WATER QUALITY EFFECTS OF HYPORHEIC PROCESSING
Alexander Fernald1, Dixon Landers2, P.J. Wigington Jr.2
ABSTRACT: Water quality changes along hyporheic flow paths may have important effects on river water quality and
aquatic habitat. Previous studies on the Willamette River, Oregon, showed that river water follows hyporheic flow paths
through highly porous deposits created by river channel meandering. To determine water quality changes associated with
hyporheic flow, we studied six bar deposits positioned between the river and closed lentic side-channel alcoves. At each site
we measured water levels and water quality in river, hyporheic, and alcove water. At all sites we found hyporheic flow paths
from the river through the bar deposits to the alcove surface water. At a majority of the sites hyporheic dissolved oxygen and
ammonium decreased relative to river water, while hyporheic specific conductance, nitrate, and soluble reactive phosphorous
increased compared to the river. At three sites with fast hyporheic flow rates, hyporheic temperature decreased relative to
river water, and there was little change in temperature at the other three sites. Hyporheic changes most affected receiving
alcove water quality at sites with fast hyporheic flow rates. Strategies to promote ecosystem functions provided by hyporheic
flow should focus on restoring natural hydrogeopmorphic river channel processes to create high porosity deposits conducive
to hyporheic flow.
KEY TERMS: Hyporheic flow, water quality, aquatic habitat.
INTRODUCTION
Hyporheic flow may have important effects on water quality and aquatic habitat in the Willamette River, Oregon.
Hyporheic flow occurs where river water enters the channel bed and banks to follow subsurface flow paths before reemerging
to main channel or off-channel surface water. Both main channel and off-channel sites are important aquatic habitat on the
upper Willamette River. Alcoves, which are high-water side channels closed by sediment plugs at the upstream end during
lower flow, have been shown to be important breeding and rearing areas for native fish including threatened salmonids (C.
Andrus, unpublished data). Biochemical reactions and physical changes in hyporheic flow affect water quality through
processes such as microbially-mediated denitrification (Duff and Triska, 1990) and metal oxidation (Harvey and Fuller,
1998). Hyporheic flow affects aquatic ecosystem functions by providing, for example, habitat for aquatic macroinvertebrates
(Stanford and Ward, 1993) and increased periphyton growth (Muiholland et al„ 1997) at hyporheic upwelling zones which
occur in low gradient pools (Harvey and Bencala, 1993).
If a large percentage of total river flow passes through hyporheic flow paths, water quality changes within hyporheic
flow may affect main channel water quality. Tracer studies on the Willamette River in 1998 showed that hyporheic flow
occurs most where the river is able to move within the active floodplain, reworking and depositing highly porous gravel
deposits (A. Fernald, unpublished data). Detailed discharge measurements showed that over a 26 km-long study area, at least
70 % of total river discharge exchanged with hyporheic flow paths at in-stream riffle and pool complexes. To identify effects
of hyporheic flow on water quality and aquatic habitat, this study sought to identify physical and chemical water quality
changes along hyporheic flow paths. By studying alcove sites, we also sought to improve our understanding of hyporheic
flow effects on these important rearing and breeding habitats. We addressed two questions in this study: 1) Do water quality
characteristics change in hyporheic flow relative to river source water? and 2) Do receiving alcove surface waters show the
effects of hyporheic flow inputs?
METHODS
Our study took place during summer low-flow in 1999 along 60 kilometers of the upper Willamette River between
Eugene and Corvallis, Oregon. We selected six sites for detailed analysis of hyporheic flow paths and water quality (Fig. 1).
JNRC Postdoctoral Associate, U.S. Environmental Protection Agency, 200 SW 35th St. Corvallis, OR 97333
U.S. Environmental Protection Agency, 200 SW 35th St, Corvallis, OR 97333

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These sites all had off-channel alcoves separated from the main river channel by a bar deposit. This type of site is excellent
for studying hyporheic flow for three reasons: 1) hyporheic flow from the river into the bar deposit is created by hydraulic
gradients from the river through the bar to the alcove surface water, 2) hyporheic flow can be accessed from land by driving
wells into the bar deposit, and 3) the absence of river flow through the alcoves facilitates identification of the effects on
alcove surface water of emerging hyporheic flow.
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Figure 1. Hyporheic study sites on the Willamette River, Oregon
At each of the six sites we installed 20-30 wells made of 1" PVC pipe driven to a depth of about 0.5 m below
summer low-flow water tables. We sampled water levels and water quality at each site twice, in early and late August. We
measured groundwater elevation in each well and surface water elevations along the river and alcoves. We used kreiged areal
averaging of the point water level measurements to determine a continuous water level surface. From this surface we
determined hyporheic flow path directions, and we measured distance from the river bank to each well along the hyporheic
flow path direction. We estimated hyporheic flow rate, qH, using Darcy's law, q=-K(dh/dl) where q is one-dimensional
discharge (m/s), K is hydraulic conductivity (m/s), and dh/dl is the hydraulic gradient (Darcy, 1856),
In each of the two sampling periods, we used calibrated YSFM probes to measure river, hyporheic, and alcove
physical water characteristics including dissolved oxygen (DO), temperature (T), and specific conductance (SC). We
continuously purged each well until SC readings stabilized before recording the data values. We also took samples for
laboratory analysis from one or two transects per site that included river, hyporheic, and alcove sample locations. We used
standard methods to analyze the samples for nitrate (N03), ammonium (NH/), and soluble reactive phosphorus (SRP). At
Site A, we installed recording YSI™ probes in river, hyporheic, and alcove water to obtain hourly values for T, DO, and SC,
RESULTS
Water level measurements show that at all of the six study sites, river water flowed out of the main channel and
followed hyporheic flow paths through the bar deposits before emerging into receiving alcoves. The hyporheic flow path
gradients of 0.0030 to 0,0045 m/m into the upstream heads of the alcoves compared to an average river surface slope of
0.0008 m/m. Mature Site F with fine substrate had the slowest qH, while recently reworked Sites C and B with coarse
alluvium had the fastest values (Table 1).
Hyporheic water quality changes relative to river source water
For the three parameters DO, SC, and T, we had measurements from all hyporheic wells at each study site. This

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enabled us to plot the changes in hyporheic water with distance from the river along the hyporheic flow paths (Fig. 2). The
patterns discussed here for the August 23-25 sampling effort were very similar to those of the August 3-6 sampling period.
At all sites we found that DO rapidly decreased from near saturation in the river to much lower 5-45% saturation in hyporheic
flow. At all the sites SC increased from 60-75 p$/cm in the river to 90-120 juS/cm in hyporheic flow. We found that T
followed two different patterns. At three sites, T decreased along the hyporheic flow paths by 1-7ฐC compared to the river.
At the other three sites T did not change or increased by up to 2ฐC relative to the river.
Table 1 : Substrate, hydraulic conductivity, gradient, and hyporheic flow rate at six Willamette River hyporheic study sites.
Site
River
km
Substrate type
Saturated hydraulic
conductivity (m/s)
River to alcove
gradient (m/rn)
Hyporheic flow
rate, qH (m/s)
Relative qH
F
275.2
Silt, sand, clay
1.0E-03
0.0030
3.0E-06
Slow
E
271.4
Gravel, sand, silt
l.OE-02
0.0031
3.1E-05
Intermediate
A
216.4
Gravel, sand, silt
1.0E-02
0.0045
4.5E-05
Intermediate
D
262.6
Gravel, sand
1.0E-01
0.0037
3.7E-04
Intermediate
C
256.1
Gravel, sand
5.0E-01
0.0035
1.8E-03
Fast
B
247.0
Gravel, sand
5.0E-01
0.0040
2.0E-03
Fast
For our analysis of the remaining parameters, we grouped measurements of SRP, NH4\ and N03" by river,
hyporheic, and alcove location. For each study site, we plotted the single river value, the median of the hyporheic values, and
the farthest upstream (head of) alcove value (Fig. 3). SRP increased in hyporheic water compared to river water at all sites
but Site B, which had the fastest %. At all sites NH4+ decreased relative to river water, Hyporheic N03' increased compared
to river water at all sites but Site F, which had the slowest c^.
Receiving alcove water quality relative to hyporheic and river water
For the physical characteristics of DO, SC, and T, alcove surface water appeared to show the influence of emerging
hyporheic water. DO in receiving alcoves was similar to hyporheic flow, which had lower DO than in the river. Alcove SC
was similar to the hyporheic water in wells closest to the alcove, following the increase in SC with distance from the river.
Alcove T was also similar to hyporheic T at wells near the alcove, and alcove T showed the same changes as hyporheic T
relative to the river.
In comparing SRP, NH4+, and N03" between alcove, hyporheic, and river water, we found that alcove water reflected
hyporheic changes in NHซ\ but did not consistently follow hyporheic changes in N03" and SRP (Fig. 3). At five of six sites,
NH4* in alcove water was lower than in river water, and at all of these sites hyporheic NH4* was lower than river NH4+.
Alcove N03* was elevated compared to river water only at Site B, although five of the six sites had hyporheic N03' higher
than river N03". Alcove SRP was unchanged or lower than river SRP at five sites, yet four of these had hyporheic water that
was elevated in SRP compared to the river.
DISCUSSION
Water quality changes related to hyporheic flow rate
The changes along hyporheic flow paths and resulting effects on receiving alcove surface water appear to be related
to q^ The greatest cooling effect on alcove water compared to river water occurred at the two sites with the fastest qH and
probably the largest volumes of hyporheic inflow. Hourly data from the recording probes at Site A showed that hyporheic
and alcove T responded gradually over many days to hourly changes in river T. This suggests that gravel deposits act to
dampen T fluctuations in hyporheic water compared to changes in river source water. When river stage rose at Site A and
created a steeper gradient from river to alcove, we found that hyporheic and alcove SC decreased. This is consistent with our
interpretation that the increases in SC along hyporheic flow paths are a result of contact with interstitial material. With faster
qH during rising river stages, there is less contact time with interstitial material and the SC in hyporheic water drops. Our
measurements of T and SC were particularly important for identifying alcove changes caused by hyporheic inflows, because
these characteristics were not as strongly affected by the bio-chemical reactions that affect water nutrient concentrations.
Although we did not directly measure microbially-mediated chemical transformations, they appear have an important

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Temperature

Dissolved oxygen

Specific conductance
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Distance from river (m)
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Distance from river (m)

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Distance from river (m)


Source river water

• Hyporheic flow
~ Receiving alcove water

Figure 2. Water physical characteristics at two example Willamette River study sites showing two different patterns
for temperature and consistent patterns for dissolved oxygen and specific conductance. Temperature decreased at
three sites as at Site B and was unchanged or increased slightly as at site A. At all six sites in the study, dissolved
oxygen decreased and specific conductance increased.
SRP
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Hyporheic flow
Receiving alcove water
Figure 3. Nutrients in river source water, hyporheic flow (median of hyporheic values), and alcove
receiving water from measurements taken August 23-25,1999 at six Willamette River study sites
(A-F) arranged in order of hyporheic flow rate, qH.

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effect on water quality changes. At site F, which had the slowest qH, low DO and long hyporheic residence time in fine
sediments may promote hyporheic denitrification as documented elsewhere (Sjodin et al., 1997). Site F hyporheic NO/and
NH/ were lower than in river water. With lower NO/ and NH4+, surface water primary productivity may be N limited,
which could explain why site F is the only site where we saw an increase in SRP. The increases in hyporheic NOj" at all but
site F could be from nitrification of NH/, since all sites showed a decrease in hyporheic NH4*. At Site B with the fastest qH,
we found the largest increase in hyporheic and alcove NO/. At this site we found the only example of a decrease in
hyporheic SRP and this could be from microbial uptake aided by high N03* availability. While complete understanding of
nutrient transformations in hyporheic flow would require a more extensive analysis of soil, vegetation, and microbial activity,
our water quality data suggest that hyporheic flow exerts important controls on water quality in receiving alcoves.
Implications of hyporheic water quality changes for river function and management
Our study shows the importance of sampling a range of sites to better understand patterns of hyporheic water quality
changes and the effects of these changes on receiving surface water. Studies at other sites have produced different conceptual
models of hyporheic flow effects on water quality, lii a generalized model of hyporheic flow paths at sites with rapid %,
nitrification led to increased nitrate concentrations along hyporheic flow paths (Edwards, 1998). On a large river with fine
substrates and slow qj,, ammonium was reduced and nitrate denitrified in hyporheic flow, causing reductions in river
dissolved nitrogen (McMahon and Bohlke, 1996). On a river with active exchange between river water and groundwater in a
glacial floodplain, exchange between groundwater and surface water minimized downstream changes in surface water quality
(Ward et al., 1999). All of these processes may occur along the Willamette River. At sites with fine substrates, nitrate may
be lost to denitrification, while at other sites with coarser substrates, nitrate may increase from nitrification. Hyporheic
cooling may provide an important ecosystem benefit for fish. Ecosystem productivity may be enhanced at hyporheic
upwelling zones downstream of riffle complexes and in off-channel alcove habitats. Movement of river water in and out of
hyporheic flow paths along the entire channel may stabilize fluctuations in river water characteristics such as temperature and
SRP. In general, hyporheic exchange may promote overall river system water quality stability while providing site-to-site
aquatic habitat diversity.
Ecological functions provided by hyporheic flow can be promoted by managing the amount of river channel
meandering. The most hyporheic flow occurs at sites where the river is free to rework large gravel deposits. In this study, we
found the greatest effects of hyporheic flow on receiving surface water at recently reworked sites with highly porous gravels.
Willamette River meandering has been limited by construction of bank-hardening structures like revetments, and there has
been a historic loss of gravel bars on the Willamette River (Benner and Sedell, 1986). Removal of revetments as a
management strategy to promote river channel movement would increase the numbers of gravel bar features and would create
high porosity sites for active hyporheic flow.
CONCLUSIONS
In this study we found that water quality of hyporheic flow changed relative to river source water, and for some
parameters the nature of these changes was related to hyporheic flow rate. Hyporheic specific conductance increased and
hyporheic dissolved oxygen decreased relative to river water at all study sites. Hyporheic temperature decreased relative to
river water at sites with relatively fast hyporheic flow rates. At sites with intermediate to fast hyporheic flow rates, hyporheic
ammonium decreased, possibly from nitrification, and there was a corresponding increased in hyporheic nitrate. At the site
with the slowest hyporheic flow rate, hyporheic nitrate decreased, possibly due to denitrification. At all sites but the one with
the fastest hyporheic flow rate, hyporheic soluble reactive phosphorus increased relative to river water. The extent to which
water quality changes were seen in receiving alcove surface waters was greatest at sites with the fastest hyporheic flow rates.
These results show that hyporheic flow has important effects on alcove aquatic habitats and has the potential to
impact overall river water quality. Alcoves provide an environment with high macrophyte food availability in a low stress
environment of quiescent surface water, and increased bio-available N and P contributed to some alcoves from hyporheic
flow may help explain why these habitats are important for fish rearing and breeding. Along the main channel, hyporheic
flow processes a large percentage of the total volume of river flow. The water quality changes we documented at the alcove
sites are likely occurring at ill-stream and off-channel locations along the entire main river channel. Management efforts to
promote the ecological functions provided by hyporheic flow may be best targeted at increasing river channel meandering
within the active channel thereby creating additional sites with a range of hyporheic flow rates. Valuable future studies could
combine analyses of hyporheic water quality effects at representative sites with analyses of hyporheic flow rates over long
river reaches to better estimate the net effects of hyporheic flow on river ecosystem function.

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ACKNOWLEDGMENTS
For their assistance with data acquisition, spatial data analysis, and manuscript review, we thank Dave Gallery,
Marilyn Erway, Patti Haggerty, Monte Pearson, and Blake Price. This study was conducted as part of a National Research
Council Postdoctoral Associateship and was funded in part by the U.S. Environmental Protection Agency. This document
has been subjected to the Agency's peer and administrative review, and it has been approved for publication as an EPA
document. Mention of trade names of commercial products does not constitute endorsement of recommendation for their use.
REFERENCES
Benner, P.A., and J.R. Sedell, 1996. Upper Willamette River landscape: an historical perspective, in River Quality:
Dynamics and Restoration, A. Laenen and D.A. Dunnette, Eds., CRC Press/Lewis Publishers.
Darcy, H., 1856. Les Fontaines Publiques de LaVille de Dijon. Paris: V. Oalmont.
Duff, J.H. and F.J. Triska, 1990. Denitrification in sediments from the hyporheic zone adjacent to a small forested stream.
Can. J. Fish. Aquat. Sci. 47:1140-1147.
Edwards, R.T., 1998. The Hyporheic Zone, in River ecology and management: Lessons from the pacific coastal eeoregion.
R.J. Naiman and R.E. Bilby, Eds. Springer Verlag.
Harvey, J. W. and C. C. Fuller, 1998. Effect of enhanced manganese oxidation in the hyporheic zone on basin-scale
geochemical mass balance. Water Resour. Res. 34:623-636.
Harvey, J.W. and K.E. Bencala, 1993. The effect of stream bed topography on surface-subsurface water exchange in mountain
catchments. Water Resour. Res. 29:89-98.
McMahon, P.B and J.K. Bohlke, 1996. Denitrification and mixing in a stream-aquifer system: effects on nitrate loading to
surface water. J. Hydro. 186:105-128.
Mulholland, P.J., E.R. Marzolf, J.R. Webster, D.R. Hart, and S.P. Hendricks, 1997. Evidence that hyporheic zones increase
heterotrophic metabolism and phosphorus uptake in forest streams. Limnol. Oceanogr. 42:443-451.
Sjodin, A. L., W. M. Lewis Jr., and J. F. Saunders HI, 1997. Denitrification as a component of the nitrogen budget for a large
plains river. Biogeochem. 39:327-342.
Stanford, J.A, and J.V. Ward, 1993. An ecosystem perspective of alluvial rivers: connectivity and the hyporheic corridor. J.
N. Am. Benthol. Soc. 12:48-60.
Ward, J. V., F. Malard, K. Tockner and U. Uehlinger, 1999. Influence of ground water on surface water conditions in a
glacial flood plain of the Swiss Alps. Hydro. Proc. 13:277-293.

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WED-00-061
TECHNICAL REPORT DATA
(Please read instructions on the reverse before completing)
1. REPORT NO.
EPA/600/A-00/026
2.
3. RECIPIENT'S ACCESSION NO.
4. TITLE AND SUBTITLE Water quality effects of hyporheic processing
5. REPORT DATE
6. PERFORMING ORGANIZATION
CODE
7, AUTHOR(S) Alexander Fernaldl1,Dixon Landers2, P.J. Wigington, Jr.2
8. PERFORMING ORGANIZATION REPORT
NO.
9. PERFORMING ORGANIZATION NAME AND ADDRESS
'NRC Postdoctoral Associate 2US EPA NHEERL WED
US EPA NHEERL WED 200 SW 35!h Street
200 SW 35"* Street Corvallis, OR 97333
Corvallis, OR 97333
10. PROGRAM ELEMENT NO.
11. CONTRACT/GRANT NO.
12, SPONSORING AGENCY NAME AND ADDRESS
US EPA ENVIRONMENTAL RESEARCH LABORATORY
200 SW 35th Street
Corvallis, OR 97333
13. TYPE OF REPORT AND PERIOD
COVERED
14. SPONSORING AGENCY CODE
EPA/600/02
15. SUPPLEMENTARY NOTES:
16. Abstract: Water quality changes along hyporbeic flow paths may have important effects on river water quality and aquatic
habitat. Previous studies on the Willamette River, Oregon, showed that river water follows hyporheic flow paths through highly
porous deposits created by river channel meandering. To determine water quality changes associated with hyporheic flow, we
studied six bar deposits positioned between the river and closed lentic side-channel alcoves. At each site we measured water
levels and water quality in river, hyporheic, and alcove water. At all sites we found hyporheic flow paths from the river through
the bar deposits to the alcove surface water. At a majority of the sites hyporheic dissolved oxygen and ammonium decreased
relative to river water, while hyporheic specific conductance, nitrate, and soluble reactive phosphorous increased compared to
the river. At three sites with fast hyporheic flow rates, hyporheic temperature decreased relative to river water, and there was
little change in temperature at the other three sites Hyporheic changes most affected receiving alcove water quality at sites
with fast hyporheic flow rates. Strategies to promote ecosystem functions provided by hyporheic flow should focus on restoring
natural hydrogeophmorphic river channed processes to create high porosity deposits conducive to hyporheic flow.
17. KEY WORDS AND DOCUMENT ANALYSIS
a. DESCRIPTORS
b. IDENTIFIERS/OPEN ENDED
TERMS
c. COSATI Field/Group
Hyporheic, Water Quality, Groundwater-surface
water exchange.


18. DISTRIBUTION STATEMENT
19. SECURITY CLASS (This Report)
21. NO. OF PAGES: 6
20. SECURITY CLASS {This page)
22. PRICE
EPA Form 2220-1 (Rev. 4-77) PREVIOUS EDITION IS OBSOLETE

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