U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2014–3073

February 2015

FORT COLLINS SCIENCE CENTER

Aquatic Systems Branch

Transdisciplinary Research to Address Water-Related Environmental Problems

Capabilities

The Aquatic Systems (AS) Branch at the Fort Collins Science Center 

(FORT) is a group of scientists dedicated to advancing interdisciplinary science and providing science support to solve water-related environmental 

issues. Natural resource managers have an increasing need for scientific 

information and stakeholders face enormous challenges of increasing and 

competing demands for water. Our scientists are leaders in ecological 

flows, riparian ecology, hydroscape ecology, ecosystem management, and 

contaminant biology. The AS Branch employs and develops state-of-thescience approaches in field investigations, laboratory experiments, remote 

sensing, simulation and predictive modeling, and decision support tools. We 

use the aquatic experimental laboratory, the greenhouse, the botanical garden and other advanced facilities to conduct unique research. Our scientists pursue research on the ground, in the rivers, and in the skies, generating and testing hypotheses and collecting quantitative 

information to support planning and design in natural resource management and aquatic restoration.

Photograph from Quan Dong, USGS.

Photograph from Robert Zuellig, USGS.

Ecological Flows

Ecological flow is a central theme of AS Branch 

studies, as our research examines how water flows affect 

populations, communities, ecosystems, and hydroscapes. 

Our studies elucidate the interactions among hydrologic, geomorphologic, biogeochemical, biological, and 

anthropogenic processes. Branch scientists identify and 

quantify the spatial and temporal attributes of water 

flow for ecological needs. Flow alternations by humans 

are a primary contributor to the degradation of aquatic 

ecosystems and the loss of freshwater biodiversity, and 

we provide innovative scientific methods and tools on 

flow-related ecological issues to decisionmakers, policymakers, and stakeholders.

Riparian Ecology

Riparian ecologists in the AS Branch study interactions 

among flow, channel change, and vegetation along rivers across the 

western United States and worldwide. Our work focuses on issues 

relevant to the management of water and public lands, including 

dam operation, climate change, invasive species, and ecological restoration. Investigations take place on a range of scales. 

For example, experimental studies in pots and growth chambers 

detect genetic, phenotypic, and species variations in response to 

environmental conditions, such as drought, frost, mycorrhizal 

inoculation, salinity, and carbon dioxide enrichment. Site-specific 

case studies examine processes and patterns of exotic species invasions, impacts of dams and consequences of climate change, while 

regional studies examine general patterns along environmental 

gradients, consequences of variation in water flow, and effects of 

human activities across the western United States.

Photograph from Quan Dong, USGS.
Decision Support Systems

It is a difficult task to determine the desirable environmental targets for aquatic resource managers, because of a myriad of 

physical, hydrological, and biological processes affecting aquatic ecosystems and hydroscapes, the complexity of interactions and the 

multifaceted information, and substantial levels of uncertainty. Computer-based Decision Support Systems (DSS) can help integrate 

and communicate scientific information and analyses, and thus provide support tools for decisionmaking.

One primary focus of the AS Branch DSS development is to generate spatially explicit indices of habitat suitability for various 

flow scenarios. DSS integrates spatially explicit environmental data, alternative water flow scenarios, flow-specific hydrodynamic 

estimates of local habitats, estimates of physical-chemical conditions, and habitat suitability criteria for key taxa. Our decision support 

work creates and improves geospatial integration and representation of flow-dependent habitat suitability and the scoring systems for 

alternative flow regimes, based on continually improving flow data and statistics and quantitative understanding of site-specific relations between flow and desired environmental conditions. We also develop and apply Bayesian approaches to characterize uncertainties. Our tools promote understanding of the relations between aquatic species and habitats, serve adaptive management strategies, 

and evaluate the consequences of climate change and other uncertainties brought by anthropogenic effects.

Hydroscape Ecology

The interdisciplinary team of hydroscape ecology develops 

and advances a broad, landscape-scale perspective of ecological 

flows for aquatic ecosystems. A hydrologic landscape, hydroscape, 

is an environmental theater, where hydrologic, geomorphologic, 

biogeochemical, biological, and anthropogenic processes play 

to provide ecological services to the society. The construction of 

water control structures, water management and diversion, land 

conversion, and other social-economic activities have fragmented 

and domesticated hydroscapes. Decisionmakers are facing great 

challenges to manage and restore aquatic ecosystems, partially 

because of the lack of a landscape perspective. Our scientists 

develop innovative conceptual models and apply novel modeling 

and survey approaches to detect and quantify the ecological effects 

of anthropogenic alterations on hydrologic and geomorphic processes. We develop spatially explicit metrics and tools to address 

the ecological responses to hydrologic and geomorphic variations 

Aquatic Ecology and Contaminants and the ecological flow needs at multiple scales.

The Aquatic Ecology and Contaminants Team investigates 

critical ecological processes operating in aquatic and riparian 

ecosystems and how these processes are affected by human 

activities. We address questions through a combination of field 

studies, laboratory experiments, and modeling, while working 

at multiple levels of biological organization from cells through 

ecosystems. Topics include land use and climate change effects 

on stream ecosystems and organisms, interactions between 

native and invasive fishes, the flux of contaminants through 

aquatic and riparian food webs, and contaminant effects on 

aquatic-riparian linkages. 

Photograph from Johanna Kraus, USGS.

Photograph from Quan Dong, USGS.
Effects of Contaminants on Linked Aquatic and Terrestrial

Food Webs

Most aquatic insects live in fresh water as larvae and move to land 

as flying adults to complete their life cycle. Although often ignored, 

the emergence of adults can transfer the effects of contamination from 

aquatic to terrestrial ecosystems as the adults are eaten by predators such 

as spiders, birds, and bats. Our scientists are investigating how contaminants move from streams, rivers, and lakes into riparian zones and how 

contamination alters the ecological linkages between these systems. Our 

investigations use large-scale field studies in various aquatic ecosystems, ranging from mountain headwater streams to the Great Lakes. We 

conduct complementary experiments at the new aquatic experimental 

laboratory at the Fort Collins Science Center to identify mechanisms 

underlying the patterns observed in these field studies. The mesocosm 

facility in our state-of-the-art laboratory is designed to replicate the 

coupled aquatic-riparian ecosystems. Our design is unique, because it 

can mimic a riparian boundary ecosystem whereas other facilities typically simulate either aquatic or terrestrial ecosystems, but not the boundary between the two. Results from these studies are helping 

managers to better evaluate water-quality criteria, to design and implement restoration plans for contaminated aquatic systems, and 

to assess the effectiveness of remedial actions.

Photograph from David Walters, USGS.

Reconstructing Flood History from Tree Rings

Shifts in river flow regimes are a major threat to water 

supplies and riverine ecosystems. Understanding and predicting flow changes and their effects on vegetation are critical to 

effective river management. AS Branch scientists analyze rings 

of riparian trees relating tree growth and establishment to historical flow. We then use the tree rings to reconstruct the flow 

in past centuries. Flow reconstructions discover the frequency 

and magnitude of past droughts and floods—information that is 

essential for management of rivers and water supplies. We also 

use downscaled climate projections and watershed models to 

predict changes in flow and tree growth resulting from humaninduced climate change. We have pioneered the use of cottonwood, a dominant riparian species, for tree ring analysis; this 

is a significant advance in arid regions where old trees of other 

species are otherwise scarce. Ongoing studies focus on rivers 

of the Upper Missouri Basin and the Tarim River, China. From Jonathan Friedman, USGS.

Selected Projects

Dams and Their Ecological Consequences

Scientists in the AS Branch have been studying the impacts 

of dams on riverscapes for more than two decades. Our scientists 

have written many reports on the effects of dams on recruitment 

of bottomland pioneer trees, such as cottonwood, along the Upper 

Missouri River and the Bill Williams River, and the effects of dams 

on channel geometry and vegetation throughout the Great Plains. 

Understanding the effects of dams and the relations between flow, 

sediment, and vegetation have allowed AS Branch scientists to 

provide valuable information for managing flow releases from dams 

to enhance native tree recruitment, or to remove exotic plant species 

that are encroaching on the channel along several rivers. Recently, 

AS Branch scientists are monitoring changes to flood plain vegetation along the Elwha River in Olympic National Park in response to 

the removal of two large dams. This study will provide lessons and guidance to the design and planning of future aquatic restoration efforts. We also study the ecological consequences of the experimental pulse flow in the Colorado River.

Date (M/D/Y)

1/1/30 1/1/40 1/1/50 1/1/60 1/1/70 1/1/80 1/1/90 1/1/00 1/1/10

Daily discharge (cubic feet per second), Missouri River,

Bismarck, North Dakota

0

100000

200000

300000

400000

Ft. Peck

1937

Garrison

1953

Dam nation: Drivers of decline

Missouri River; Garrison reach

x = 136,372 cfs

x = 35,894 cfs

Last major

cottonwood

recruitment 

event

Garrison dam

early work

From Mike Scott, USGS.
ISSN 2327-6932 (online)

http://dx.doi.org/10.3133/fs20143073

Contact Information

Quan Dong, Ph.D., Branch Chief

U.S. Geological Survey 

Fort Collins Science Center

2150 Centre Avenue, Building C

Fort Collins, Colorado 80526-8118

Tel. 970.226.9175 Fax 970.226.9230

qdong@usgs.gov

Learn more about FORT science, products, and resources at 

http://www.fort.usgs.gov

Aquatic Systems Branch web site: 

http://www.fort.usgs.gov/ASB/

Climate Change and Trout

Cold-water fishes like trout, salmon, and charr are especially 

vulnerable to shifting conditions related to climate change; for 

example, warmer temperatures and more variable hydroclimate. 

Native cutthroat trout of the southern Rocky Mountains now 

only occupy a tiny fraction of their historic habitats because of 

stressors such as non-native fishes, habitat fragmentation, and detrimental land management practices. Using a combination of field 

and modeling approaches, we address how climate may influence 

native cutthroat trout and how conservation strategies can be 

tailored in a climate-smart approach to maximize conservation 

benefits under recent (late 20th–early 21st century) and projected 

climate conditions. One fundamental question we are addressing is how changes in thermal and hydrologic conditions may 

affect native cutthroat trout imbedded in mountain lake-stream 

networks. Our research includes modeling surface temperatures 

for mountain lakes at a regional scale, and examining how altered 

thermal and hydrologic regimes affect critical life history events, 

such as spawning migrations. Ultimately, we will integrate these 

ecological patterns into state-of-the-art decision support models 

and use these models as tools to aid in the conservation of native 

cutthroat trout populations.

Using Unmanned Aircraft System Technology to Support 

Natural Resource Management

Unmanned Aircraft Systems (UAS) provide an affordable 

and safe method to collect high resolution imagery needed for 

the management of natural resources. Sensors on these airframes collect spatially explicit data for wildlife monitoring, 

vegetation analysis, habitat mapping, and erosion monitoring 

in areas where it has been previously difficult or impossible to 

obtain information. AS Branch research pilots are testing and 

integrating UAS technology to collect data in order to inform 

decisionmaking across Federal, State, and Tribal agencies. 

Our collaborations with other U.S. Geological Survey science 

centers, U.S. Fish and Wildlife Service, Bureau of Land Management, U.S. Department of Agriculture, Colorado Parks and 

Wildlife, and private landowners have demonstrated that this 

state-of-the-art technology is useful and has a place in natural 

resource management.

Photograph from Leanne Hanson, USGS.

Photograph from Jeremy Monroe, Freshwaters Illustrated.

Scientists

Branch Chief: Quan Dong, Ph.D., Supervisory Ecologist, 

 qdong@usgs.gov

Andersen, Douglas, Ph.D., Emeritus Research Ecologist,

 doug_andersen@usgs.gov

Auble, Gregor, Ph.D., Research Ecologist, aubleg@usgs.gov

Daniels, Joan, M.S., Botanist, joan_daniels@usgs.gov

Friedman, Jonathan, Ph.D., Research Hydrologist,

 friedmanj@usgs.gov

Grantham, Theodore, Ph.D., Research Biologist,

 tgrantham@usgs.gov

Haegele, Jeanette, Ph.D., Emeritus Fisheries Biologist, 

 haegelej@usgs.gov 

Hanson, Leanne, M.S., Biologist, hansonl@usgs.gov

Holmquist-Johnson, Chris, Ph.D., Hydrologist,

 h-johnsonc@usgs.gov

Kraus, Johanna, Ph.D., Research Ecologist, jkraus@usgs.gov

Muths, Erin, Ph.D., Research Zoologist, muthse@usgs.gov

Perry, Laura, Ph.D., Research Ecologist, perryl@usgs.gov

Reynolds, Lindsay, Ph.D., Research Ecologist,

 reynoldsl@usgs.gov

Roberts, James, Ph.D., Research Ecologist, jroberts@usgs.gov

Schmidt, Travis, Ph.D., Research Ecologist, tschmidt@usgs.gov

Scott, Mike, Ph.D., Emeritus Research Ecologist,

 scottm@usgs.gov

Shafroth, Pat, Ph.D., Research Ecologist, shafrothp@usgs.gov

Venarsky, Mike, Ph.D., Research Ecologist,

 mvenarsky@usgs.gov

Walters, David, Ph.D., Research Ecologist, waltersd@usgs.gov

Zuellig, Robert, Ph.D., Ecologist, rzuellig@usgs.gov

And a continuous team of supporting staff.