U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2007–3079

September 2007

Understanding Contaminants 

Associated with Mineral Deposits

Printed on recycled paper

Overview

The potential environmental effects associated with abandoned and inactive mines, 

resulting from the complex interaction of a variety of chemical and physical processes, is 

an area of study that is important to the USGS Mineral Resources Program. Understanding 

the processes responsible for the environmental effects of abandoned and inactive mines 

is also of interest to a wide range of stakeholders, including both those responsible for 

managing lands with historical mined areas and those responsible for anticipating environmental consequences of future mining operations. The recently completed USGS project 

entitled “Process Studies of Contaminants Associated with Mineral Deposits” focused on 

abandoned and inactive mines and mineralized areas in the Rocky Mountains of Montana, 

Colorado, New Mexico, Utah, and Arizona, where there are thousands of abandoned 

mines.

Red Mountain #3

Lark Mine

Yankee Girl Mine

Natural acidic spring

Photo 1. In the Red Mountain Mining District, Colorado, a complex mixture of 

source material for metals and acidity includes abandoned gold, silver, copper, and 

lead mines and the surrounding mineralized but unmined areas.

Photo 2. Red Mountain Creek, within the Red Mountain 

Mining District, receives waters from mined areas as well 

as waters that are naturally acidic and metal rich.

Recent interdisciplinary studies by the U.S. Geological Survey 

(USGS) have resulted in substantial progress in understanding the 

processes that control 

•	 the release of metals and acidic waters from inactive mines and 

mineralized areas,

•	 the transport of metals and acidic waters to streams, and

•	 the fate and effect of metals and acidity on downstream 

ecosystems. 

Results from these studies provide new information that 

advances our understanding of the physical and biogeochemical 

processes responsible for the mobilization, transport, reaction, 

and fate of potentially toxic elements in mineralized near-surface systems and their effects on aquatic and riparian habitat. 

The significant chemical elements of interest include aluminum, 

arsenic, cadmium, copper, iron, lead, and zinc. These interdisciplinary studies provide the basis for scientific decision making 

and remedial action by local, State, and Federal agencies charged 

with minimizing the impacts of potentially toxic elements on the 

environment.

Current USGS research highlights the importance of 

understanding (1) the geologic sources of metals and acidity, 

as well as the geochemical reactions that release them from 

their sources; (2) the pathways that facilitate transport from 

those sources; and (3) the processes that control the fate of the 

elements once released from the sources. Experts in the fields of 

economic geology, structural geology, mineralogy, geophysics, 
bioavailability 

screening tests 

Zn map 

SPHALERITE Zn map Cd map

50 microns

$RILLCOREWITHPYRITEZONES

$OWNCORERECORDOFROCKTYPE

HYDROTHERMALALTERATIONINTENSITY

$RILLINGWELLSIN(ANDCART'ULCH ANDPYRITECONTENT



0YRITE	 

$EPTH ,ITHOLOGY !LTERATION







FEET	



































Figure 2. Integrated studies of Handcart Gulch document a link between acidic, 

metal-rich ground water and the intensity of hydrothermal alteration and pyrite 

content.

Figure 1. Geologist conducting field studies of mine-waste 

material. Samples used for detailed microchemical analyses 

to determine mineralogical and chemical variability and for 

developing metal bioavailability screening tests.

geochemistry, hydrology, ground-water modeling, microbiology, and 

toxicology came together for a series of studies that address these 

relationships on scales ranging from the watershed to the microscopic. 

Highlights include:

•	 Microscopic studies and laboratory experiments on mine waste 

material to understand the complex relationship between primary 

and secondary minerals and the release and transport of metals;

•	 Laboratory experiments designed to document the role microbial 

communities play in the release and concentration of metals in 

mine-waste rock;

•	 Design, testing, and screening of protocols to identify potential toxicity associated with leaching and weathering of mine waste rock;

•	 Detailed studies of existing deep exploration boreholes in the 

mineralized but unmined Handcart Gulch area (Colo.) to identify 

the link between the physical and mineralogical properties of the 

sulfide-bearing rock and the release of metals and acidity into a 

receiving stream;

•	 Multidisciplinary studies of bedrock geology including field 

mapping, geophysical surveys, mineralogical determinations, and 

laboratory leaching experiments to identify favorable rock units for 

use in remediation projects;

•	 Multidisciplinary studies of a highly mineralized and extensively mined 

alpine catchment, Prospect Gulch, Colo., to identify mining and natural 

sources of metals and acidity to receiving streams;

•	 Use of geophysical techniques to identify water pathways through wasterock piles;

•	 In extensively altered areas, using Airborne Visible/Infrared Imaging Spectrometer 

(AVIRIS) data and geologic mapping to document the spatial extent of mineralized rock; 

and 

•	 Analysis of time-series data to assess downstream effects of mine-site remediation efforts 

and the subsequent recovery of aquatic ecosystems.

Sources of Metals and Acidity

Metal and acidity are released from both 

abandoned mines and mineralized but unmined 

areas as water and oxygen react with sulfide 

minerals. Weathering of pyrite, a common 

iron sulfide mineral (FeS2), produces iron and 

sulfuric acid, which in turn can leach major 

elements such as aluminum, calcium, and magnesium and trace elements such as copper and 

zinc from surrounding rocks. Newly-formed 

acidic, metal-rich waters can then flow into 

receiving streams. Waste rock, material from 

the mine site that is not processed for ore or 

is left over after ore processing, is generated 

during mining operations and usually stored on 

site. Waste rock is a complex mixture of rocks 

and minerals from the mine workings that has 

been broken up to varying degrees, from a fine 

powder to the size of boulders. In most cases, 

mine-waste material is stored on the ground 

surface and is susceptible to weathering. U.S. 

Geological Survey research has focused on 

understanding the generation of metals and 

acidity from waste-rock piles (fig. 1) and from 

mineralized but unmined areas (fig. 2).

In order to examine the processes that 

control acid generation and metal release 

from mine-waste material, samples were 

collected from different geologic settings and 

examined in the laboratory for geochemical and 

mineralogical changes related to weathering 

of the mine-waste piles. Methods such as 

quantitative X-ray diffraction, bulk chemical 

analysis, optical mineralogy, microanalysis 
techniques, acid-base accounting, 

leaching techniques, microbial assays, and 

toxicological modeling were employed to 

understand the complex mixture of primary 

and secondary minerals as well as the effects 

of seasonal, water-soluble precipitates. The 

trace mineral content of primary minerals can 

be variable, and the weathering of wasterock material results in changes in grain size 

and texture and the potential for secondary 

minerals to coat primary minerals all of which 

adds to the complexity of the study. Standard 

methods for waste-rock pile sampling and 

waste-rock material leaching experiments 

assessing the toxicology of waste-rock 

material were developed, tested, and presented 

at international meetings and workshops.

In Colorado, one example of a mineralized but unmined alpine catchment can be 

found in Handcart Gulch (fig. 2), a watershed 

that lies along the Continental Divide and 

is underlain by a low-grade copper-molybdenum deposit. The area provides a unique 

opportunity to study natural sources of metals 

and acidity and their movement through 

the surface and ground water in the fragile 

alpine watershed (Caine and others, 2006). 

Cooperators provided USGS personnel with 

access to four deep mineral exploration wells 

(365–1,065 m) in the upper part of the catchment. Geophysical borehole logging of the 

wells provided characteristics of the physical 

properties of the rocks, mineralogical 

studies contributed to an understanding of the primary and secondary 

sources of metals, ground-water 

chemistry determined the concentration of metals and acidity released 

from the weathering of mineralized 

rocks, and ground-water ages provided constraints on ground-water 

transport rates through the upper 

watershed.

Pathways that Transport 

Metals and Acidity

An important aspect in evaluating the potential environmental 

effects of mineralized areas and 

abandoned mines is the determination of pathways and fluxes of 

metals from their sources to the 

receiving streams and ground water. 

Integration of geological, geochemical, and geophysical techniques led 

to substantial advances in our understanding of ground-water flow in 

alpine basins and waste-rock piles.

Integrated geophysical and 

geochemical studies were used 

by USGS scientists to identify 

ground-water pathways through a 

typical waste-rock pile at the Waldorf 

mine in central Colorado (fig. 3). 

Electromagnetic surveys and resistivity 

profiles are two complimentary geophysical 

methods that measure how conductive the 

underlying material is and help delineate 

water flowpaths. Using these geophysical 

techniques, two primary sources of water were 

identified as entering the waste-rock pile: (1) 

water from the mine adit infiltrates the upper 

part of the pile and (2) ground water from 

shallow fracture-flow in bedrock infiltrates at 

the bedrock interface (McDougal and Wirt, 

2007). Understanding the water pathways 

through the waste-rock pile is critical to 

understanding the source and movement of 

metals and acidic water that, visible as metalrich seeps, represent potential environmental 

challenges.

Fate of Released Metals

After metals and acidity have been 

mobilized from their sources and transported 

to receiving streams, determining their fate 

and effect on the ecosystem is an important 

aspect of addressing abandoned mines and 

mineralized but unmined areas. To determine 

the fate of potentially toxic metals, USGS 

research included detailed stream sampling events to determine where metal-rich 

waters enter receiving streams, geochemical 

modeling of water chemistry to determine 

the potential toxicity of different waters, and 

post-remediation chemical analysis to evaluate 

changes in environmental indicators.

Historically, water-quality criteria, as 

pertaining to aquatic organisms, have been 

based on the total dissolved concentration of 

a metal adjusted for hardness. In concert with 

recent advances in understanding toxicity of 

metals that focus on the importance of the bioavailable fraction of the metal, project studies 

have utilized complete water chemistry and 

speciation calculations to evaluate processes 

that control variations in the bioavailable fraction of metals in waters draining mined and 

mineralized rock. The Biotic Ligand Model, 

which is a computational approach used to 

determine metal speciation and potential 

acute toxicological effects developed by Allen 

(2002), has been used to determine the effects 

of watershed lithology on potential metal 

toxicity in streams.

The effect of metals and acidity on 

ecosystems has been closely monitored 

by mining companies, land managers, 

and government regulators involved in 

mine sites. Different factors contribute to 

the movement of metals and acidic water 

through our environment. Examples of the 

effects of these factors can be found at three 

different locations: (a) the Morenci copper 

mine in Arizona is set in a relatively simple 

hydrogeologic setting; (b) the Boulder River 

basin, Montana, represents a slightly more 

WALDORF MINE 

Electromagnetic Survey Resistivity Survey 

Low

Conductivity

High

Adit

Low

Conductivity

High

7.5 meter

 depth

15 meter

 depth

Figure 3. The Waldorf mine, central Colorado, and images showing results from geophysical studies 

including an electromagnetic survey and resistivity profiles. Brighter colors in graphical images 

delineate more conductive areas of waste-rock pile, which are interpreted to be water saturated.
complex hydrogeologic setting; and (c) the 

upper Animas River watershed in Colorado 

contains thousands of abandoned mines in 

an extremely complex hydrogeoloic setting 

with extensive areas of intense hydrothermal 

alteration. Time-series data collected as part 

of the downstream monitoring effort of all 

three sites (fig. 4) can be used to evaluate the 

changes in water chemistry that effect the 

recovery of the aquatic ecosystem. Timeseries data document that in relatively simple 

hydrogeologic systems success of remedial 

actions can be observed on a scale of years, 

but in complex settings, where many natural 

and anthropogenic sources of metals and 

acidity are generated, downstream results of 

remedial actions likely will take longer.

Summary

The recently completed USGS Mineral Resources Program integrated effort to 

determine processes that control the release, 

transport, and fate of contaminants associated 

with the near-surface weathering of mineral 

deposits highlights important links between 

source material and the release of metals and 

generation of acid. For more information on 

these and other project-related studies, please 

visit the project website at http://minerals.

cr.usgs.gov/projects/contaminants/index.html. 

The website includes a detailed description of 

each study and a complete bibliography.

McDougal, R.R., and Wirt, L., 2007, Characterizing infiltration through a mine-waste dump 

using electrical geophysical and tracer-injection methods, Clear Creek County, Colorado, 

in DeGraff, J.V., ed., Geological Society of 

America Reviews in Engineering Geology, v. 

XVII, p. 9–24.

For More Information

Contact:

Philip L. Verplanck

U.S. Geological Survey, MS 973

Denver, CO 80225

Telephone: 303-236-1902

Email: plv@usgs.gov

Stanley E. Church

U.S. Geological Survey, MS 973

Denver, CO 80225

Email: sechurch@usgs.gov

Kathleen S. Smith

U.S. Geological Survey, MS 964D

Denver, CO 80225

Email: kssmith@usgs.gov

Figure 4. Three examples of time-series data display the extent of post-remediation recovery. A, Copper concentrations in sediment 

from cores collected down stream of the Morenci porphyry copper mine site, Arizona. This plot documents the release of copper from 

the mine site with peak concentrations from 1978 to 1983 and demonstrates the immediate results of the successful remedial action at the 

mine site (Church and others, 2005). B, Decrease in dissolved metal concentrations observed after remedial actions (2002–2007) at three 

small-scale mines and associated fluvial tailings in the Boulder River basin, Montana. C, Time-series water chemistry data for copper and 

zinc from the upper Animas River downstream of Silverton, Colo. Although substantial remedial efforts have been undertaken within the 

upper Animas River watershed, only minor improvements in water quality have been achieved after more than a decade of remedial work 

(Church and others, 2007).

References

Allen, H.E., 2002, The biotic ligand model 

addresses effects of water chemistry on metal 

toxicity: International Council on Mining and 

Metals Fact Sheet 7, 5 p.

Caine, J.S., Manning, A.H., Verplanck, P.L., 

Bove, D.J., Kahn, K.G., and Ge, S., 2006, 

Well construction information, lithologic logs, 

water level data, and overview of research in 

the Handcart Gulch, Colorado—An alpine 

watershed affected by metalliferous hydrothermal alteration: U.S. Geological Survey 

Open-File Report 2006-1189, 13 p.

Church, S.E., Choate, L.M., Marot, M.E., Fey, 

D.L. Adams, M., Briggs, P.H., and Brown, 

Z.A., 2005, Geochemical assessment of 

metals and dioxin in sediment from the San 

Carlos Reservoir and the Gila, San Carlos, 

and San Francisco Rivers, Arizona: U.S. 

Geological Survey Scientific Investigations 

Report 2005-5086, 61 p. 

Church, S.E., Owen, J.R., von Guerard, P., 

Verplanck, P.L., Kimball, B.A., and Yager, 

D.B., 2007, The effects of acidic mine drainage from historical mines in the Animas River 

watershed, San Juan County, Colorado—

What is being done and what can be done to 

improve water quality?, in DeGraff, J.V., ed., 

Geological Society of America Reviews in 

Engineering Geology, v. XVII, p. 47–83.

Copper

Zinc

DISCHARGE, IN CUBIC FEET PER SECOND

Cadmium

Copper

0 200 400 600 800 1,000 1,200

DEPTH, IN CENTIMETERS

A B C

1983

1978

0

100200300400500600700

320

300

280

260

240

220

200

180

160

140

120

100

80

60

40

20

0

Sediment toxicity

level

0

45

-45

90

-90

135

-135

0

1

-1

2

-2

3

-3

4

-4

5

-5

Oct Apr Oct Apr Oct Apr Oct Apr Oct Apr Oct Apr Oct Apr Oct Apr Oct Apr Oct Apr Oct Apr

94 95 95 96 96 97 97 98 98 99 99 00 00 01 01 02 02 03 03 04 04 05

Oct Apr Oct Apr Oct Apr Oct Apr Oct Apr Oct Apr Oct Apr Oct Apr Oct Apr Oct Apr Oct Apr 94 95 95 96 96 97 97 98 98 99 99 00 00 01 01 02 02 03 03 04 04 05

0

2

4

6

8

10

12

14

0.0

0.2

0.4

0.6

0.8

1.0

COPPER, IN PARTS PER MILLION

DISSOLVED CONCENTRATION, IN MICROGRAMS PER LITER

SHIFT IN MEAN DISSOLVED, IN 

MICROGRAMS PER LITER

1996-2002

2002-2007