring oxide
of nitrogen, an essential component of all living
things, a primary source of nitrogen for plants, and
a pollutant (Steward, 2012). When concentrations
of nitrogen get too high in a system, it can lead to
adverse consequences for ecosystems and human
health. High levels of nitrate can result in eutrophica-
tion, lower quality drinking water, toxic algal blooms,
fish kills, and a variety of other negative effects
(Fewtrell, 2004). Health risks to humans include

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blue baby syndrome (methaemoglobinemia), where
nitrate interferes with the ability of blood to carry
oxygen to vital tissues in infants six months old or
younger. Drinking water that is treated chemically
to remove algae (e.g, from algal blooms present in
the source water) may contain elevated levels of
disinfection by-products which have been linked
to increased cancer and reproductive health risks
as well as liver, kidney and central nervous system
problems (Hans and Scott, 2010). Sources of high
levels of nitrogen include fertilizers, septic systems,
wastewater treatment seepage, animal wastes,
industrial wastes, and food processing (Fenn et
al., 1998).
At Green Island, we presume that nitrogen primar-
ily enters the system from agricultural sources.
Since agricultural application of nitrogen fertilizer
is a common practice, the solution to nitrogen
pollution requires a multi-part, all-inclusive ap-
proach that can help reduce nitrogen pollution.
For example, in addition to managing fertilizer
use, there is evidence that nitrogen management
should focus on restoration of streams, because
greater stream surface area-to-volume of water
ratios (i.e. increasing the size and connectivity of
the floodplain) favors nitrate uptake (Forshay and
Dodson, 2011).
Microbial communities consume and transform
nutrients bv processes such as denitrification.
In particular, these processes are enhanced by
the cycling of surface water and groundwater.
This cycling provides the medium for dissolved
components (oxygen, nutrients, and pollutants) to
make direct contact with carbon sources, microbial
communities, and both oxidative and high reducing
biogeochemical conditions (Hester and Gooseff,
2010). We have observed that low elevation and
hydrologic connection increases potential for mi-
crobial processes and biogeochemical reactions.
In addition, the increased residence time of water
and solutes in the porous media of the hyporheic
zone increases the potential formicrobial processes
and biogeochemical reactions to occur relative to
the water moving in the stream channel above
(Hancock et al., 2005; Baker et al., 2000). Thus,
when greater river connectivity is developed, for
example through restoration of side channels or
removal of levees and armoring, it allows for larger
floodplains and consequently larger hyporheic zone
surface area, in turn creating greater fish and mi-
crobial habitat, nutrient cycling and nitrate removal.
Coupled with denitrification benefits, the hyporheic
zone supports stream ecosystem functions for
biota—such as providing a refuge zone from high
flows for aquatic life, providing a habitat away from
predators, and housing organisms responsible for
biogeochemical cycling (Fischer et al., 2005).This
floodplain hyporheic ecotone is often overlooked
Error Bars +/-1 SE
I
Habitat Type
Surface denitrification rates in different habitats of
floodplain.
Wet Temp Wet Dry
Surface denitrification rates below different habitats
of floodplain.
5

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in restoration strategies, yet has potential to be
a cornerstone of holistic ecosystem restoration
in floodplain areas where nitrate concentrations
pose problems.
Take-home story about Green Island
Our research shows that the floodplain at Green
Island is well-connected with the river, showing
distinct flow path changes based on seasonal varia-
tion. Within this well functioning ecotone proximal
to the floodplain, there is
•	more microbial habitat
•	increasing the potential for denitrification
The hyporheic zone is beneficial for the entire
ecosystem, providing
•	increased habitat
•	enhanced nutrient cycling
•	pollutant buffering, and
•	temperature regulation.
The hyporheic zone's ability to produce cold water
refuges during warm water times of the year is
particularly important, as this directly enhances
habitat for aquatic life, in particular increasing
salmon habitat (Weston, 1998). Given this wide
range of ecosystem services ranging from improved
physical, chemical, and thermal conditions along
the river, which translate to improved habitat,
greater nutrient cycling, measureable pollutant
buffering, and significant temperature regulation,
it is beneficial to restore and maintain the Green
Island hyporheic zone.
Larger Scope: EPA intentions
Green Island
Because we examined the connectivity and poten-
tial for nutrient processing, our research at Green
Island sets the stage forhighlighting the capabilities
of a restored, more naturally functioning floodplain.
This can be applied at similar locations on the Wil-
lamette River. The main intention of river restoration
is to reestablish the ecological integrity of a river
as judged by the ability of the river to self-sustain
ecological functions, species and processes (Whol
et al., 2005). Restoration efforts focus on recreat-
ing "natural" rates of specific ecological, biogeo-
physical, and chemophysical processes, as well
as potentially replacing damaged or missing biotic
elements. The core biogeochemical processes of
rivers depend upon connectivity and geomorphic
setting: water, sediment, organic matter, nutrients
and chemicals move from uplands, through tribu-
taries, and across and under floodplains before
interacting with the main channel (Whol et al., 2005).
Broadening restoration practices to include near-
channel processes creates an ecosystem-wide
effect, because the hyporheic zone is the critical
ecotone linking stream water and groundwater
flow. Restoration efforts over time may become
a new type of farming of the benthos, microbial
films, and hyporheic microscopic communities, with
stewards managing the land and supporting self-
sufficient sustainable resources resulting in clean
water, salmon and wildlife populations, esthetic
pleasure^on a timescale surpassing generations.
Our research develops the scientific underpin-
nings of restoration efforts, by measuring benefits
beyond those normally associated with healthy,
dynamic river ecosystems. The research that we
are conducting at Green Island is part of a broader
project examining large river floodplains in the Pa-
cific Northwest and the ecosystem services that
they, and restoration projects in them, can provide.
The EPA is attempting to create a framework for
an ecological understanding of restoration out-
comes. The expansive goal of this research is to
create a more holistic approach to regulation that
includes industry, land trusts, and local community
involvement to protect the nation's water quality. A
comparison site is based along the Yakima River,
located in a highly agricultural valley in south-eastern
Washington.
Yakima Basin, Washington
Built over the course of the last century, large pro-
tective levees near the Yakima River disconnect
the floodplain from the main river channel and
contribute to loss of salmon spawning and rear-
ing habitat. The Gap-to-Gap reach of the Yakima
(from the Selah gap to Union Gap) was identified as
having the most potential for successful restoration
6

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as well as beneficial, community wide ecosystem
services (Stanford etal., 2002; HilldaleandGodaire,
2010). While Green Island is an active, developed
restoration project, the Yakima River is still con-
fined— particularly in the Gap-to-Gap reach, but a
local consortium has received funding to set levees
back and re-establish floodplains. Work performed
in this project will establish baseline measures of
floodplain indicators on ecosystem services "pre-
restoration", or prior to levee breach. Monitoring
sites will be established along and through levee
setback locations, incorporating existing monitor-
ing wells established by local municipalities and
government agencies as well. Inconclusion, Green
Island acts an example of the potential benefits of
restoring the Yakima River and other locations on
the Willamette River. The ultimate goal is to create
support for river restoration practices as a whole,
so the EPA can bring a more holistic approach to
regulation.
Literature Cited
Baker, M.A.; Dahm, C.N.; Valett, H.M. (2000).
"Anoxia, anaerobic metabolism and biogeo-
chemistry of the stream-water—groundwater
interface. (In) Jones, J.B. Jr., and Mulholland,
RJ. (Eds.), Surface-Subsurface Interactions
in Stream Ecosystems. Pages 259—283.
Elsevier, Inc.
Brooks, J.R.; Wigington, P. J. Jr.; Phillips, D. L;
Comeleo, R.; Coulombe, R. (2012). "Wil-
lamette River Basin surface water isoscape
(5180 and 52H): temporal changes of source
water within the river." Ecosphere 3(5):39.
http: - dx.doi. org/10.1890/ESl1-00338.1
Faulkner, B. R.; Brooks, J. R.; Forshay, K. J.; Cline,
S. P. (2012). "Hyporheic Flow Patterns in relation
to large river floodplain attributes." Journal of
Hydrology 448-449: 161 -173.
Fenn, M.E.; Poth, M.A.; Aber, J.D.; Baron, J.S.;
Bormann, B.T.; Johnson, D.W.; Lemly, A.D.;
McNulty, S.G.; Ryan, D.F.; and Stottlemyer R.
7

-------
(1998). "Nitrogen excess in North American
ecosystems: predisposing factors, ecosystem
responses, and management strategies." Eco-
logical Applications 8:706-733. http://dx.doi.
or 2/10.1890/1051-0 761(1998) 008fO 706:NEINA
El 2.0. CO: 2
Fewtrell, L. 2004. "Drinking-Water Nitrate, Methe-
moglobinemia, and Global Burden of Disease:
A Discussion." Environmental Health Perspec-
tives. 112, 14.
Fischer, H.; Kloep, F.: Wilzcek, S.; Pusch, M.T.
(2005). "A river's liver™microbial processes
within the hyporheic zone of a large lowland
river." Biogeochemistry 16:349-371.
Forshay, K. J. and Dodson, S. I. (2011). "Macro-
phyte presence is an indicator of enhanced
denitrification and nitrificiation in sediments
of a temperate restored agricultural stream."
Hydrobiologia, 668:21-34.
Hancock, P.J.; Boulton, A.J.; and Humphreys, W.F.
(2005), "Aquifers and hyporheic zones: Towards
an ecological understanding of groundwater."
Hydrogeology Journal 13(1), 98-111.
Hans, P.W.; Scott, J.T. (2010). "Throwing Fuel on
the Fire: Synergistic Effects of Excessive Ni-
trogen Inputs and Global Warming on Harmful
Algal Blooms." Environmental Science and
Technology. 44, 77556-7758.
Hester, E. T. and Gooseff, M. N. (2010). "Moving
Beyond the Banks: Hyporheic Restoration is
Fundamental to Restoring Ecological Services
and Functions of Streams." Environmental Sci-
ence and Technology 44:1521 -1525.
Hilldale, R. and Godaire, J. (2010). "Yakima River
Geomorphology and Sediment Transport
Study: Gap to Gap Reach, Yakima, WA, Techni-
cal Report No. SRH-2010-09". US Department
of the Interior Bureau of Reclamation.
Hulse, D.; Gregory, S.; Baker. J. (2002). Willamette
River Basin Atlas: Trajectories of Environmental
and Ecological Change. Oregon State Univer-
sity Press.
McKenzie River Trust. "Green Island" Mtp://www.
McKemieriver.ore/vrolected-lands/ownder-Drov-
erties/zreen-island/. Accessed 2013.
Rathert, D., D. White, J. Sifneos, and R. M. Hughes.
(1999). Environmental correlates of species
richness in Oregon freshwater fishes Journal
of Biogeography 26:257-73.
Stanford, J.A.; Snyder, E.B.: Lorang, M. N.: Whited,
D. C,; Matson, P. L; and Chaffin, J. L. (2002)."
The Reaches Project: Ecological and Geomor-
phic Studies Supporting Normative Flows in the
Yakima River Basin, Washington." US Depart-
ment of the Interior, Bureau of Reclamation.
Steward, S. (2012). Fact Sheet: Nitrate in Drink-
ing Water. State of Oregon Department of
Environmental Quality.
Weston, R.F. (1998). Final Report: Groundwater/
Surface Water Interactions, Conceptual Models
and Assessment Endpoints. USEPA Work As-
signment No. 3-353. July 1998.
Whol, E; Angermeier, PL., Bledsoe, B., Kondolf,
M.; MacDonnell, L; Merritt, D.M.; Palmer, M.A.;
Poff, N.L; and Tarboton, D. (2005). "River
Restoration." Water Resources Research,
41, W10301.
Acknowledgements
The authors thank the Board ofthe McKenzie River
Trust and Chris Vogel and Joe Moll ofthe McKenzie
River Trust, Ryan Anderson of the City of Yakima,
and Jason Smith of the Washington Department
of Transportation for providing access and logistic
support for the use of the properties described in
this report. We thank Bruce Duncan, David Hulse,
Dixon Landers fortheir input and review comments.
Martha Williams (SRA International, Inc.) assisted
with final editing and formatting for publication.
Glossary
Armoring- A natural or artificial process where an
erosion-resistant layer of relatively large particles
is established on the surface of the stream bed
through the removal of finer particles by stream
flow. A properly armored stream bed generally re-
sists movement of the bed material at discharges
8

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up to approximately "threefourths" bank-full depth.
Biogeochemistry- involves the study of chemical,
physical, geological, and biological processes and
reactions that govern the composition of the natural
environment.
Chemicophysical- of or relating to physics and
chemistry,
Confluence- the junction of two rivers.
Ecotone- a transitional zone in which one ecosys-
tem gives way to its neighbor; typically this will be
a zone in which elements of both ecosystems are
identifiable.
Ecological Entities- A general term that may refer
to a species, a group of species, an ecosystem
function or characteristic, or a specific habitat. An
ecological entity is one component of an assess
ment endpoint.
Ecosystem Services- humankind benefits from
a multitude of resources and processes that are
supplied by natural ecosystems; those compo-
nents of nature that are directly valued by people,
or combined with other factors to produce valued
goods and services.
Eutrophication-excess richness of nutrients which
causes a dense growth of plant life and death of
animal life from lack of oxygen.
Hydraulic connectivity- essentially a measure of
permeability of a given body of rock with respect
to water; a measure of how fast fresh water can
move among surface and ground water.
Hydrologic- addresses water occurrence, distribu-
tion, movement and balances in an ecosystem.
Hyporheic- Denoting an area or ecosystem beneath
the bed of a river or stream that is saturated with
water and that supports invertebrate fauna which
play a role in the larger ecosystem.
Reach- a continuous extent of water, often a stretch
of river between two bends.
Riparian- region of land near the banks of a river.
Piezometer- a small-diameter well specially con-
structed to measure the head at a specific depth
within an aquifer.
Subsurface path lines- direction of flow of water
beneath the ground surface during the course of
time.
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