COVER

1 View of Red Mountain mining district, Silverton, Colorado.

2 U.S. Geological Survey scientist performing a stream survey, Red Mountain Creek, Colorado.

3 Silver Ledge mine, Silverton, Colorado.

4 U.S. Geological Survey scientist sampling natural acid spring, Crested Butte, Colorado.

All photographs by Philip L. Verplanck

1

3

2

4
Understanding Contaminants Associated

with Mineral Deposits

Edited by Philip L. Verplanck

Circular 1328

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2008

This and other USGS information products are available at http://store.usgs.gov/

U.S. Geological Survey

Box 25286, Denver Federal Center

Denver, CO 80225

To learn about the USGS and its information products visit http://www.usgs.gov/

1-888-ASK-USGS

Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the 

U.S. Government.

Although this report is in the public domain, permission must be secured from the individual copyright owners to 

reproduce any copyrighted materials contained within this report.

Suggested citation:

Verplanck, P.L., ed., 2008, Understanding contaminants associated with mineral deposits: U.S. Geological Survey 

Circular 1328, 96 p.
iii

CONTENTS

Introduction by Philip L. Verplanck ..................................................................................................... 1

Part 1—Laboratory- and Site-Scale Studies of the Sources and Release of Metals................ 2

Chapter A: What is weathering in mine waste? Mineralogic Evidence 

for Sources of Metals in Leachates

by Sharon F. Diehl, Philip L. Hageman, and Kathleen S. Smith ................................................. 4

Chapter B: Understanding Jarosite—From Mine Waste to Mars

by Gregg A. Swayze, George A. Desborough, Kathleen S. Smith, Heather A. Lowers, 

Jane M. Hammarstrom, Sharon F. Diehl, Reinhard W. Leinz, and Rhonda L. Driscoll.................. 8

Chapter C: In-Situ Acid Weathering Reactions in Areas Affected by Large-Scale 

and Pervasive Hydrothermal Alteration in the Southern Rocky Mountains

by Dana J. Bove, Heather A. Lowers, Geoff S. Plumlee, and Philip L. Verplanck.................. 14

Chapter D: Bacterial Processes Can Influence the Movement of Metal Contaminants

in Wetlands that Have Been Affected by Acid Drainage

by Mark R. Stanton........................................................................................................................... 18

Chapter E: Simple Screening Tests to Determine the Potential Metal Toxicity

of Mining-Waste Leachates

by LaDonna M. Choate, James F. Ranville, Eric P. Blumenstein, and Kathleen S. Smith............. 24

Part 2—Basin-Scale Studies of the Sources and Release of Metals .......................................... 28

Chapter F: Determination of Flow Paths and Metal Loadings from Mine Waste 

Using Geophysical and Geochemical Methods at the Waldorf Mine, Clear Creek 

County, Colorado

by David L. Fey, Robert R. McDougal, and Laurie Wirt .............................................................. 30

Chapter G: Geologic Controls on Metal Transport in Ground Water Within 

an Alpine Watershed Affected by Historical Mining

by Raymond H. Johnson.................................................................................................................. 36

Chapter H: Electrical Geophysical Characterization of a Mining-Affected Subbasin, 

Prospect Gulch, Colorado

by Robert R. McDougal.................................................................................................................... 42

Chapter I: U.S. Geological Survey Research in Handcart Gulch, Colorado—

An Alpine Watershed Affected by Metalliferous Hydrothermal Alteration

by Jonathan Saul Caine, Andrew H. Manning, Philip L. Verplanck, 

Dana J. Bove, Katherine Gurley Kahn, and Shemin Ge ............................................................. 50
iv

Chapter J: Developing a Conceptual Model of Ground-Water Flow 

in an Alpine Watershed

by Andrew H. Manning and Jonathan Saul Caine...................................................................... 58

Chapter K: Environmental Rock Properties at Abandoned Mine Lands

that Generate or Neutralize Acid Drainage, Silverton, Colorado

by Douglas B. Yager...................................................................................................................... 64

Chapter L: Connecting Airborne Geophysical Data to Geologic Structures 

in the Upper Animas River Watershed, Silverton, Colorado

by Anne E. McCafferty and Robert R. McDougal..................................................................... 70

Chapter M: Using a Geographic Information System (GIS) to Determine the 

Physical Factors that Affect Water Quality in the Western San Juan Mountains, 

Silverton, Colorado

by Douglas B. Yager, Raymond H. Johnson, and Bruce D. Smith.......................................... 76

Part 3—Postremediation Recovery of Stream Ecosystems........................................................ 84

Chapter N: Recovery of Aquatic Life in Surface Streams Affected by Mining 

Following Remediation

by Stanley E. Church..................................................................................................................... 86
Introduction

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 water from inactive 

mines and mineralized areas,

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

•	 the fate and effect of metals and acidity on downstream 

ecosystems.

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 contributing 

to 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 historically 

mined areas and those responsible for anticipating environmental consequences of future mining operations. The recently 

completed (2007) 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.

Results from these studies provide new information that 

advances our understanding of the physical and biogeochemical processes causing the mobilization, transport, reaction, 

and fate of potentially toxic elements (including aluminum, 

arsenic, cadmium, copper, iron, lead, and zinc) in mineralized 

Understanding Contaminants Associated 

with Mineral Deposits

near-surface systems and their effects on aquatic and riparian 

habitat. These interdisciplinary studies provide the basis for 

scientific decisionmaking and remedial action by local, State, 

and Federal agencies charged with minimizing the effects of 

potentially toxic elements on the environment.

Current (2007) USGS research highlights the need to 

understand (1) the geologic sources of metals and acidity and 

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

toxicology came together for a series of studies that address 

these relationships on scales ranging from the microscopic to 

the watershed.

This Circular presents results and highlights from the 

detailed, interdisciplinary studies that include investigations 

in both mining-affected areas and mineralized but unmined 

areas. The first section of the Circular describes laboratory 

and site-scale field investigations that primarily focus on 

mineralogic and biologic controls on the source and release 

of metals and acidity from mine-waste rock and hydrothermally altered areas. The second section describes a set of 

basin- to watershed-scale studies that not only investigate the 

source and release of metals and acidity but also the transport 

of these constituents away from the source areas. The third 

section is a summary of results from postremediation ecosystem monitoring. For more information on these and other 

project-related studies, please visit the project Web site at 

http://minerals.cr.usgs.gov/projects/contaminants/index.html. 

The Web site includes a complete bibliography and detailed 

descriptions of each interdisciplinary study.

Edited By Philip L. Verplanck
2 Part 1—Laboratory- and Site-Scale Studies of the Sources and Release 

of Metals

One objective of this project was to better understand the mineralogical controls of metals 

and acidity in the acid weathering environment of hard-rock mining waste-rock piles and in mineralized but unmined areas. This section includes detailed mineralogical studies highlighting (1) the 

importance that mineral chemistry has concerning the sources of metals and acidity and (2) how 

mineral chemistry can be used to determine the potential for the release of metals and acidity from 

mine-waste material. Furthermore, detailed work on a weathering profile in an extensively hydrothermally altered area documents the change in mineralogy as a result of weathering in an acidic 

environment and the potential for a once-stable area to become unstable. Bacterial processes serve 

as another potentially important control on the release of metals and acidity in the acid weathering 

environment. This section includes results of recent field and laboratory investigations on the function of bacteria in the release and removal of metals from sulfide-rich rocks. To complement these 

field and laboratory studies, results of an evaluation of a new field screening test of water toxicity 

from the leaching of mine-waste rock are presented.
3
4 Chapter A: What is weathering in mine waste?

Mineralogic Evidence for Sources of Metals in Leachates

Introduction

Sulfide minerals such as pyrite (iron sulfide) commonly 

contain trace metals such as arsenic, lead, zinc, cobalt, and 

nickel. Sphalerite (zinc sulfide) commonly contains cadmium, 

and galena (lead sulfide) commonly contains silver. These trace 

metals render the lattice unstable and increase the solubility of the 

host sulfide mineral. This chapter describes how metals leaching into the environment at each locality are a result of mineralogic controls such as the residence of trace elements in sulfide 

minerals, weathering of these minerals, and formation of soluble 

secondary evaporative salts.

Two abandoned mine waste sites (Dinero, Lower 

Chatauqua) and one mine-waste-affected wetland site 

(Saints John) were sampled and subjected to the USGS FLT 

(U.S. Geological Survey Fact Sheet 2005–3100; Hageman, 

2007). The elements that were leached from the samples exhibited a unique geochemical fingerprint that is related to their ore 

deposit mineralogy (fig. 1).

Overview

Mine waste is discarded, uneconomical rock from 

active and inactive mine sites, and it covers hundreds of 

thousands of acres in the United States. Case studies of 

mine waste in the Colorado Rocky Mountains demonstrated a link between the weathering of trace-elementbearing sulfide minerals in mine waste and resulting 

metal contamination and acidity in receiving streams 

(Diehl and others, 2006). This study compares mineralogy, weathering textures, and leachate chemistry 

between the Dinero and Lower Chatauqua mine-waste 

piles, and the Saints John mine tailings-affected wetland 

to determine the source of leachable metals. Leaching 

experiments are a commonly used technique to identify 

metals that are released from mine waste and enter the 

environment, thereby affecting ecosystems.

This study identifies mineralogic sources of potentially hazardous metals such as lead, zinc, cobalt, and 

copper and explains why concentrations of different metals are elevated in surface water at different mine-waste 

sites. Metals in USGS Field Leach Test (FLT) leachates 

show a relationship between weathering and mobility of 

elements from minerals in the mine waste and leachate 

geochemistry. The two waste piles and wetland are close 

to timberline, at about 10,500 feet, situated on steep 

slopes where they are subject to rapid runoff and erosion 

during precipitation events. The weathering of minerals 

in mine waste is evidenced by oxidation by-products such 

as secondary sulfate minerals and dissolution textures 

such as etch pits on surfaces of sulfide grains.

The Dinero and Lower Chatauqua mine-waste piles are 

composed of hydrothermally altered and mineralized granite, 

schist, and gneiss rock fragments, ranging from boulder to silt 

sized. Two waste-rock piles at Dinero were sources of contaminant metals and acid drainage that negatively affected the 

downstream ecosystem, including fish populations (Walton-Day 

and others, 2005). Zinc, cadmium, and lead are major metals of 

concern in drainages from Dinero waste and an open adit.

The abandoned mine waste in the Lower Chatauqua site 

is in a similar geological setting as the Dinero waste. The 

Lower Chatauqua mine-waste pile remains a potential source 

of zinc, lead, cadmium, cobalt, and nickel contaminants to a 

downstream drainage, Deer Creek, where aquatic life had high 

uptake of metals (Yang, 2006). The reason we see high lead 

content in the Lower Chatauqua mine waste is because galena 

at this site is not a pure mineral; it contains silver. Figures 2C

and 4C show that galena has weathered to anglesite in the 

mine waste, and the anglesite has undergone partial dissolution, resulting in releasing lead into the environment.

The Saints John wetland received fluvial tailings from an 

upstream mill site. The tailings have been deposited as sandbars 

composed of layered, crossbedded, sand-size grains. Mercury, 

lead, and zinc are the primary elements of concern in the wetland.

Methods and Techniques

Microanalytical techniques, such as optical mineralogy, 

scanning electron microscopy, electron microprobe, and laser 

ablation inductively coupled mass spectrometer (LA–ICP–MS), 

were used to identify minerals, weathering textures, and the 

distribution of trace elements in minerals. These microanalytical 

techniques provide insight into why some minerals are more 

soluble than others.

In addition, the USGS FLT, which is designed to rapidly characterize the water reactive, readily soluble, mobile 

phases of mineralogic materials, was used to identify metals 

in solution (U.S. Geological Survey, 2005; Hageman, 2007). 

Using FLT leachates, researchers have described geochemical 

fingerprints for different mined areas (fig. 1).

Weathering of Minerals in Mine Waste 

and Leachate Geochemistry

Exposure to weathering processes (for example, freezethaw cycles, solar radiation, atmospheric oxygen, meteoric 

precipitation, and microbial activity) causes the breakdown of 

mineral grains and the formation of reactive, readily soluble 

secondary mineral phases (figs. 2 and 3). Metals in these 

soluble mineral phases are released as the mineral dissolves 

in rainwater or snowmelt.

by Sharon F. Diehl, Philip L. Hageman, and Kathleen S. Smith
Sphalerite

Fe oxides

Void

50 MICRONS

Pyrite

Void

K-clay

Etched, partially

dissolved pyrite

Fe-oxide

rim

Galena

Anglesite

A Dinero waste B Dinero waste C Lower Chatauqua waste

EXPLANATION

Selected FLT Leachate Results, Showing Geochemical Fingerprints

of the Dinero, Lower Chatauqua, and Saints John Sites

10,000

1,000

100

10

1 Dinero Lower Chatauqua Saints John

MINE-WASTE SITE

ELEMENT CONCENTRATION, IN PARTS PER BILLION

Al

Cd

Co

Cu

Fe

K

Mn

Ni

SO4

Sr

Pb

Ti

Zn

pH 3 pH 5 pH 3.5

5

Figure 2. Trace-element-rich sulfide minerals commonly show partial to total dissolution in mine-waste piles. (A) Sphalerite ([Zn,Fe]S) 

shows partial dissolution and remnant iron-oxide rims. (B) Pyrite (FeS) is deeply embayed and etched by dissolution processes. 

(C) Galena (PbS) has partially altered to anglesite (PbSO4

). Fine-grained, porous anglesite rinds show partial to total dissolution, 

indicating that weathering of galena and the subsequent dissolution of the secondary weathering product, anglesite, is the primary 

source for lead in solution.

Figure 1. Metals in high concentration leached from Dinero mine waste are zinc, manganese, potassium, iron, and 

aluminum. In contrast to results from Dinero, lead is high in concentration in solution in Lower Chatauqua waste, and iron is 

not detected in the leachate. In Saints John leachate, neither potassium nor iron is detected in solution, but elevated levels 

of manganese, lead, and zinc are going into solution.
A

B

C

D

Dissolution

embayments

Dinero

Void

Sphalertie

50 MICRONS

S map

Lower Fe map

Chatauqua

Lower

Chatauqua

S map Pb map Ag map

1 Cd map 3

3

1 2 3 4 5

3 As map 4

2

S map1 2 Cd map

Saints John

20 MICRONS

Sphalerite

1 Fe map 2 Co map

Pyrite

Galena

Pyrite

100 MICRONS

2 MICROMETERS

Chapter A

6 Understanding Contaminants Associated with Mineral Deposits

Figure 4. Element distribution maps 

gathered by electron microprobe show 

trace-metal enrichment and residence sites 

in sulfide minerals. (A) Sphalerite that hosts 

cadmium is deeply etched and embayed by 

dissolution processes. (B) Sphalerite that 

lacks cadmium has not undergone the pitting 

and deep weathering as its cadmium-rich 

counterpart in (A). (C) Silver-rich galena, 

a sulfide, has undergone partial alteration 

to anglesite, a sulfate. In turn, the rinds of 

anglesite have undergone partial dissolution. 

(D) Cobalt and nickel are concentrated in a 

pyrite within healed fractures (green areas 

in image 3). The elements arsenic (image 4) 

and cobalt do not overlap in area, suggesting 

that these elements precipitated during 

different times in the deformation history of 

the ore deposit.

Element distribution maps, also called element intensity 

maps, show that sulfide minerals such as galena, sphalerite, and 

pyrite contain varying amounts of trace metals that increase 

the mineral’s susceptibility to dissolution (fig. 4). Warm, 

yellow-green to red colors in figure 4 indicate relatively high 

concentrations of an element, and cool, blue colors indicate low 

concentrations. Figure 4 shows element distribution maps of 

cadmium in sphalerite, silver in galena, and metals such as cobalt 

and arsenic in pyrite. Figure 4A shows a cadmium-rich sphalerite grain from Dinero mine waste that is highly etched and has 

undergone partial dissolution. In comparison, a cadmium-poor 

sphalerite grain from the Saints John tailings (fig. 4B) does not 

show deep etch embayments or the high degree of weathering 

as the grain in 4A.

During dry periods, secondary evaporative minerals 

form at seeps on the surfaces of mine-waste piles (fig. 5). Element 

distribution maps show that these highly soluble secondary minerals have a preferred order of precipitation, from early magnesiumand zinc-rich minerals to later manganese-rich minerals and 

gypsum (CaSO4

).

Figure 3. Silicate minerals undergo weathering and dissolution, 

thereby contributing cations to the formation of secondary minerals. 

Here, mica [KAl3

(Si3Al)O10(OH,F)2] from the Saints John tailings has 

altered by splitting along cleavage planes. Bright spots of leadbearing jarosite [lead substitutes for potassium in KFe3+(SO4

)

2

(OH)6)] 

have formed between the cleavage planes.
1

S map

2 3

Mg map

4

Mn map

5

Zn map 20

MICROMETERS

A

B

Chapter A

Chapter A: What is weathering in mine waste? 7

Figure 5. (A) U.S. Geological Survey scientist notes development of secondary salts at seep on reclaimed mine-waste 

material. During dry periods, soluble secondary minerals 

form on the surfaces and in pore spaces in mine-waste piles. 

(B) Secondary minerals (1) readily dissolve during precipitation 

events. Yellow color indicates high concentration as shown 

in the sulfur (S) map (2). The minerals have a preferred order 

of metal precipitation; magnesium-rich zinc-bearing minerals 

precipitate first (3), followed by manganese-rich minerals (4). 

Zinc (5) preferentially precipitates early with magnesium. During 

wet periods, these minerals will readily dissolve, and magnesium, 

manganese, and zinc will be flushed downstream.

geochemical fingerprints of a waste pile can be used to assess 

and profile the release and mobility of potential toxic elements 

into the environment.

In addition, secondary mineral precipitates are observed 

to be more soluble than original sulfide minerals, as evidenced 

by the dissolution and reprecipitation of sulfates during 

wetting and drying cycles. The study also verifies that the 

USGS FLT is an effective tool to characterize or predict waterreactive, readily soluble phases of mine-waste samples.

References Cited

Diehl, S.F., Hageman, P.L., and Smith, K.S., 2006, What’s 

weathering? Mineralogy and field leach studies in mine 

waste, Leadville and Montezuma Mining Districts, 

Colorado, in Barnhisel, R.I., ed., Gateway to the future: 

Society for Mining, Metallurgy, and Exploration (SME) 

Annual Meeting and 7th International Conference on Acid 

Rock Drainage (ICARD), March 26–30, St. Louis, Mo. 

CD–ROM, p. 508–527.

Hageman, P.L., 2007, U.S. Geological Survey field leach 

test for assessing water reactivity and leaching potential of 

mine wastes, soils, and other geologic and environmental 

material: U.S. Geological Survey Techniques and Methods, 

book 5, chap. D3, 14 p.

U.S. Geological Survey, 2005, A simple field leach test to 

assess potential leaching of soluble constituents from mine 

wastes, soils, and other geologic materials: U.S. Geological Survey Fact Sheet 2005–3100 (Contact: P.L. Hageman). 

http://pubs.usgs.gov/fs/2005/3100/

Walton-Day, K., Flynn, J.L., Kimball, B.A., and Runkel, 

R.L., 2005, Mass loading of selected major and 

trace elements in Lake Fork Creek near Leadville, Colorado, September–October 2001: U.S. Geological Survey 

Scientific Investigations Report 2005–5151, 52 p.

Yang, Chi, 2006, Effects of acid mine drainage on nesting tree 

swallows: Boulder, University of Colorado, Master’s thesis, 

94 p.

Effects

Leachate analytical data produced during this study show 

that metals from the three mine-waste samples are mobilized 

and may become bioavailable (fig. 1). The FLT leachates 

produced as part of this study were also the source leachate for 

bioavailable toxicity studies (Choate and others, this volume.) 

The uptake of leached metals by flora and fauna was observed 

in a study of benthic invertebrates in Deer Creek downstream 

from the Lower Chatauqua mine-waste pile (Yang, 2006). 

An interesting finding during that study was that no swallows 

nested along the stream where the highest metal content in 

aquatic food sources was recorded.

Summary

This study documents that the microscale alteration of 

mineral grains due to weathering leads directly to the leaching 

and mobility of acid and metals from the waste materials into 

the environment upon exposure to and leaching by water. Geochemical fingerprints derived from the FLT leachates, along 

with the etched, partially dissolved minerals observed in these 

samples, serve as evidence of this weathering process. The 
8 Chapter B: Understanding Jarosite—From Mine Waste to Mars

Introduction

In 1852, a German mineralogist named August Breithaupt 

discovered a yellowish-brown mineral in Barranco del Jaroso 

(Jaroso Ravine) in the Sierra Almagrera along the southeastern 

coast of Spain. He named this potassium-iron-sulfate-hydro

xide mineral “jarosite” (Anthony and others, 1990). Jarosite 

has the chemical formula KFe3

(SO4)

2

(OH)6 but its “garbage 

can”-like structure can accommodate many other elements 

to produce chemically diverse varieties like natrojarosite 

[NaFe3

(SO4)

2

(OH)6], hydronium jarosite [H3OFe3(SO4)

2

(OH)6], 

ammoniojarosite [NH4

Fe3(SO4)

2

(OH)6], and plumbojarosite 

[PbFe6

(SO4)

4

(OH)12], among others. These are examples of 

endmember jarosites; intermediate jarosites consist of mixtures 

of alkali-site cations (for example, K+

 and Na+, or H3O+ and K+).

Jarosite has been in the headlines as one of the hydrated 

minerals discovered using the Mossbauer spectrometer on 

the Opportunity Rover at Eagle Crater on Mars (Klingelhöfer 

and others, 2004). Here on Earth jarosite is common in acidic 

soils, in mine waste formed by oxidation of sulfide minerals, 

or as a product of iron precipitation prior to electrolytic refining of zinc. Because of its association with sulfide minerals, 

acidic conditions, and heavy metals in mine waste, jarosite can 

be used as a proxy in remote-sensing studies to locate areas of 

high acidity and metal leachability (Swayze and others, 2000), 

thereby providing a rapid way to screen mined areas for potential sources of acidic drainage (fig. 1).

Jarosite’s function as a potential source of acid in mine 

waste is not completely understood. The traditional view is 

that acid can be generated in mine waste due to the oxidation 

of sulfide minerals, the dissolution of highly soluble sulfate 

salts, and the dissolution of less-soluble sulfate minerals, 

such as jarosite. In waste where all of these materials are 

mixed together, it is difficult to decipher which ones contribute the most to acid generation. As a further complication, jarosite’s compositional variability allows multiple 

levels of chemical reactivity. Because natural endmember 

jarosites are very difficult to physically segregate, synthetic 

jarosites have been used as analogs to determine solubility 

and dissolution properties of the natural jarosites. Solubility 

data from synthetic jarosites are used to predict the acidgeneration potential of mine-waste materials. Hydroniumbearing jarosite, in particular, is thought to contribute to acid 

generation in mine wastes because the hydronium ion (H3

O+) 

accelerates jarosite dissolution (Gasharova and others, 2005, 

and references therein).

Overview

The presence of jarosite, an iron-sulfate mineral, in 

soil or in mining waste is an indicator of acidic, sulfaterich conditions. Physical and chemical properties of 

synthetically prepared jarosites are commonly used as 

analogs in laboratory studies to determine solubility 

and acid-generation potential of naturally occurring 

jarosites. In our work we have mineralogically and 

chemically characterized both natural and synthetic 

jarosites. Analyses of natural potassium (K)- and 

sodium (Na)-jarosites from hydrothermal and weathering environments indicate that there is little solid solution 

(chemical mixing); instead, they revealed that samples 

consist of discrete mixtures of potassium- and sodiumendmembers. Hydronium (H3

O+)-bearing jarosite was 

detected in only one relatively young natural sample, 

suggesting that terrestrial H3

O-bearing jarosites are 

unstable over geologic timescales. Although the presence 

of H3O+ in jarosite is very difficult to measure directly 

with traditional analytical methods, we found that heating H3

O-bearing samples at high temperatures (greater 

than 200 to 300 degrees Celsius) produces an Fe(OH)SO4

compound. Fe(OH)SO4 is easily detected by X-ray 

diffraction and reflectance spectroscopy; hence, it can 

be used as a “post-mortem” indicator of the presence 

of H3

O+ in jarosite. Results from our synthetic jarosite 

studies indicate that natural H3

O-bearing jarosite, 

alkali-site deficient, and iron-deficient forms of natural 

jarosite are metastable and likely are significant factors in acid generation of some mining wastes, but that 

these natural phases are not accurately represented by 

synthetic jarosite prepared by commonly used methods. 

The widespread practice of heating synthetic jarosites to 

at least 110 degrees Celsius (°C) after synthesis appears 

to drive off structural water, resulting in samples with 

crystal structures similar to those of the hydrothermal 

jarosites, which are a much more stable form of jarosite. 

Therefore, synthetic jarosite should not be heated above 

60°C if it is to be used as an analog for low-temperature 

natural jarosite found in mine waste. An extension of our 

work on jarosite reveals that reflectance spectroscopy 

can be used in remote sensing studies to identify H3

Obearing and iron-deficient jarosites on the surface of the 

Earth and Mars.

by Gregg A. Swayze, George A. Desborough, Kathleen S. Smith, Heather A. Lowers, Jane M. Hammarstrom, 

Sharon F. Diehl, Reinhard W. Leinz, and Rhonda L. Driscoll
In this study, a detailed laboratory examination of the 

mineralogical, microscopic, thermal, and spectral characteristics of jarosite was conducted in order to find clues to its place 

in the acid-mine drainage story. We studied both natural and 

synthetic jarosites to see if lessons learned from past research 

on synthetic jarosites can be used to accurately predict the 

geochemical behavior of natural ones and to define the environmental conditions under which their comparison to natural 

samples is valid. While conducting this research we were 

mindful of how these findings might be used to better understand jarosite formation on Mars and how its presence there 

constrains Martian surface chemistry.

Jarosite Geochemistry

Jarosites found in mining wastes generally are very fine 

grained (<5 micrometers), making it very difficult to determine 

the composition of individual grains. The unit cell of a mineral 

is the smallest group of atoms that possess the crystallographic 

symmetry and chemical properties of the mineral. Changes in 

unit cell parameters can be diagnostic of element substitutions 

or vacancies within the unit cell, which can lead to decreased 

stability of a mineral phase. The a- and c-cell dimensions 

of natural jarosites were examined using X-ray diffraction 

(XRD) analysis, and it was found that both hydrothermal and 

low-temperature samples consisted of single K- or Na-jarosite 

endmembers or pairs of endmembers. This is in contrast to the 

existence of complete solid solution (chemical mixing) across 

the sodium-potassium compositional series in jarosites synthesized at hydrothermal temperatures (>100°C). We concluded 

from these observations that natural jarosites rarely, if at all, 

form crystals with intermediate composition.

N

Venir waste

rock pile

A

0 25 50 METERS

Neutral

Low leachability

Jarosite Jarosite + Goethite

Goethite Hematite

EXPLANATION

EXPLANATION

Venir waste-rock pile

Samples from spectral zones:

Jarosite

Jarosite + Goethite

Goethite

2 3 4 5 6 7

LEACHATE pH

LEACHABLE HEAVY METALS

Zn + Cu +Cd + Pb + Co + Ni,

IN MILLIGRAMS PER LITER

100,000

10,000

1,000

100

B

pH: Acidic

Metals: High leachability

Secondary minerals:

9

Figure 1. (A) Airborne Visible and InfraRed Imaging Spectrometer 

(AVIRIS) mineral map overlaid on a color aerial photograph of the 

Venir mine-waste pile located 5 kilometers southeast of Leadville, 

Colorado. In the aerial photograph white areas are snow, rectangular 

objects are abandoned mine structures, and dark green objects are 

lodgepole pines casting shadows. The mineral map overlay shows 

the spectrally dominant iron-bearing secondary minerals, jarosite, 

goethite, hematite, and mixtures, for each 20-by-15-meter pixel on 

the ground. (B) Comparison of field and laboratory measurements 

with AVIRIS mapping demonstrates that jarosite-bearing areas 

have low pH and higher metal leachability and goethite-bearing 

areas have more neutral pH and lower metal leachability. Because 

imaging spectroscopy measures reflected sunlight, it cannot be 

used to detect minerals deeper than can typically be seen with the 

human eye; hence, the data can only provide information on minerals 

exposed in the top few millimeters of the surface.
Quantitative electron probe microanalysis data of several 

natural hydrothermal jarosite samples show only endmember 

compositions for individual grains or zones, and no detectable 

alkali-site deficiencies, which indicates that there is no H3

O+

substitution within the analytical uncertainty of the method 

(fig. 2). In addition, there is no evidence of deficiencies in the 

natural hydrothermal jarosite samples. X-ray diffraction data 

for the natural low-temperature (<100°C) K- and Na-jarosites 

we studied have cell dimensions similar to the “mature” 

high-temperature hydrothermal jarosites. Hence, it is inferred 

that these samples also lack alkali- or iron-site vacancies, 

lack an H3

O+ component, and instead consist of a mixture of 

potassium- and sodium-jarosite endmembers. In other words, 

they chemically resemble the more stable hydrothermal jarosites 

and do not resemble low-temperature synthetic jarosites.

There is an explanation for the apparent discrepancy 

between low-temperature synthetic jarosites and natural 

low-temperature jarosites. A series of five synthetic jarosites 

were prepared in pressure vessels at 95°C and dried at 60°C 

for one hour. These samples vary from H3

O-poor and irondeficient to H3

O-rich (fig. 3). After heating these samples at 

110°C for 20 and 40 hours, respectively, structural water losses 

ranged from 3.5 to 9 weight percent and cell dimensions were 

reduced significantly. Post-synthesis heating is a common 

practice used to remove “excess” water from nonstoichiomeric 

(non-ideal chemical formula) jarosite samples. Heating these 

samples causes some H3

O+ in alkali sites near iron vacancies 

to permanently transfer protons to hydroxyls surrounding these 

iron vacancies, thereby converting this H3

O+ to H2O and the 

hydroxyls to protonated hydroxyls (OH2

), which are then both 

lost as water vapor at temperatures near 200°C. Samples with 

little to no H3

O+ tend to gradually lose their protonated hydroxyl 

component as H2

O vapor at temperatures lower than 200°C. 

Both water-loss processes produce relatively stable stoichiometric (ideal chemical formula) jarosite that may no longer be representative of the chemically reactive type of nonstoichiometric 

jarosite, which can potentially contribute to acid-mine drainage.

Identification of HydroniumBearing Jarosite

Heating synthetic H3O-bearing jarosite samples up to 

240°C results in the production of an XRD-detectable compound with the chemical formula Fe(OH)SO4

. The loss of H3O+

from the jarosite crystal structure is accompanied by a small but 

significant change in cell dimensions, which coincides with the 

development of endmember K-jarosite (Desborough and others, 

2006). Formation of crystalline Fe(OH)SO4

 from H3O-bearing 

jarosite requires the loss of water and formation of amorphous 

iron hydroxide, as shown in the reaction equation:

(H3O)Fe3(SO4)

2

(OH)6 → 2Fe(OH)SO4 + 2H2O + Fe(OH)3,

hydronium-jarosite amorphous

Fe-hydroxide

5 m

200 MICROMETERS

5 MICROMETERS

20 MICROMETERS

20 MICROMETERS

A

B

C

D

Potassium

Sodium

Chapter B

10 Understanding Contaminants Associated with Mineral Deposits

Figure 2. (A) Backscattered electron image 

of a potassium-jarosite sample, originally 

identified by X-ray diffraction, from a wasterock pile showing the typical small grain size of 

low-temperature jarosite minerals observed in 

mine waste. (B) Blowup of (A) where the circle 

represents the diameter of the electron beam 

defocused to 10 micrometers (μm) for electron 

microprobe analysis of jarosite, which illustrates 

the difficulty of obtaining an elemental analysis 

of compositional zoning within individual grains. 

(C) and (D) Electron microprobe X-ray intensity 

maps of potassium (K) (top) and sodium (Na) 

(bottom) of about 5- to 10-micrometer jarosite 

crystals from the Richmond Mine at Iron 

Mountain in California. Green and orange areas 

depict regions with greater elemental intensity 

than blue regions. Note the K- and Na-zoning is 

less than 2 micrometers across, which suggests 

that potassium- and sodium-jarosites grew at 

different times and have limited solid solution 

(chemical mixing).
Chapter B

Figure 3. Crystallographic unit-cell dimensions for eight synthetic 

jarosites with variable hydronium (H3

O+) content prepared in a 

pressure vessel at 95 degrees Celsius and then dried in air at 

60 degrees Celsius for one hour. Unit-cell dimensions refer to the 

lengths, usually given in Angstroms (one ten-millionth of a millimeter), 

of the sides of a unit cell, the smallest group of atoms whose 

arrangement produces a crystal’s symmetry and whose repetition 

in three dimensions produces a crystal’s lattice. Unit-cell values 

for endmember H3

O-jarosite, sodium (Na)-jarosite, and potassium 

(K)-jarosite are also shown for reference. Arrow shows trend of 

unit-cell dimension changes as samples become H3

O-rich. Unit-cell 

dimensions calculated from X-ray diffraction analysis can be used to 

measure the H3

O+ content of natural jarosites, thus helping scientists 

predict how much acidity and leachable metals they can potentially 

contribute to acidic mine drainage.

with the remaining jarosite recrystallizing to endmember 

K-jarosite. Thermogravimetric analysis of synthetic H3

O-bearing 

jarosite shows evidence of rapid H2

O loss near 200°C (fig. 4), 

although there is no evidence of rapid H2

O loss at this temperature when H3

O+ is absent. There is also no XRD-detectable 

Fe(OH)SO4

 produced by heating when H3O+ is absent from 

jarosite samples. Therefore, we conclude that H3

O+ loss from 

jarosite is the cause of Fe(OH)SO4

 production. Consequently, the 

easily XRD-detectable Fe(OH)SO4

 phase can be used as a “postmortem” indicator of the presence of H3

O+ in jarosite.

In the natural jarosites studied, no Fe(OH)SO4

 was 

detected after heating, in agreement with the quantitative electron probe microanalysis results that show no detectable alkalisite deficiencies or H3

O+ substitution. The sole exception is a 

sample from the Richmond mine in California, where jarositerich stalactites are actively forming from dripping acidic water 

(Jamieson and others, 2005). These samples yield Fe(OH)SO4

after thermal treatment at 240°C, which indicates that their 

jarosite contains H3

O+.

Spectroscopic Studies of Jarosite

Reflectance spectroscopy can be a useful tool for jarosite 

identification in remote-sensing studies and for detecting the 

presence of H3

O+ and iron-deficiencies in jarosite with portable 

field spectrometers. In the spectral region spanning the ultraviolet 

to the near-infrared wavelengths (about 0.35 to 2.5 micrometers 

[μm]), jarosite has many diagnostic absorptions (fig. 5). Most 

Synthetic H3O-bearing jarosite

H3O0.27K0.73Fe3+

2.82(SO4)2(OH2)0.54OH5.46

Loss of

H3O and OH2

Loss of

OH–

Loss of SO4

2–

QMS

DTG

QMS

SAMPLE MASS,

 IN PERCENT

TGA 100

80

60

100 200 300 400 500 600 700 800 900 1,000 °C

H2O SO2

K-H3O compositional series

Low H3

O+,

high iron-deficiency

7.30

7.31

7.32

7.33

7.34

7.35

7.36

16.6 16.7 16.8 16.9 17.0 17.1 17.2 17.3

A CELL DIMENSION, 

IN ANGSTROMS

C CELL DIMENSION, IN ANGSTROMS

Na-jarosite

H3

O-jarosite

K-jarosite

High H3

O+,

low iron-deficiency

Chapter B: Understanding Jarosite—From Mine Waste to Mars 11

Figure 4. Top: Thermogravimetric Analysis (TGA) curve shows the 

mass loss as a function of heating a synthetic H3O-bearing jarosite 

at a rate of 10 degrees Celsius per minute up to 1,100 degrees 

Celsius in an inert gas. Middle: Derivative thermogravimetry (DTG) 

curve shows the first derivative of the TGA curve highlighting 

changes in the rate-of-mass-loss during heating. Bottom: 

Quadrupole Mass Spectrometer (QMS) curves record the ion 

current associated with masses 18 (H2

O) and 64 (SO2) released 

during heating. In this jarosite sample, progressive heating drives 

off H3

O+ and OH2 at about 200 degrees Celsius. Near 400 degrees 

Celsius hydroxyl (OH) is converted to H2

O, and near 680 degrees 

Celsius SO4

 is converted to SO2. These kinds of measurements help 

scientists understand the composition of jarosite.

notable is the wide absorption band near 0.9 μm caused by an 

Fe3+-electronic transition. This spectral feature was used to 

map for the presence of jarosite in mine waste near Leadville, 

Colorado (fig. 1A). Variations in the wavelength position and 

shape of vibrational absorptions near 1.4, 1.85, and 2.26 μm 

can be used to differentiate potassium- from sodium-jarosite 

and assess the temperature of jarosite formation (Swayze and 

others, 2006). Hydronium-bearing and iron-deficient jarosites 

have relatively weak spectral features compared to those of the 

potassium- and sodium-endmembers, thus allowing them to be 

recognized using airborne and orbital imaging spectrometers. 

The relative proportion of protonated hydroxyl (OH2

) to H3O+

can be directly measured based on the depth of absorption bands 

at 1.93 and 1.96 μm, respectively (see vertical arrows in fig. 5). 

Using this information, it may now be possible to spectrally 

identify which areas of mine waste have the highest concentrations of H3

O-bearing jarosite and are thus more likely contribute 

to acidic drainage.

Is synthetic jarosite a suitable analog 

for natural jarosite in mine waste?

The chemical composition, cell dimensions, and other properties of synthetic jarosites formed at low temperature (<100°C) 

may simulate relatively young jarosites in mining wastes. Most 

of the low-temperature synthetic jarosites seem to be metastable 

(easily changed and more chemically reactive) due to either 

substitution of H3

O+ in the mineral’s structure or to iron- and 
WAVELENGTH, IN MICROMETERS

SCALED REFLECTANCE

Hydronium

jarosite

(140°C)

Fe-deficient

jarosite

(95°C)

H3O+

OH2

K-jarosite

Vibrational

absorptions

Fe-electronic

absorptions

Na-jarosite

1.0

0.5

0

0.5 1.0 1.5 2.0 2.5

Types of jarosite: Compositional changes:

Hydrothermal

Old supergene, speleogenic

and acid-saline lacustrine

stoichiometric 

(K, Na) Fe3

 (SO4)

2

(OH)6

Loss of H3O+, OH2,

alkali and iron

deficiencies

Young supergene, speleogenic,

and acid-saline lacustrine

nonstoichiometric

(H3

O, K, Na) Fe3–n (SO4)

2

(OH2)

3n(OH)6–3n

Recrystallization

and desiccation

Metastable conditions:

sAlkali deficiencies

sH3

O+-bearing

s Protonated hydroxyls

 charge-compensate

 iron deficiencies

Chapter B

12 Understanding Contaminants Associated with Mineral Deposits

alkali-site deficiencies in the mineral structure. Heating synthetic 

jarosite samples drives off “excess” water (OH2

) and changes 

the properties of the jarosites. Over time, recrystallization and 

desiccation may do the same thing to natural jarosites (fig. 6). 

Metastable or “modern” low-temperature natural jarosites and 

synthetic jarosites have larger a- and smaller c-unit-cell dimensions than do “mature” natural jarosites. In addition, mature 

natural jarosites do not appear to have the site vacancies, irondeficiencies, or significant H3

O+ substitutions in the mineral 

structure that are observed in some synthetic and modern natural 

jarosites. Recognition of metastable jarosite phases is important 

because they tend to have different solubility and acid-generation 

properties than mature or high-temperature synthetic jarosites. In 

order for synthetic jarosites to be representative of young jarosites 

from mining wastes, the synthetic jarosites should not be dried at 

temperatures above 60°C.

Figure 5. Reflectance spectra of synthetic jarosites (upper 

two curves) and natural jarosites (lower two curves). Hydronium 

(H3

O+)-bearing jarosites have a diagnostic H3O+ spectral 

absorption at 1.96 micrometers. The iron (Fe)-deficient jarosite 

is potassium (K)-rich with about 10 percent vacancies in the iron 

site and a diagnostic H2

O spectral absorption at 1.93 micrometers. 

Synthesis temperatures are listed in parentheses for synthetic 

samples. Spectra of the natural samples have stronger vibrational 

absorptions than spectra of the synthetic samples because they 

do not contain H3

O+ or protonated hydroxyl (OH2). Spectra are 

offset vertically for clarity.

Figure 6. Terrestrial environments in which jarosites are known to 

form. Hydrothermal formation of jarosite usually involves precipitation 

from hot (greater than 100 degrees Celsius) fluids. Low-temperature 

(less than 100 degrees Celsius) sulfide oxidation is responsible for 

most supergene jarosite formation. Sulfuric acid associated with 

hydrocarbons may form speleogenic jarosite in caves, whereas 

highly acidic-saline fluids can cause precipitation of jarosite in 

lakes. Most hydrothermal jarosites are stoichiometric, having ideal 

jarosite chemical formulas. The other types of jarosite may be 

nonstoichiometric initially, but through long-term desiccation they 

usually recrystallize to stoichiometric forms. In the nonstoichiometric 

jarosite formula the letter “n” indicates the level of iron deficiency, 

and if this value is known it can be used to calculate the amount of 

protonated hydroxyl (OH2

) and normal hydroxyl (OH).

What can jarosite tell us about Mars?

As mentioned previously, one of the Mars exploration rovers 

found jarosite in what many interpret as sedimentary rocks on 

Mars (fig. 7). A remaining question about this jarosite occurrence 

is the type of geochemical environment in which it was deposited. One hypothesis suggests that this jarosite may have been 

deposited in shallow, acid-saline water, but another hypothesis 

suggests that hydrothermal fluids may have been instrumental in 

the formation of the jarosite (Golden and others, 2008). In 2007, 

jarosite was observed on Mars from orbit by the CRISM imaging 

spectrometer in layered materials south of the Valles Marineris 

Canyon System (Milliken and others, 2008). A spectrum of this 

jarosite shows H3

O+ and protonated hydroxyl (OH2) absorptions 

near 1.9 μm, which is consistent with formation of this mineral 

in an acidic, low-temperature environment. This observation supports an emerging picture of Mars as an initially wet planet that 

dried up over time. The ability to differentiate spectrally between 

low-temperature lake sediments and relict high-temperature 

hydrothermal deposits from Martian orbit can help focus future 

rover deployment and sample collection on areas with the highest 

potential of having preserved possible evidence of ancient life. In 

summary, our studies have led to the recognition that jarosite can, 

under the right conditions, preserve evidence of the geochemical 

and thermal conditions in which it formed.
Chapter B

Chapter B: Understanding Jarosite—From Mine Waste to Mars 13

References Cited

Anthony, J.W., Bideaux, R.A., Bladh, K.W., and Nichols, 

M.C., 1990, Handbook of mineralogy, volume I. 

Elements, sulfides, sulfosalts: Tucson, Arizona, Mineral 

Data Publishing, 588 p.

Desborough, G.A., Smith, K.S., Lowers, H.A., Swayze, G.A., 

Hammarstrom, J.M., Diehl, S.F., Driscoll, R.L., and Leinz, 

R.W., 2006, The use of synthetic jarosite as an analog for 

natural jarosite: Proceedings of the Seventh International 

Conference on Acid Rock Drainage (ICARD 7), St. Louis, 

Missouri, March 26–30, 2006, p. 458–475.

Gasharova, B., Gottlicher, J., and Becker, U., 2005, Dissolution at the surface of jarosite—An in situ AFM study: 

Chemical Geology, v. 215, p. 499–516.

Golden, D.C., Ming, D.W., Morris, R.V., and Graff, T.G., 

2008, Hydrothermal synthesis of hematite spherules and 

jarosite—Implications for diagenesis and hematite spherule 

formation in sulphate outcrops at Meridiani Planum, Mars: 

American Mineralogist, v. 93, p. 1201–1214.

Jamieson, H.E., Robinson, C., Alpers, C.N., Nordstrom, D.K., 

Poustovetov, A., and Lowers, H.A., 2005, The composition 

of coexisting jarosite-group minerals and water from the 

Richmond Mine, California: Canadian Mineralogist, v. 43, 

no. 4, p. 1225–1242.

Klingelhöfer, G., Morris, R.V., Bernhardt, B., Schröder, C., 

Rodionov, D.S., de Souza, Jr., P.A., Yen, A., Gellert, R., 

Evlanov, E.N., Zubkov, B., Foh, J., Bonnes, U., Kankeleit, 

E., Gütlich, P., Ming, D.W., Renz, F., Wdowiak, T., Squyres, 

S.W., and Arvidson, R.E., 2004, Jarosite and hematite 

at Meridiani Planum from Opportunity’s Mössbauer 

spectrometer: Science, v. 306, p. 1740–1745.

Milliken, R.E., Swayze, G.A., Arvidson, R.E., Bishop, J.L., 

Clark, R.N., Ehlmann, B.L., Green, R.O., Grotzinger, J.P., 

Morris, R.V., Murchie, S., Mustard, J.F., Weitz, C., and 

the CRISM Science Team, 2008, Opaline silica in young 

deposits on Mars: Geology, v. 36, no. 11, p. 847–850.

Swayze, G.A., Smith, K.S., Clark, R.N., Sutley, S.J., Pearson, 

R.N, Rust, G.S., Vance, J.S., Hageman, P.L., Briggs, P.H., 

Meier, A.L., Singleton, M.J., and Roth, S., 2000, Using 

imaging spectroscopy to map acidic mine waste: Environmental Science and Technology, v. 34, no. 1, p. 47–54.

Swayze, G.A., Desborough, G.A., Clark, R.N., Rye, R.O., 

Stoffregen, R.E., Smith, K.S., and Lowers, H.A., 2006, 

Detection of jarosite and alunite with hyperspectral 

imaging—Prospects for determining their origin on Mars 

using orbital sensors, in Martian sulfates as recorders of 

atmospheric-fluid-rock interactions: Lunar and Planetary 

Institute, 7072.pdf. available at http://www.lpi.usra.edu/

meetings/sulfates2006/pdf/7072.pdf and accessed 

07/22/08.

Figure 7. Approximate true-color mosaic of “Burns Cliff” along the southeastern inner wall of Endurance Crater in Meridiani Planum 

on Mars. Images were collected by the panoramic camera on the Opportunity Rover. In-situ Mossbauer analyses of these crossbedded 

sediments indicate that they contain spherical hematite-rich concretions known as “blue berries,” magnesium sulfates, and jarosite. 

The mosaic spans more than 180 degrees from side to side.

NASA/JPL/Cornell
14 Chapter C: In-Situ Acid Weathering Reactions in Areas Affected by 

Large-Scale and Pervasive Hydrothermal Alteration in the Southern 

Rocky Mountains

Overview

Weathering of pyrite-rich, hydrothermally 

altered rocks can produce acidic, metal-rich waters. 

This study of large-scale, pervasively altered, 

unmined areas in Colorado and New Mexico 

documents the in-situ mineralogical changes of the 

hydrothermally altered rocks (altered protolith) in 

response to this acid weathering. Quantitative X-ray 

diffraction analyses document a decrease in the 

amount of chlorite, illite, pyrite ± plagioclase in the 

protolith as weathering progresses. The decreased 

abundance of these minerals is associated with a concurrent increase in smectite (a highly swelling clay), 

kaolinite, and jarosite. The data indicate that waters 

related to pyritic weathering are initially acidic and 

result in the precipitation of kaolinite. As solutions 

evolve locally to more neutral compositions, they precipitate and equilibrate with smectite. These in-situ 

mineralogical changes can decrease the strength of 

the rock and enhance physical weathering. Understanding the mineralogical evolution of these altered 

and mineralized rocks has implications as to minewaste pile stability.

to 20 km2) of hydrothermally altered rock. Natural weathering in each of these areas produces low-pH and metal-rich 

water (fig. 2). These study areas include (1) Webster Pass, in 

the central Colorado Front Range, near Keystone, Colorado 

(Caine and others, 2006); (2) Prospect Gulch in the upper 

Animas River watershed, southwest Colorado (Bove and 

others, 2007); (3) Alum Creek, tributary to the upper Alamosa 

River, near Summitville Colorado (Bove and others, 1996); 

and (4) Straight Creek, near Questa and the Red River, 

New Mexico (Ludington and others, 2004).

The results of our studies demonstrate that the fundamental processes of acidic weathering of rocks are remarkably similar in each of these four hydrothermally altered 

areas. Although results from a compendium of these studies 

will be presented, we will specifically focus on our findings 

in Straight Creek, northern New Mexico, which provide an 

exceptional example of what we have observed elsewhere.

Results and Discussion 

of Weathering Studies

Gullies incised into the eroded slopes of the four study 

areas expose relatively unweathered (absence of recent and 

low-temperature alteration), pyrite-rich rocks. These characteristically light-gray, clay-rich rocks were hydrothermally 

altered millions of years ago by hot, caustic solutions driven 

by magmas rising high into the Earth’s crust. In geologic terms, 

we classify the hydrothermally altered rock as the altered 

protolith. The altered protolith is classically characterized as 

quartz-sericite-pyrite (qsp)-altered because the original mineral 

constituents—rich in calcium, sodium, magnesium, and iron—

were largely stripped of these elements during their transformation to an assemblage dominated by quartz, fine-grained muscovite (sericite), pyrite, and in some instances chlorite. In many 

instances, however, some of the original mineral components 

of the protolith remained partially intact during hydrothermal 

alteration; these include a variety of feldspars and rarely biotite. 

Recent weathering of pyrite in the qsp-altered protolith ultimately results in the formation of sulfuric acid, which initiates a 

cycle called “acid weathering.” Quantitative analyses by X-ray 

diffraction (XRD) document a decrease in chlorite, illite, and 

pyrite ± plagioclase in the altered protolith as acid weathering 

progresses. The loss of these minerals during low-temperature 

weathering is associated with a correlated increase in smectite 

(a clay that swells when wet), kaolinite, and jarosite (formed 

from the alteration of pyrite). A spectacular rock sequence from 

the Straight Creek alteration “scar” (fig. 1D) exemplifies the 

progressive transformation of the altered protolith during the 

acid-weathering process (fig. 3). Scanning Electron Microscopic 

(SEM) observations support our quantitative mineralogical data 

that show an inversely linear decrease in chlorite (89-percent 

reduction) and pyrite (100-percent reduction) in the altered 

Introduction

Numerous studies during the past decade have documented 

the presence of acidic, metal-rich surface and ground waters 

derived from pervasively clay-altered rocks that were stripped 

of their original mineralogic constituents in the geologic past by 

caustic solutions. These hydrothermally altered rocks, called the 

“altered protolith,” contain exceptionally high quantities of finegrained pyrite. Weathering of the pyrite-rich altered protolith 

produces highly acidic water that is largely unbuffered owing to 

the general lack of calcite and other acid-neutralizing minerals. 

Even in the absence of human-induced disturbances such as 

mining or prospecting, waters draining these rocks are highly 

acidic (pH, 2 to 4) and contain aluminum, iron, and sulfate concentrations that far exceed aquatic-life standards.

Prior to our current work, the understanding of acid 

weathering reactions in hydrothermally altered rock has 

been largely based on theoretical models simulating mineral 

reactions. In contrast, our study documents the actual in-situ 

mineralogical response of the pyrite-bearing protolith due to 

attack by low temperature and highly acidic waters. During 

the course of various geoenvironmental investigations by the 

U.S. Geological Survey (USGS), we conducted studies in 

four principal areas (fig. 1) that hosted large expanses (1.7 

by Dana J. Bove, Heather A. Lowers, Geoff S. Plumlee, and Philip L. Verplanck
A B

C D

pH, IN STANDARD UNITS

0

100

10

1

0.10

0.01

0

2 4 6 8 10

Cu+Pbf+Zn,

IN MILLIGRAMS PER LITER

15

Figure 1. Large areas of hydrothermally altered rock in the four study areas. (A) Webster Pass, near Keystone, Colorado; (B) Prospect 

Gulch in the headwaters of the upper Animas River, near Silverton, Colorado; (C) Alum Creek, a tributary to the Alamosa River, near 

Summitville, Colorado; and (D) Straight Creek, near Questa, northern New Mexico. 

Figure 2. Plot of pH relative to sum of dissolved copper (Cu), lead 

(Pb), and zinc (Zn) for stream and spring samples in the four study 

areas. Data from Mast and others (2000); Verplanck and others 

(2006, 2007).

protolith with an increase in smectite ± kaolinite (fig. 4). 

Decreases in illite (32-percent reduction) and plagioclase 

feldspar (26-percent reduction) from altered protolith to the 

final weathering products are still considerable but have a less 

linear relationship with respect to increasing smectite (fig. 4). 

SEM textures and clay XRD studies suggest that smectite grew 

largely as newly formed crystals (fig. 5A). The precipitated 

smectite derived its elemental components from the concurrent 

dissolution of chlorite, illite, and plagioclase (fig. 5B–D). However, SEM data and mapping of elements by electron microprobe show zones of reaction around illite grains with a loss of 

potassium, magnesium, and iron. These reacted zones show the 

original illite crystal shapes, but chemical analyses suggest that 

some of the illite has been altered to smectite. Smectite and kaolinite are always the latest clays formed in the weathered rocks, 

and smectite always postdates kaolinite.
A

C

D

E

2025 15 10 5 0

A

C

D

E

SAMPLESAMPLESAMPLE

SAMPLESAMPLESAMPLE

Illite

A

C

D

E

A

C

D

E

A

C

D

E

A

C

D

E

4 3 2 1 0 14 681012 4 2 0

Smectite + Kaolinite

A

C

D

E

681012 4 2 0

Jarosite

16 12 8 4 0

Plagioclase

16 12 048

WEIGHT PERCENT WEIGHT PERCENT WEIGHT PERCENT

WEIGHT PERCENT WEIGHT PERCENT WEIGHT PERCENT

Chlorite

Pyrite

Chapter C

16 Understanding Contaminants Associated with Mineral Deposits

Figure 3. Acid-weathering sample sequence from a 

steeply incised gulley in Straight Creek, New Mexico. 

Sample A represents the quartz-sericite-pyrite-altered 

protolith that is relatively unaffected by low temperature 

weathering. Acid weathering increases upward from 

samples A through E. Quantitative XRD results from 

samples A, C, D, and E are presented in figure 4. Note 

shovel for scale in photograph on the right near sample 

site C. Scale bars on the left represent 2.5 centimeters. 

Figure modified from Ludington and others (2004).

Figure 4. Quantitative XRD mineral analyses in weight percent for samples A, C, D, and E from the Straight Creek sequence 

(see figure 3). Methodology for XRD quantitative analyses described in Eberl (2003).
Smectite

S

Smectite

Chlorite

Plagioclase

Smectite

Plagioclase

A B

C D

Illite

Sm

Sm

Kaol

20 MICRONS 20 MICRONS

20 MICRONS 100 MICRONS

Chapter C

Chapter C: In-Situ Acid Weathering Reactions in the Southern Rocky Mountains 17

Simple reactions written from our data suggest that the 

weathering of pyrite forms goethite (iron hydroxide), which 

generates acidity that further drives the weathering reaction. 

Minerals in the altered protolith then react with the acid. 

Where the water is most acidic, kaolinite is formed. As fluids 

become less acidic and probably accumulate more solutes, 

smectite is formed. The more permeable pathways in the rock 

may conduct acidic waters and promote kaolinite formation. In 

low-permeability regions where solutions reside for a longer 

time, chlorite dissolution may locally increase the pH and 

cation concentrations, promoting smectite precipitation. 

Figure 5. Scanning electron microscope photographs of samples 

from several study areas showing neoformed smectite morphology 

(A) and smectite that formed from the dissolution of chlorite (B), 

plagioclase (C), and illite and plagioclase (D). Note the opening of 

illite due to smectite alteration in figure B.

References Cited

Bove, D.J., Wilson, A.B., Barry, T.H., Hon, K., Kurtz, J., 

VanLoenen, R.E., and Calkin, W.S., 1996, Geology, alteration, 

and rock and water chemistry of the Iron, Alum, and Bitter 

Creek areas, upper Alamosa River, southwestern Colorado: 

U.S. Geological Survey Open-File Report 96–039, 34 p.

Bove, D.J., Mast, M.A., Dalton, J.B., Wright, W.G., and 

Yager, D.B., 2007, Major styles of mineralization and 

hydrothermal alteration and related solid- and aqueousphase geochemical signatures, chap. E3, in Church, S.E., 

von Guerard, Paul, and Finger, S.E., eds., Integrated 

investigations of environmental effects of historical mining 

in the Animas River watershed, San Juan County, Colorado: U.S. Geological Survey Professional Paper 1651, 

p. 161–230.

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 

Handcart Gulch, Colorado—An alpine watershed affected 

by metalliferous hydrothermal alteration: U.S. Geological 

Survey Open-File Report 2006–1189, 15 p.

Eberl, D.D., 2003 User guide to RockJock—A program for determining quantitative mineralogy from X-ray diffraction data: 

U.S. Geological Survey Open-File Report 2003–78, 36 p.

Ludington, S., Plumlee, G.S., Caine, J.S., Bove, D., Holloway, 

J.M., and Livo, K.E., 2004, Questa baseline and pre-mining 

ground-water quality investigation 10. Geologic influences on ground and surface waters in the lower Red River 

watershed, New Mexico: U.S. Geological Survey Scientific 

Investigations Report 2004–5245, 41 p.

Mast, M.A., Evans, J.B., Leib, K.J., and Wright, W.G., 2000, 

Hydrologic and water-quality data at selected sites in the upper 

Animas River watershed, southwestern Colorado, 1997–99: 

U.S. Geological Survey Open-File Report 2000–53, 20 p.

Verplanck, P.L., McCleskey, R.B., and Nordstrom, D.K., 

2006, Questa baseline and pre-mining ground-water quality 

investigation. 20. Water chemistry of the Red River and 

selected seeps, tributaries, and precipitation, Taos County, 

New Mexico 2000–2004: U.S. Geological Survey Scientific 

Investigations Report 2006–5028, 139 p.

Verplanck, P.L., Manning, A.H., Kimball, B.A., McCleskey, 

R.B., Runkel, R.L., Caine, J.S., Adams, Monique, 

Gemery-Hill, P.A., and Fey, D.L., 2007, Ground- and 

surface-water chemistry of Handcart Gulch, Park County, 

Colorado, 2003–2006: U.S. Geological Survey Open-File 

Report 2007–1020, 31 p.

Conclusions and Implications

Although this study focuses on acidic rock weathering in 

natural settings, highly pyritic and altered rock of a very similar 

character typically compose a large portion of the material in 

mine-waste piles. Based on our studies, we suggest that mine 

waste that contains hydrothermally altered wall rock with abundant pyrite may undergo similar reactions and form smectite. Mine 

dump instability, a common problem on very steep slopes, may be 

exacerbated by the production of this highly swelling clay. 
18 Chapter D: Bacterial Processes Can Influence the Movement of Metal 

Contaminants in Wetlands that Have Been Affected by Acid Drainage

Background

Many bacteria that live and bring about chemical changes 

in acid drainage environments are known as lithotrophs (“rockeaters”). These microbes utilize just a few inorganic compounds 

or elements for energy or growth. Iron-oxidizing bacteria obtain 

energy by oxidizing ferrous iron (Fe2+) to ferric iron (Fe3+). 

The best-known lithotrophic iron oxidizer, Acidithiobacillus 

ferrooxidans, thrives in acidic (low pH) environments.

Bacteria that use organic compounds for energy or 

growth are known as heterotrophs (“diverse eaters”). Important 

heterotrophs are sulfate reducers that use sulfate (SO4

2–), rather 

than oxygen as most bacteria do, to aid their decomposition of 

organic matter. The end product of this decomposition, sulfide 

(S2–), is produced almost exclusively by sulfate-reducing bacteria (Widdell, 1988). Sulfide reacts to form H2

S(g) (hydrogen 

sulfide gas), the compound that produces the odor of rotten 

eggs. The best-known sulfate-reducing bacteria are in the 

genus Desulfovibrio, but many other sulfate reducers are present in nature (Widdell, 1988; Ehrlich, 1990).

Bacterial processes involving iron and sulfate can be 

especially important in depositional sites such as wetlands that 

receive acid drainage. Sulfate is present in high concentration 

in acid drainage because of the oxidation of sulfide minerals. 

High sulfate and abundant organic matter promote sulfatereducer growth (which in turn supports near-neutral [7.0] pH 

values). Sulfate reduction permits chemically reducing conditions to develop and persist in water-saturated, oxygen-poor 

portions of the sediment. Other areas of the sediment, such as 

areas at or near the surface, remain oxygenated. Thus, wetlands can have chemically reducing and chemically oxidizing 

zones in close proximity. In general, reducing conditions tend 

to immobilize metals and prevent them from moving in the 

surface-water/ground-water system, whereas oxidizing conditions tend to mobilize metals and allow them to move in the 

surface-water/ground-water system. The mobility of metals is 

important because metals usually are the source of toxicity in 

acid drainage.

Four of the most prominent metals in acid drainage are 

iron (Fe), copper (Cu), lead (Pb), and zinc (Zn). Under suitable 

geochemical conditions, aqueous sulfide produced by Desulfovibrio reacts with a dissolved metal to form a solid precipitate, 

for example, Pb2+ + S2– → PbS(solid). Amorphous iron sulfide 

(FeS(am)), the most common metal-sulfide precipitate (Davison 

and others, 1992), is not soluble in waters of near-neutral pH 

(7.0) but tends to dissolve at about pH 5.0 or less (Pankow and 

Morgan, 1980). When iron-sulfide precipitates are dissolved in 

strong hydrochloric acid (6N HCl), they produce H2

S gas and 

hence are called “acid-volatile sulfide” (Berner, 1970); other 

strong HCl-soluble sulfides that might be present include Cu2

S 

(chalcocite), PbS (galena), and ZnS (sphalerite). Metal-sulfide 

precipitates formed by bacterial sulfide production are called 

“secondary” sulfides, whereas “primary” sulfides are those 

that are present in ore deposits.

Analytical Methods

The chemical composition of the natural sulfides 

and number of associated sulfate-reducing bacteria were determined from samples collected at the Forest Queen mine wetland 

near Silverton, Colorado (fig. 1). Details of the sampling, 

geochemistry, sedimentology, and hydrology of this site can be 

found in Stanton (2000) and Pavlik and others (1999).

Iron-sulfide-rich, black solids were present at depths to 

3 meters in a matrix of silt and fine-grained sand or associated 

with organic matter. Orange-red iron oxides were present at 

the surface (fig. 2) and in the uppermost sections (0 to 60 cm 

depth) of the sediment column.

Complete separation of the black metal sulfides from 

other materials was not possible, and some samples contained 

an estimated 20–30 wt. % (weight percent) of silicate minerals 

(silt, sand, clay), plus traces of organic matter. The iron sulfides are in a complex matrix, but it is likely that the trapping 

of most metals had occurred because of the reducing (sulfidic) 

nature of the sediments. Filtered water samples were analyzed 

onsite to define the geochemical conditions under which the 

bacteria were living (fig. 3).

Overview

Two important bacterial processes that can 

affect the removal (precipitation) or release (solubilization) of metal contaminants in wetlands affected 

by acid drainage are sulfate reduction resulting in 

metal-sulfide precipitation and bacterial iron oxidation potentially resulting in sulfide mineral dissolution. These processes were studied under natural and 

laboratory conditions by (1) characterizing metalsulfide precipitates that formed in wetland sediments 

(“natural” sulfides) for total metal, acid-extractable 

metal, and total sulfide concentrations, and by number of sulfate-reducing bacteria, and (2) examining 

the potential function of iron-oxidizing bacteria in 

the release of metals from sulfide-bearing materials, specifically, fine-grained zinc sulfide (sphalerite, 

ZnS). The results confirm the importance of bacterial 

sulfate reduction as an agent for removal of metals as 

sulfide precipitates; the results also confirm that bacterial oxidation of iron in ZnS does not appear to greatly 

enhance ZnS dissolution over periods of several weeks.

by Mark R. Stanton
COLORADO

Denver

Durango

Silverton

Grand

Junction

Mineral

Creek

Silverton

Animas

River

Canyon

Forest Queen

Wetland

Animas

River

N

19

The flowchart in figure 3 shows the procedures applied 

in this study. Water analyses included pH, dissolved oxygen (DO), specific conductivity (SpC), alkalinity, temperature, total iron (Fe[tot]), ferrous iron (Fe2+), and ferric iron 

(Fe3+ = Fe[tot] – Fe2+). Slight modifications of the acid 

volatile sulfide method described by Tuttle and others (1986) 

and Rice and others (1993) were made. Sulfide recovered 

from the strong acid (6N HCl) leach is reported as parts per 

million (ppm) total sulfide (S2–

(tot)). Major and trace-element 

aqueous concentrations from the strong acid leach and dissolution experiments were obtained using atomic emission 

(Briggs, 2002) or mass spectrometric (Lamothe and others, 

2002) methods, respectively (fig. 3). Metal concentrations are 

reported as parts per million in the solids and as micrograms 

or milligrams per liter (μg/L or mg/L) in the solutions. X-ray 

diffraction was used to evaluate the crystallinity of the natural 

sulfides and to characterize the mineralogy of the sulfides and 

reactant sphalerite.

Quantification of the sulfate-reducing bacteria in the 

natural sulfides was undertaken to see if there was any relation 

between the numbers of cells and the chemical composition 

(metals, sulfide). Similarly, numbers of iron oxidizers in the 

dissolution experiments were obtained to see if the ZnS dissolution rate was related to cell numbers. Methods to quantify 

the numbers of the sulfate-reducing and iron-oxidizing bacteria are based on standard microbiological culturing and staining techniques (Gerhardt and others, 1994; Atlas, 1995). The 

number of bacterial colonies grown on agar plates (or sometimes in liquid medium), adjusted by the appropriate dilution 

or concentration factor, produces the final number of cells in 

the original sample (cells per gram or cells per milliliter).

Figure 1. Location map of Forest Queen mine 

wetland, near Silverton, Colorado. (Topographic 

image from Douglas Yager, U.S. Geological Survey.)

Figure 2. Forest Queen mine wetland (before remediation; 

looking north) showing the inflow of iron-bearing acid drainage. 

Core samples were collected in the green area between the red 

solids and road (top of picture).

Experimental Dissolution 

of ZnS: Abiotic and Biotic 

Reactions

The sphalerite was powdered to an average 

particle size of approximately 10 μm (Stanton and 

others, 2008). This grain size is among the smallest mineral particle sizes that might be present in 

the wetland sediments, except for clays. The ZnS 

contained 6.7 wt.% Fe, 380 ppm Cu, 1,400 ppm 

Pb, and 61.8 wt.% Zn.

The Acidithiobacillus bacteria (maintained 

in culture medium at pH 4.5) and prepared ZnS were added to 

the acid solution (pH ≤ 4.0, 25°C) to begin the reaction. Three 

abiotic experiments (no bacteria) at starting pH values of pH 2, 

3.3, and 4 were performed; a similar set of three experiments 

was run in the presence of the iron-oxidizing bacteria (biotic). 

All experiments were open to the air and used a high rate of 

stirring to permit oxygenation; most were maintained at constant 

pH by adding 0.1 N HCl as needed. Filtered samples for metal 

analysis were taken at about 48-hour intervals over a 2–3-week 

period; plate count samples were taken at approximately 

100-hour intervals.
(1) NATURAL SULFIDE SAMPLES

Wetland core samples

Water chemistry data:

pH, DO, SpC, Temp (C),

Alkalinity, Fe(tot), Fe2+, Fe3+

Black FeS Solids

Number of

sulfate-reducing

bacteria

(a)

Mineralogical

(X-ray) analysis

Acid volatile

sulfide analysis

Filtration

Metal analysis:

ICP–AES

(3) BACTERIAL NUMBERS

(a) Natural sulfide sediment or

(b) Sphalerite inoculum or

(c) Reaction mixture

Serial dilution (as needed)

Sulfate-reducing medium,

agar plates

Iron-oxidizing medium,

agar plates

Count number of colonies

at 5-day intervals for

up to 3 months

Apply correction factor

for dilution (or concentration)

(2) SPHALERITE DISSOLUTION

Number of

iron-oxidizing

bacteria

(b)

Reaction vessel:

Powdered sphalerite (ZnS)

and iron-oxidizing bacteria

Filtration

Number of

iron-oxidizing

bacteria

Metal analysis:

ICP–MS

(c)

Chapter D

20 Understanding Contaminants Associated with Mineral Deposits

Figure 3. Flowchart showing the major sample treatment and analysis procedures used in this study.
EXPLANATION

0.01

0.1

1

10

100

1,000

10,000

0 50 100 150 200 250 300 350 400 450 500

TOTAL SULFIDE [S2–

(tot)], IN PARTS PER MILLION

CONCENTRATION OF METALS LEACHED,

IN MILLIGRAMS PER LITER

Zinc

Sulfate-reducing

bacteria, cells/gram

Iron

Copper

Lead

10

100

1,000

CONCENTRATION, IN PERTS PER MILLION

OR IN MILLIGRAMS PER LITER

0 50 100 150 200 250 300 350 400 450 500

TOTAL SULFIDE [S2–

(tot)], IN PARTS PER MILLION

1

Iron, milligrams per liter

Silicon, parts per million

Chapter D

Chapter D: Bacterial Processes Can Influence the Movement of Metal Contaminants 21

Results and Discussion 

of Bacterial Studies

Natural Metal Sulfides

Acid-extractable metal concentrations and bacterial numbers 

in the natural iron sulfides showed little relation to each other or 

to total sulfide (fig. 4). The sulfides had a wide range of metal 

concentrations but generally low numbers of sulfate-reducing 

bacteria; in fact, 8 of the 20 samples produced no viable bacteria. 

The plate counts translate to cell numbers from zero up to about 

3,000 per gram.

High values of total sulfide are not always found in 

samples with high metal concentrations (whether total or acidextractable metals), and low values of total sulfide may have 

high metal concentrations (fig. 4). Strong HCl-extractable metal 

content is high even in samples containing less than 100 ppm 

S2–

(tot). Acid-extractable iron ranges from 10 to 100 times higher 

than total sulfide recovered. The metal-sulfide precipitates do 

not appear to amass metals in a consistent, predictable manner.

One likely reason for high metal content in samples lacking 

sulfide is that metals are sorbed onto silicates or undetectable 

(X-ray amorphous) ferric oxides. Solid-phase silica (Si) exhibits 

a pattern similar to leachable iron with respect to sulfide (fig. 5), 

suggesting metals are also bound by silicates within the sediment. 

The amount of metal associated specifically with the sulfide or 

silicate phase is unknown because of sample heterogeneity.

Figure 4. Acid-extractable (6N HCl) metal and numbers of sulfatereducing bacteria plotted relative to total sulfide concentrations 

from natural sulfide samples.

Figure 5. Solid-phase silica (Si), acid-extractable iron (Fe), and 

total sulfide concentrations from natural sulfide samples indicating 

the likelihood of metal being adsorbed onto silicate phases.

Another possible reason for the poor correspondence of 

metals and sulfide is that accumulation and enrichment of metals 

might occur over time. As ground or surface water move through 

the sediment column, preexisting metal sulfides may be able to 

adsorb more metals in concentrations greater than would be predicted on an ideal 1:1 ratio of metal to sulfide (for example, Fe:S).

Some sediments had low values of metals except iron, 

indicating there had been little or no copper, lead, and zinc 

available. Lack of a metal source, or location away from 

a metal source and flow path, is a potential reason for the 

samples having lower metal contents. Competition for metals 

by silicates or organic matter along a flow path might also 

contribute to low metal values in some sulfides.

Only slight differences in crystallinity were observed 

among the natural sulfides in that some had X-ray reflections 

indicative of a poorly crystalline FeS phase (possibly mackinawite); no other sulfides were detected. Pyrrhotite, a crystalline 

form of FeS, was found in trace amounts in the reactant ZnS.

Metal Release During Abiotic 

and Biotic ZnS Dissolution

The initial release of all metals in the biotic run was 

slightly higher than in the abiotic run, suggesting perhaps a 

slight increase in the ZnS dissolution rate by bacteria. Soluble 

total iron was slightly higher at all sampled intervals (fig. 6A), 

indicating the preference of iron oxidizers to release this 

metal. However, there was little change in metals released in 

the presence of iron-oxidizing microbes after about 48 hours 

(fig. 6A). The plot for zinc (fig. 6B) confirms that there was 

only minor variation between the abiotic and biotic reactions.
10

100

1,000

10,000

100,000

1,000,000 CONCENTRATION, IN MICROGRAMS PER LITER

0 25 50 75 100 125 150 175 200 225

TIME, IN HOURS

Open = Abiotic

Filled = Biotic

Iron

Copper

Lead

Zinc

A

0

20,000

40,000

60,000

80,000

100,000

120,000

140,000

ZINC, IN MICROGRAMS PER LITER, ABIOTIC

0 20,000 40,000 60,000 80,000 100,000 120,000 140,000

ZINC, IN MICROGRAMS PER LITER, BIOTIC

r

2 = 0.98

B

Chapter D

22 Understanding Contaminants Associated with Mineral Deposits

Figure 6. (A) Metal concentrations from acidic dissolution of 

zinc sulfide in the absence (abiotic) and presence (biotic) of ironoxidizing bacteria (initial pH = 3.3). (B) Plot of zinc concentrations 

from the same abiotic and biotic zinc sulfide dissolution 

experiments shown in figure 6A.

The (ferric) iron concentration during the reaction 

apparently was not sufficient to promote faster decomposition through ferric iron oxidation (Perez and Dutrizac, 1991; 

de Giudici and others, 2002). Ferric iron did not become significant (that is, equal to the ferrous concentration) until about 

100 hours of reaction time, and despite high oxygenation, the 

ferric iron and bacteria did not seem to accelerate the rate of 

dissolution of sphalerite during the time of the experiment. 

The bacteria may have enhanced the release of iron from pyrrhotite in the sphalerite, which might explain the higher total 

iron concentrations with little increase in other metals.

The results are in agreement with Fowler and Crundwell 

(1998), who noted that there were no direct microbial mechanisms involved in the short-term dissolution of ZnS. However, 

if the microbes were allowed sufficient time to produce significant quantities of ferric iron, perhaps they could enhance the 

rate of ZnS dissolution (Weisener and others, 2003) because 

Fe3+ is a known strong oxidant of ZnS (Rimstidt and others, 

1994; Perez and Dutrizac, 1991). The fact that metal concentrations did not vary between the two types of experiments 

suggests the iron-oxidizing bacteria were incapable of directly 

solubilizing metals from the ZnS structure (at least in the 

time period of these experiments). The results with ZnS are 

in contrast to what is known about the important function of 

iron-oxidizing bacteria in the decomposition of pyrite (Berner, 

1970; Nordstrom and Southam, 1997).

Plate counts indicated some difficulty in bacterial growth 

and viability during the reaction because cell numbers declined 

with increasing reaction time. The cells had been grown in a 

chemically defined medium prior to addition to the vessel and 

likely were unable to quickly adapt to the abrupt change of 

growing in a medium devoid of several nutrients. Thus, the cells 

were probably less viable at longer reaction times. Although the 

bacteria did not greatly accelerate the acid dissolution of ZnS, 

there were indications they may have done this in the earliest 

stages (0–48 hours) when their viability was highest.

Conclusions

In organic-rich, reducing sediments, many trace metals 

can be immobilized by precipitation as acid volatile sulfide; 

thus, bacteria that produce sulfide are geochemical agents in 

acid drainage environments. Relatively high concentrations of 

metal can be associated with the natural sulfides. However, the 

results indicate metal-sulfide formation is a process controlled 

primarily by inorganic (abiotic) geochemical factors and is not 

directly mediated by sulfate-reducing bacteria. Total sulfide 

and metal concentrations were independent of the sulfatereducing bacteria cell numbers. One reason for this may be 

that in the natural samples, the bacteria are not continuously 

active or are active at different times. A sulfate-reducing bacterial population may be inactive (dormant) or perhaps absent 

from one precipitate for many reasons (exhaustion of nutrients, 

and so forth); cell numbers might vary greatly from an active 

population in another precipitate.
Chapter D

Chapter D: Bacterial Processes Can Influence the Movement of Metal Contaminants 23

The metal sulfides are neither crystalline nor formed in 

proportions according to ideal chemical formulas. Aging of 

the natural sulfides rather than any direct microbial action 

likely is the dominant process for the FeS precipitates to 

become increasingly crystalline and exhibit ideal ratios of 

metal to sulfide. The enclosing sediments are young (less than 

12,000 years before present; Stanton, 2000) and the sulfides 

have not had time to crystallize into more-ordered phases. 

Most of the metal leached from the sediment was probably 

immobilized as a result of the reducing conditions established 

by the sulfide, but the amount of metals associated with the 

silicates was not determined. And as noted earlier, the source 

location and transport of dissolved metals can influence the 

metal content of the sulfide precipitates.

Iron-oxidizing bacteria may have the potential to release 

metals during oxidative decomposition of ZnS, but the experimental results were not conclusive because of limited reaction 

time. Longer term experiments are likely needed to determine if bacterially mediated iron oxidation can contribute to 

enhanced dissolution of ZnS.

References Cited

Atlas, R.M., 1995, Handbook of media for environmental 

microbiology: Boca Raton, Fla., CRC Press, 540 p.

Berner, R.A., 1970, Sedimentary pyrite formation: American 

Journal of Science, v. 268, p. 1–23.

Briggs, P.H., 2002, The determination of forty elements in 

geological and botanical samples by inductively coupled 

plasma–atomic emission spectrometry, in Taggart, J.E., Jr., 

ed., Analytical methods for chemical analysis of geologic 

and other materials: U.S. Geological Survey Open-File 

Report 2002–0223–F, p. F1–F11.

Davison, W., Grime, G.W., and Woof, C., 1992, Characterization 

of lacustrine iron sulfide particles with proton-induced x-ray 

emission: Limnology and Oceanography, v. 37, p. 1770–1777.

de Giudici, Giovanni, Voltolini, Marco, and Moret, Massimo, 

2002, Microscopic surface processes observed during the 

oxidative dissolution of sphalerite: European Journal of 

Mineralogy, v. 14, p. 757–762.

Ehrlich, H.L., 1990, Geomicrobiology: New York, Marcel 

Dekker, Inc., 646 p.

Fowler, T.A., and Crundwell, F.K., 1998, Leaching of zinc 

sulfide by Thiobacillus ferrooxidans—Experiments with 

a controlled redox potential indicate no direct bacterial 

mechanism: Applied and Environmental Microbiology, 

v. 65, p. 3570–3575.

Gerhardt, Philipp, Murray, R.G.E., Wood, W.A., and Krieg, N.R., 

eds., 1994, Methods for general and molecular bacteriology: 

Washington, D.C., American Society for Microbiology, 791 p.

Lamothe, P.L., Meier, A.M., and Wilson, S.A., 2002, The 

determination of forty-four elements in aqueous samples by 

inductively coupled plasma–mass spectrometry, in Taggart, 

J.E., Jr., ed., Analytical methods for chemical analysis of 

geologic and other materials: U.S. Geological Survey OpenFile Report 2002–0223–H, p. H1–H11.

Nordstrom, D.K., and Southam, Gordon, 1997, Geomicrobiology of sulfide oxidation, in Banfield, J.F., and Nealson, 

K.H., eds., Geomicrobiology—Interactions between 

microbes and minerals: Mineralogical Society of America 

Reviews in Mineralogy, v. 345, p. 361–390.

Pankow, J.F., and Morgan, J.J., 1980, Dissolution of tetragonal 

ferrous sulfide (mackinawite) in anoxic aqueous systems; 

2. Implications for the cycling of iron, sulfur, and trace metals: 

Environmental Science and Technology, v. 14, p. 183–186.

Pavlik, M.C., Kolm, K.E., Winkler, S., Emerick, J., Wildeman, 

T.R., and Robinson, Rob, 1999, Hydrogeologic controls 

on the geochemical function of the Forest Queen wetland, 

Colorado—Proceedings of 6th International Conference on 

Tailings and Mine Waste, Fort Collins, Colo., January 1999: 

Rotterdam, Balkema, p. 647–655.

Perez, I.P., and Dutrizac, J.E., 1991, The effect of iron content 

of sphalerite on its rate of dissolution in ferric sulphate and 

ferric chloride media: Hydrometallurgy, v. 26, p. 211–232.

Rice, C.A., Tuttle, M.L., and Reynolds, R.L., 1993, The analysis 

of forms of sulfur in ancient sediments and sedimentary 

rocks—Comments and cautions: Chemical Geology, v. 107, 

p. 83–95.

Rimstidt, J.D., Chermak, J.A., and Gagen, P.M., 1994, Reactions of sulfide minerals with Fe(III) in acidic solutions, 

in Alpers, C.N., and Blowes, D.W., eds., Environmental 

geochemistry of sulfide oxidation: ACS Symposium Series, 

American Chemical Society, Washington, D.C., p. 1–13.

Stanton, M.R., 2000, Trace metal and acid-volatile sulfide 

concentrations in sediments from the Forest Queen wetland 

near Silverton, Colorado—Implications for removal of 

metals from acid drainage waters: U.S. Geological Survey 

Open-File Report 2000–115, 43 p.

Stanton, M.R., Gemery-Hill, P.A., Shanks, W.C. III, and 

Taylor, C.D, 2008, Rates of zinc and trace metal release 

from dissolving sphalerite at pH 2.0–4.0: Applied Geochemistry, v. 23, p. 136–147.

Tuttle, M.L., Goldhaber, M.B., and Williamson, D.L., 1986, 

An analytical scheme for determining forms of sulfur in oil 

shale and associated rocks: Talanta, v. 33, p. 953–961.

Weisener, C.G., Smart, R.St.C., and Gerson, A.R., 2003, 

Kinetics and mechanisms of the leaching of low Fe sphalerite: Geochimica et Cosmochimica Acta, v. 67, p. 823–830.

Widdell, Friedrich, 1988, Microbiology and ecology of the 

sulfate- and sulfur-reducing bacteria, in A.J.B. Zehnder, 

ed., Biology of anaerobic microorganisms: New York, 

John Wiley and Sons, p. 469–585.
1 MILLIMETER

24 Chapter E: Simple Screening Tests to Determine the Potential Metal 

Toxicity of Mining-Waste Leachates

Overview

The leaching of metals from mining waste 

remaining after mining operations have ended can 

be toxic to aquatic organisms. Determination of water 

toxicity due to the presence of metals can be experimentally difficult. Standard aquatic toxicity tests also 

are expensive and time intensive. Therefore, development of screening methods that are experimentally 

simpler, cost effective, and more time efficient is 

beneficial. The results of our screening tests indicate 

that replacing the stock culture of a standard test species, Ceriodaphnia dubia, with hatched, dormant eggs 

(ephippia) of that species yields similar results while 

reducing cost, time, and labor required. MetPLATETM, 

which uses bacteria as a test organism, is also a promising screening tool to determine which disturbed sites 

require further investigation.

Introduction

Mine-waste leachates are assumed to be toxic to aquatic 

organisms if the pH value is less than 5 (Ohio River Valley 

Water Sanitation Commission, 1955; Wildeman and others, 

2007), but toxicity is uncertain and must be tested above this 

pH threshold. Standard toxicity testing using Ceriodaphnia 

dubia (C. dubia, a type of water flea) requires maintaining 

a stock culture of the organism, making it time and labor 

intensive. The U.S. Geological Survey (USGS) has compared 

the use of stock C. dubia with the use of C. dubia ephippia, a 

dormant form that is rehydrated within a few days prior to the 

test. The 48-hour C. dubia test is a measure of acute toxicity, 

which is the toxicity determined by the percentage of mortality of the organisms (generally on the order of 20 individuals) 

after a single exposure. Acute toxicity commonly is reported 

as lethal concentration 50 (LC50) or lethal dose 50 (LD50), 

specifically the concentration or dose of a substance where 

50 percent of the organisms die. Both standard C. dubia and 

ephippia-based tests are 48 hours long; however, the standard 

test usually requires long-term maintenance of a culture and 

is thus expensive to use in the screening of large numbers 

of samples and (or) sites. The USGS has also compared 

the 48-hour C. dubia toxicity test with the enzymatic assay 

MetPLATETM (Bitton and others, 1996) for use as a screening 

tool. MetPLATETM measures the acute toxicity of a substance 

where the endpoint is a sublethal effect such as abnormal 

development, growth, reproduction, behavior, and (or) other 

physiological or biological functions. Since the toxicity is 

based on factors other than mortality, it is reported as effected 

concentration 50 (EC50) or effected dose 50 (ED50), specifically the concentration or dose at which 50 percent of the 

organisms have been adversely affected. The USGS is also 

investigating nonlaboratory methods such as the Biotic Ligand 

Model (BLM) and the Mining Waste Decision Tree (MWDT). 

These methods use water-chemistry parameters, such as hardness, alkalinity, pH, and dissolved organic matter, to predict 

the aquatic metal toxicity and (or) determine potential toxic 

threats to aquatic organisms.

Ceriodaphnia dubia

Ceriodaphnia dubia (water flea) (fig. 1) is a freshwater 

zooplankton that is generally never larger than one millimeter 

(mm) in length. They are used in effluent toxicity testing because 

they are common among vegetation in shallow surface waters 

(that is lakes, ponds, and marshes) throughout most of the world 

(U.S. Environmental Protection Agency, 1993). With regard to 

metal toxicity, C. dubia are a relatively sensitive species. Standard 

U.S. Environmental Protection Agency (USEPA) test conditions 

were followed using both a stock cultured C. dubia and hatched 

C. dubia ephippia. Results of this comparison for copper toxicity 

in a number of simulated test waters are shown in figure 2. The 

Figure 1. Ceriodaphnia dubia (water flea).

by LaDonna M. Choate, James F. Ranville, Eric P. Blumenstein, and Kathleen S. Smith
SAMPLE

PW+Ca

PW+DOC

PW+DOC+Fe

SW(A)

SW(A)+Ca

SW(B)+Ca+Fe

SW+DOC

SW+DOC+Fe

LC50

0

20

40

60

80

100

In-house culture LC50

Ephippia LC50

PW

25

their production of enzyme is inhibited and less of the colored 

substrate is cleaved. The inhibition is determined by color 

(purple) measured as absorbance at 575-nanometer wavelength. Figure 4 is a developed MetPLATETM; columns 1 and 

2 are controls, and columns 3 to 12 are samples. Each sample 

column is an individual sample with varying concentrations 

of a toxic substance, in this case copper. The copper concentration decreases going down the rows from A to H, and the 

inhibition (also referred to as toxicity) decreases with decreasing concentration. The less toxic the sample, the darker the 

color and the higher the absorbance measured. Absorbance is 

used to determine an EC50 for the E. coli. Comparison of this 

EC50 to the LC50 for the C. dubia is presented in figure 5. It can 

be seen from figure 5 that the EC50 for the E. coli is frequently 

higher than the LC50 for either C. dubia, but water-quality 

Figure 2. Lethal concentrations (LC50) of copper (milligrams per 

liter) to Ceriodaphnia dubia for nine water samples: PW (pluton 

water), SW (sedimentary water), and PW or SW amended with Ca 

(calcium), DOC (dissolved organic carbon), and (or) Fe (iron).

simulated test waters PW and SW refer respectively to “pluton 

water,” which is based upon the composition of stream-water 

samples collected from 10 Colorado stream-drainage basins 

underlain by plutonic (intrusive igneous) rocks, and “sedimentary 

water,” which is based upon the composition of stream-water 

samples collected from 13 Colorado stream-drainage basins 

underlain by various sedimentary rocks associated with the 

Maroon and Morrison Formations. Figures 2 and 5 show the 

toxicity results of these simulated test waters amended with Ca 

(calcium), DOC (dissolved organic carbon), Fe (iron), or a combination of these. Figure 2 demonstrates that, for the simulated 

and amended simulated waters, the LC50 for copper varies but the 

results for the use of C. dubia stock culture and hatched ephippia 

are similar.

MetPLATETM

MetPLATETM is an enzymatic bioassay kit where the 

toxicity is determined by the inhibition of the production 

of the enzyme β-galactosidase in Escherichia coli (E. coli) 

(fig. 3). When the E. coli bacteria are not stressed, they produce β-galactosidase, which cleaves the bonds of a colored 

substrate, causing the color of the solution to change. However, when the bacteria are stressed by the presence of metals, 
Negative Control

(column 1)

Samples

(columns 3–12)

DECREASING CONCENTRATION

Empty well

Positive control

(column 2)

DECREASING TOXICITY

Chapter E

26 Understanding Contaminants Associated with Mineral Deposits

Figure 4. A developed 96-well MetPLATETM bioassay, showing negative (toxic) and positive 

(nontoxic) controls and dilution series for several water samples.

trends in the data are the same for both organisms, indicating 

that relative copper toxicity to E. coli also responds to water 

chemistry. Therefore, MetPLATETM could be used as an initial 

screening tool to determine which samples would require more 

extensive toxicity testing and which samples are less toxic.

Figure 3. Escherichia coli (bacteria).

Copyright Shirley Owens, Center for Electron Optics,Michigan State University, 1996.

Other Approaches

Metal bioavailability and toxicity are a function of 

complex water chemistry (Sunda and Guillard, 1976). Historically, scientists have investigated the toxicity of individual metals. More recently the effects of other aqueous 

constituents, due to interactions with the metal and (or) 

organism, have been realized to be significant in metal toxicity. The Biotic Ligand Model is a computational approach 

that incorporates metal speciation and the protective effects 

of other chemicals in the water (Allen, 2002). The Biotic 

Ligand Model can be used to predict the potential toxicity of mining-waste leachates when they are released into 

the environment.

A simple decision tree (Mining Waste Decision Tree, 

MWDT) has been developed that uses simple physical and 

chemical tests to determine whether mine-waste material 

poses a potential toxicity threat to aquatic biota (Wildeman 

and others, 2007). The MWDT makes a distinction between 

leachates or waters with pH less than or greater than 5. The 

MWDT provides an inexpensive and reliable approach for 

preliminary assessment of the potential metal toxicity of 

mine-waste piles.
SAMPLE

PW

PW+Ca

PW+DOC

PW+DOC+Fe

SW(A)

SW(A)+Ca

SW(B)+Ca+Fe

SW+DOC

SW+DOC+Fe

LC50 or EC50

0

20

40

60

80

100

120

In-house culture LC50

Ephippia LC50

MetPLATE EC50

Chapter E

Chapter E: Simple Screening Tests to Determine the Potential Metal Toxicity of Mining-Waste Leachates 27

Figure 5. Lethal concentration (LC50) of copper (milligrams per 

liter) to Ceriodaphnia dubia and effective concentration (EC50) of 

copper (milligrams per liter) to Escherichia coli for nine water 

samples, PW (pluton water), SW (sedimentary water), and PW or 

SW amended with Ca (calcium), DOC (dissolved organic carbon), 

and (or) Fe (iron).

References Cited

Allen, H.E., 2002, The Biotic Ligand Model addresses effects 

of water chemistry on metal toxicity: Fact Sheet on 

Environmental Risk Assessment, no. 7, January 2002, London, 

International Council on Mining and Metals (ICMM), 5 p. 

http://www.icmm.com/document/52 and accessed July 30, 2008.

Bitton, Gabriel, Garland, E., Kong, I-C., Morel, J.L., and 

Koopman, B., 1996, A direct solid-phase assay specific for 

heavy metal toxicity. I. Methodology: Journal of Soil Contamination, v. 5, no. 4, p. 385–394.

Ohio River Valley Water Sanitation Commission, Aquatic 

Life Advisory Committee, 1955, Aquatic life water quality 

criteria: Sewage Industrial Wastes, 27, p. 321–331.

Sunda, W.G., and Guillard, R.R.L., 1976, The relationship 

between cupric ion activity and the toxicity of copper to phytoplankton: Journal of Marine Research, v. 34, p. 511–529.

U.S. Environmental Protection Agency, 1993, Methods for 

measuring the acute toxicity of effluents and receiving 

waters to freshwater and marine organisms: U.S. Environmental Protection Agency /600/4–90/207F.

Wildeman, T.R., Smith, K.S., and Ranville, J.F., 2007, A 

simple scheme to determine potential aquatic metal toxicity from mining wastes: Environmental Forensics, v. 8, 

p. 119–128.
28 Part 2—Basin-Scale Studies of the Sources and Release of Metals

A second focus of this project was to investigate sources, pathways, and fate of metals 

and acidity at the watershed scale. 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. In particular, integration of 

geological, geochemical, and geophysical techniques has led to substantial advances in our understanding of ground-water flow in alpine basins and waste-rock piles.

This section includes a variety of approaches that emphasize the need for understanding 

the factors controlling water quality in mineralized watersheds. Three studies of headwater catchments highlight the integration of geologic, geochemical, and geophysical data to develop conceptual models for the release and transport of metals. Two other studies describe the application 

of airborne geophysical and graphic information system (GIS) techniques to determine watershed 

attributes that may affect water quality.
29
30 Chapter F: Determination of Flow Paths and Metal Loadings from 

Mine Waste Using Geophysical and Geochemical Methods at the 

Waldorf Mine, Clear Creek County, Colorado

Overview

Mine waste, adit drainage, and mill tailings were 

studied at the Waldorf mine to determine water-flow 

paths and their relative contributions to contaminant 

loadings. Water draining from the adit and infiltrating through and under the waste pile, as well as 

shallow ground water flowing through the waste pile 

and through dispersed tailings, have affected nearby 

Leavenworth Creek with toxic metals, notably copper and zinc. The copper and zinc concentrations in 

the creek downstream from the mine-related inputs 

exceed standards for aquatic wildlife. 

Geophysical and geochemical methods were 

applied to study waterflow through the mine waste 

and to assess metal sources and loads to Leavenworth 

Creek. Geophysical conductivity and resistivity 

surveys revealed two probable subsurface waterflow 

paths through the Waldorf mine waste. A geochemical tracer-dilution study delineated where contaminants were coming from, how and where they reached 

the creek, and their effect on water quality in the 

creek. Diversion of the adit drainage from the top to 

around the side of the mine-waste pile did not result 

in improved water quality of the creek.

Introduction

The Waldorf mine is located within the Colorado mineral belt near the Continental Divide in an alpine setting, near 

3,540 meters (11,600 feet) elevation, in Clear Creek County, 

Colorado (fig. 1). Developed in the early part of the 20th century 

to mine polymetallic vein deposits for silver, lead, gold, copper, and zinc, the Waldorf mine is one of many thousands of 

inactive/abandoned hard-rock mines in the Western United States 

(Church and others, 2007) (fig. 2). Adit drainage and groundwater infiltration through waste material affect surface water in 

Leavenworth Creek, about 0.5 kilometer (0.3 mile) away.

Water Infiltration Through Waste Dump

The Waldorf mine and higher elevation, interconnected 

mine workings were drained by the Wilcox Tunnel, which 

is excavated about 1,200 meters (3,900 feet) into McClellan 

Mountain (Lovering, 1935). The drainage exits through a 

collapsed adit at the west end of the Waldorf waste pile; 

in July 2003, the discharge was 8 liters per second. The 

waste pile contains approximately 50,000 metric tons of 

material. There was at one time a 50-ton mill at the mine 

site (Lovering, 1935), and its tailings were dispersed some 

800 meters to the northeast by a ditch; these tailings cover an 

area of about 12 hectares (30 acres) and are up to 1 meter in 

depth (McDougal and Wirt, 2007) (fig. 3). Previous to the first 

year of this study (2002), adit water had discharged across the 

top of the waste pile, where some of it infiltrated and some 

flowed across the face and into a wetland before flowing 

toward Leavenworth Creek.

After the first year’s study, adit drainage was diverted 

through a culvert around the southwest side of the waste 

pile. Water samples from seeps at the toe of the dump were 

collected to see whether any surface drainage had infiltrated 

through the mine waste. A sodium chloride solution added 

to the adit discharge before the diversion traveled 92 meters 

through the dump and was detected at some of the seeps 

within 24 hours (McDougal and Wirt, 2007). However, surface 

infiltration of rainwater and snowmelt appears to be limited 

by a hardened crust, as evidenced by long-standing pools 

(generally lasting days) of water observed on the dump after 

summer rainstorms.

To determine possible waterflow paths, two kinds of 

geophysical techniques were applied to the waste pile, both 

involving the measurement or calculation of apparent conductivity. Electrical conductivity is a property of earth materials that varies with rock type, porosity, and the quality and 

quantity of subsurface water. Higher conductivity generally 

implies poor-quality subsurface water, that is, water with high 

dissolved-solids concentrations (McDougal and Wirt, 2007). 

Thus, higher conductivity zones or trends can be inferred 

as waterflow paths in the waste. An electromagnetic (EM) 

survey based on a grid on the top of the dump yielded a model 

with two horizontal layers, depicting apparent conductivity at 

about 7 and 15 meters below ground surface (fig. 4). Warmer 

colors denote more conductive areas. The surface topography 

of the waste pile is shown above the geophysical layers; the 

EM stations are depicted as dots. The upper layer shows an 

inferred water pathway from points B to B' and B". The outer 

base of the waste pile (B' to B") coincides with a conductive 

zone, which is interpreted as seepage of ground water containing relatively high dissolved-solids concentrations. Chemical 

analyses of water from these seeps confirmed that they are low 

in pH and high in dissolved metals (Fey and Wirt, 2007).

In the second year of the study, after the adit discharge 

was diverted, some seeps continued to issue low-quality water, 

implying that infiltration from the surface of the waste pile 

was not the only source of water, but that shallow ground 

water was infiltrating through the waste pile below the surface 

and (or) mine drainage was flowing down and through the 

dump before exiting the adit. The 15-meter EM layer revealed 

a deeper water pathway, A to A' (fig. 4).

by David L. Fey, Robert R. McDougal, and Laurie Wirt
31

Figure 1. Location map of the Waldorf mine site and surrounding area.

Road

Stream

South Clear Creek

Cont ni ental Div di e

105°47'30" W 105°45' W 105°42' 30" W

39°37'30" N

39°40' N

I-70

FR 248

A R A P A H O N A T I O N A L F O R E S T

A R A P A H O N A T I O N A L F O R E S T

FOREST BOUNDARY (APPROXIMATE)

COLORADO

Study area

 location

Denver

0 1 2 MILES

0 1 2 KILOMETERS

WALDORF 

MINE

Georgetown

Silver Plume

Leavenworth

Creek

Clear Creek

McClellan Mountain

EXPLANATION

39°42'30" N

Utilizing results from the second geophysical technique 

(a resistivity survey), we produced an apparent-conductivity 

model (inverted from resistivity) in four vertical cross sections 

(fig. 5; lines 1 through 4 shown in fig. 4). Connecting the inferred 

conductive zone at depth between lines 1, 2, and 3 (gray arrows 

in fig. 5) showed similar subsurface hydraulic pathways to the 

horizontal conductivity model. Line 4 was located away from the 

toe of the waste pile on a flat, water-saturated former railroad bed. 

The conductive zone shown on the surface of line 4 (fig. 5) indicates conductive water that collects there after issuing from the 

mine-waste pile and before it flows toward Leavenworth Creek. 

Sources, Loads, and Transport

to Leavenworth Creek

To determine the loadings of different chemical constituents to the creek and to locate inflows, whether point surface 

or diffuse ground water, a tracer-dilution study was conducted 

along about 1 kilometer of Leavenworth Creek, beginning 

about 300 meters upstream from where mine-affected water 

enters (Fey and Wirt, 2007). A nonreactive, conservative 

tracer (LiBr) was injected into the creek and allowed to reach 
Chapter F

32 Understanding Contaminants Associated with Mineral Deposits

Figure 2. View of the Waldorf waste pile from south. Collapsed 

adit is at center left margin; drainage visible flowing around lobes 

of waste pile from left to right. Leavenworth Creek is 0.5 kilometer 

off to right.

Figure 3. Photograph of dispersed mill tailings to the northeast 

of the Waldorf mine. These tailings are from a few centimeters to 

more than 1 meter thick. Rainwater runoff, snowmelt, and shallow 

ground water flow down these rills and enter Leavenworth Creek 

near the base of the hill in the center of photograph.

Leavenworth Creek

500 meters

Collapsed adit

Leavenworth

Creek

Hill shown at

arrow 3 in figure 6

in the wetland slope. Downstream about 200 meters, a small 

surface drainage introduces a mix of adit water and shallow 

ground water that has infiltrated through the area of dispersed 

mill tailings (arrow 2 in fig. 6). The concentrations and loads 

of copper and zinc in Leavenworth Creek increased slightly. 

At the end of the study reach, another surface discharge 

introduced mining-affected water. Its geochemical signature indicated that it was almost wholly composed of shallow ground water that had infiltrated downward through a 

large area of the dispersed tailings (arrow 3 in fig. 6). The 

magnitude of the zinc load of this tributary was larger than the 

load issuing at the site of the collapsed adit. There appeared 

to be some loading between sources 2 and 3 by input of 

unsampled diffuse ground water that had infiltrated through 

the area of dispersed tailings (arrow 4 in fig. 6; Fey and 

Wirt, 2007).

Comparing Sources and Loads 

Between Two Years

The purpose of the second year’s efforts was to 

determine whether the diversion of the adit drainage around 

the waste pile had reduced loadings to Leavenworth Creek. 

In the second year of the study, the adit flow, waste-pile 

seeps, and Leavenworth Creek and its inputs were again 

sampled. In place of conducting another tracer study, manual 

steady-state conditions throughout the stream reach. Within a 

short timeframe (about 2 hours), 25 water samples were collected along the length of the reach and from identified surface 

tributaries. The downstream concentration of the tracer varies 

inversely proportionally to the increasing discharge; therefore, 

with a known, measured stream discharge at the beginning of 

the reach, subsequent discharges of the stream can be calculated from the analyzed water samples (Kimball and others, 

2002). The discharges of tributaries are determined by the 

difference of the main stem upstream and downstream from 

each inflow. Unsampled ground-water inflow is determined 

by an increase in main-stem flow where tributaries are absent. 

The loads of various constituents (for example, copper, zinc, 

and sulfate) at every sampling point are calculated by multiplying discharge by measured concentration, giving the mass 

per day flowing past a given point. This calculation results in a 

loading profile, from which one can identify the locations both 

of surface and subsurface inputs.

At about 300 meters downstream from the uppermost 

site, the pH of the creek decreased and specific conductance increased, as did the concentrations of deposit-related 

constituents (for example, copper, lead, zinc, cadmium, and 

sulfate) due to the input of the surface drainage, which flows 

about 0.5 kilometer downslope from the mine site (arrow 1 

in fig. 6). Comparing the loads of the adit with the loads of 

Leavenworth Creek just downstream from the mine-drainage 

input showed attenuation along the path from the waste 

pile (about 75 percent for copper and zinc), implying that 

some of the dissolved constituents were being sequestered 
Chapter F

Chapter F: Determination of Flow Paths and Metal Loadings from Mine Waste 33

measurements were made along the creek to determine discharge. The discharge of Leavenworth Creek was substantially 

higher in 2003 than in 2002 due to increased precipitation and 

snowpack of the previous winter (Fey and Wirt, 2007). The 

discharge of Leavenworth Creek at the most upstream part of 

the study reach was 100 liters per second in 2003 and 14 liters 

per second in 2002. Tributary inflows also were higher by 

varying amounts. The result of these different conditions is 

that any potential relative reduction of loading from the adit 

discharge was masked by increased discharges of all sources. 

The loadings of Leavenworth Creek at the downstream part 

of the study reach were all higher than the previous year, and 

the percent contributions of loadings from the adit discharge 

were also actually higher in 2003. This latter finding may 

have resulted from the dispersed mill tailings having been 

flushed of soluble salts during the wetter spring of 2003, 

yielding lower relative loadings from them (and higher relative 

loadings from the adit discharge) compared to the previous 

year (Fey and Wirt, 2007). Figure 7 shows these results in a 

graphical representation.

0

2

4

6

8

10

12

14

16

18

20

22

24

26

28

30

32

34

36

B"

Digital Elevation

Model

CONDUCTIVITY,

IN MILLISIEMENS

PER METER

Adit

A

A'

Flow path A

Flow path B B

B'

A

C

D

Seeps EXPLANATION

Line 1

Line 3

Line 2

Line 4

Vertical magnetic

Dipole (about 

15 meter depth)

Horizontal magnetic

Dipole (about 

7.5 meter depth) 

Figure 4. Digital Elevation Model of the waste-pile surface (top), 

Horizontal Magnetic Dipole conductivity contour map (middle), 

and Vertical Magnetic Dipole conductivity contour map (bottom).

Figure 5. Conductivity profiles converted from DC resistivity profiles. Flow paths A and B 

refer to same in figure 4.

Line distance, in meters

3,520

3,530

3,540

3,515

3,525

3,505

3,515

Southwest

ADIT

Northeast

CONDUCTIVITY,

IN MILLISIEMENS

PER METER

Line 1

Line 2

Line 3

Line 4

Flow path A Flow path B

ELEVATION, 

IN METERS

ELEVATION, 

IN METERS

Line distance, in meters

Line distance, in meters 

Line distance, in meters 

3,510

3,520

3,530

ELEVATION, 

IN METERS

ELEVATION,

 IN METERS

0 10 20 30 40 50 60 70 80 90 100 110 120 130 140

0 10 20 30 40 60 70 80 90 100 110 120 50

0 10 20 30 40 50 60 70 80 90 100 110 130 140 120

0 10 20 30 40 50 60 70 80 90 100 110 120

0

2

4

6

8

10

12

14

16

18

20

22

24

26

28

30

32

34

36

38

40

42

44

46

48

50

EXPLANATION
Chapter F

34 Understanding Contaminants Associated with Mineral Deposits

Figure 6. Aerial photograph of the Waldorf 

mine and Leavenworth Creek area. Arrows 

indicate surface flow of affected water. 

Affected shallow ground water enters creek 

between (2) and (3). Arrow (3) is location of the 

hill in figure 3.

Figure 7. Pie charts illustrating relative contributions of zinc and copper to Leavenworth Creek in 2002 and 2003. Note higher loads

in 2003 compared to 2002.

Metal Concentrations and Comparison 

to Aquatic-Life Standards

Elevated concentrations of certain metals in stream water 

can adversely affect fish health and (or) potentially contaminate 

their food sources. Copper is toxic to fish, and zinc and cadmium 

are toxic to the benthic macroinvertebrates (caddisflies and mayflies). Acute and chronic aquatic-life toxicity standards, developed by the U.S. Environmental Protection Agency (USEPA), 

can be calculated based on hardness (calcium and magnesium 

content) of site water (Colorado Department of Public Health and 

Environment [CDPHE], 2007) and compared with site traceelement concentrations. Such standards have been developed for 

copper, zinc, nickel, lead, cadmium, and manganese. In this study, 

copper and zinc proved to exceed the standards at numerous sites.

Table 1 shows copper and zinc concentrations for six different sampling sites and 

the calculated chronic and acute toxicity 

standards. Upstream from the study reach, 

the copper concentration in Leavenworth 

Creek water is only at about 25 percent of 

the standards. The zinc concentration is 

already near the acute and chronic limits 

(about 85 percent). This may be due to an 

elevated background of this deposit-related 

element in rock and soil. Not surprisingly, the mine drainage that enters the creek from the wetland (TR–295) greatly 

exceeds the standards (6–10 times for copper and 12–14 times 

for zinc). As a result, Leavenworth Creek water (LC–325) 

reaches the toxicity standard for copper and exceeds the zinc 

standard by a factor of 4 just downstream from this drainage.

At the most downstream part of the study reach, 

600 meters downstream from the first mine inputs, additional 

inputs from the sources previously discussed maintain the 

copper concentrations near the chronic and acute standards 

and increase the zinc concentration by a factor of six over the 

zinc standards. The copper concentration is diluted/attenuated 

to below standards at the mouth of Leavenworth Creek where 

it enters South Fork Clear Creek, 7 kilometers downstream. 

The zinc concentration at the mouth, however, is still at twice 

the chronic and acute standards.

0 500 METERS

0 500 1,000 1,500 FEET

N

Dispersed mill tailings

Waldorf adit 2002 flow path

2003 flow path

Dispersed mill tailings

seeps

Leavenworth Creek

Tracer study

sampling sites

Waste pile

1

2

3

4

2002 2002

2003 2003

ZINC COPPER

Leaching

of mill tailings

65 percent

Leaching

of mill tailings

21 percent

Adit drainage/waste

pile leaching

25 percent

Adit drainage/waste

pile leaching

54 percent

Adit drainage/waste

pile leaching

69 percent

Leaching

of mill tailings

28 percent

Mix

33 percent

Mix

18 percent

Cumulative inflow load, 2,100 grams per day Cumulative inflow load, 33 grams per day

Cumulative inflow load, 3,300 grams per day Cumulative inflow load, 105 grams per day

Mix

25 percent

Mix

10 percent

Leaching

of mill tailings

13 percent Adit drainage/waste

pile leaching

39 percent

A B
Chapter F

Chapter F: Determination of Flow Paths and Metal Loadings from Mine Waste 35

Conclusions

Geophysical and geochemical tools were used to identify 

ground-water flow paths and sources of metals and acidity to 

a receiving stream from a mine site. Integrating results from 

various techniques was essential in determining the hydrogeochemistry at this complex site. Adit water from the Waldorf 

mine flows around, under, and through the waste pile and enters 

Leavenworth Creek. Ground water also flows through dispersed 

mill tailings and into the creek. Concentrations of copper and zinc 

exceed aquatic-life standards along much of Leavenworth Creek.

References Cited

Church, S.E., Owen, J.R., von Guerard, P.B., 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., Understanding and responding to hazardous substances at mine sites 

in the Western United States: Geological Society of America 

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

Colorado Department of Public Health and Environment 

(CDPHE), Water Quality Control Commission, 2007, Regulation 31, The basic standards and methodologies for surface 

water (5CCR 1002–31): Accessed November 8, 2007, at 

http://www.cdphe.state.co.us/regulations/wqccregs/index.html

Table 1. Dissolved concentrations and hardness-based and chronic aquatic standards for copper and zinc, Leavenworth Creek and inflows.

[μg/L, micrograms per liter; L, Leavenworth]

Field number Dissolved copper

(μg/L)

Hardness-based chronic 

copper standard (μg/L)

Site copper/chronic 

standard (percent)

Hardness-based acute 

copper standard (μg/L)

Site copper/acute 

standard (percent)

Adit drainage Adit 190 20 960 32 590

LC–200 L. Creek 0.54 2.7 20 3.5 15

TR–295 Tributary 160 15.4 1,040 24 660

LC–325 L. Creek 3.5 3.4 102 4.7 74

TR–902 Tributary 49 4.6 1,070 6.4 770

LC–930 L. Creek 5.2 3.7 140 5.1 100

Field number Dissolved zinc

(μg/L)

Hardness-based chronic 

zinc standard (μg/L)

Site zinc/chronic 

standard (percent)

Hardness-based acute 

zinc standard (μg/L)

Site zinc/acute

standard (percent)

Adit drainage Adit 7,440 270 2,700 320 2,300

LC–200 L. Creek 30 34 88 39 76

TR–295 Tributary 2,580 190 1,400 220 1,200

LC–325 L. Creek 175 44 390 51 340

TR–902 Tributary 2,780 67 4,900 58 4,800

LC–930 L. Creek 288 47 510 55 520

Fey, D.L., and Wirt, L., 2007, Mining-impacted sources of 

metal loading to an alpine stream based on a tracer-injection 

study, Clear Creek County, Colorado, in DeGraff, J.V., ed., 

Understanding and responding to hazardous substances at 

mine sites in the Western United States: Geological Society of America Reviews in Engineering Geology, v. XVII, 

p. 85–103.

Kimball, B.A., Runkel, R.L., Walton-Day, K., and Bencala, 

K.E., 2002, Assessment of metal loads in watersheds 

affected by acid mine drainage by using tracer injection 

and synoptic sampling, Cement Creek, Colorado, 

USA: Applied Geochemistry, v. 17, no. 9, p. 1183–1207.

Lovering, T.S., 1935, Geology and ore deposits of the 

Montezuma quadrangle, Colorado: U.S. Geological 

Survey Professional Paper 178, 119 p.

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., Understanding and responding to hazardous substances at mine 

sites in the Western United States: Geological Society 

of America Reviews in Engineering Geology, v. XVII, 

p. 9–23.
36 Chapter G: Geologic Controls on Metal Transport in Ground Water 

Within an Alpine Watershed Affected by Historical Mining

drainage (Church and others, 2007; Kimball and others, 2002; 

Kimball and others, 2007; Paschke and others, 2005). Understanding the ground-water flow and dissolved-metal transport 

is essential in determining whether sampled metal loads to 

streams are related to acid-mine drainage or acid-rock drainage, 

and thus, whether or not an identified source of metal loading 

should be remediated. The ultimate objective of this research 

is to provide the necessary scientific information for public 

land managers to select effective remedial approaches that will 

improve water quality in the watershed. 

In an effort to understand the ground-water flow system 

in the upper Animas River watershed, we selected Prospect 

Gulch (fig. 1) for further study because of the amount of 

existing multidisciplinary data in and around that particular 

watershed (Church and others, 2007). These data include 

stream tracer-dilution studies (Kimball and others, 2002; 

Wirt and others, 2001) that provide detailed streamflow and 

geochemistry information and detailed maps of the hydrothermal alteration in the bedrock (Bove and others, 2007b). In 

addition, Prospect Gulch has several inactive mines that are on 

land managed by the Bureau of Land Management (BLM).

An integrated-science approach was taken to address 

surface-water metal contributions from mining and the interaction of hydrothermally altered, sulfide-rich, volcanic rock 

with ground water. Three-dimensional geologic data include 

mineral analyses of rock cores (Bove and others, 2007a), 

maps of mineral alteration and structural features (Bove and 

others, 2007b), and seismic and ground-conductivity surveys 

(McDougal, 2006). For this study, the flow and geochemistry 

Overview

In the upper Animas River watershed in southwestern Colorado, ground-water discharge to streams 

is a significant pathway for surface-water metal 

loading from both acid-mine drainage and acid-rock 

drainage. However, the delineation of metal transport 

through ground water is difficult in fractured-rock 

terrain. Prospect Gulch, a small alpine catchment in 

San Juan County, Colorado, was selected for study 

because of (a) a high degree of mineral alteration, 

(b) effects from historical mining, and (c) preexisting 

multidisciplinary data sets. Data on the hydrogeology 

of the Prospect Gulch system include geologic mapping, rock core analyses, multilevel ground-water 

monitoring wells, geochemistry of ground and surface 

water, stream tracer-dilution studies, and groundwater modeling. An integrated-science approach was 

taken to assemble these multiple datasets and provide 

a detailed conceptual model of the geologic controls on 

metal transport in ground water of Prospect Gulch.

Data analysis provided the following insights: 

(a) the presence of shallow and deep ground-water flow 

with distinct pathways, residence times, and geochemistry, which affect metal concentrations throughout the 

year, (b) distinct ground-water flow paths that can be 

delineated using geochemistry and modeling, and (c) the 

presence of different recharge and discharge zones for 

ground water and surface water due to structural control 

in the bedrock. This detailed conceptual model provides 

information that may assist stakeholders in making 

science-based decisions regarding long-term monitoring 

and remediation activities in Prospect Gulch.

Introduction

Although most mining activity in San Juan County, 

Colorado, and the upper Animas River watershed ceased by the 

1990s, the effects of historical mining continue to release metals 

to ground water and surface water. These increased metal concentrations degrade stream-water quality and can be toxic to fish 

and other aquatic organisms. As a result, viable fish and aquatic 

habitat is now more limited than what existed before mining 

(Besser and others, 2007). Streams in this area have naturally 

low pH and elevated metal loads due to acid-rock drainage, but 

the effects of acid-mine drainage from historical mining activity 

have degraded preexisting ground-water and surface-water quality (Church and others, 2007). Ground-water discharge has been 

identified as a significant pathway for the loading of metals to 

surface water both from acid-mine drainage and from acid-rock 

Figure 1. Location of Prospect Gulch in the upper Animas River 

watershed in southwestern Colorado.

by Raymond H. Johnson

107°50'30" 107°45' 107°37'30" 107°30'

37°

58'

37°

52'

30"

37°

45'

Upper

Animas River

watershed

COLORADO

Prospect

Gulch

Mineral Creek

Cement Creek

Upper Animas River

Animas

Forks

Eureka

Silverton
37

of ground and surface water were defined through additional 

stream-tracer dilution studies (Johnson and others, 2007), the 

installation of ground-water monitoring wells (Johnson and 

Yager, 2006), and ground-water flow modeling (Johnson, 

2007). This research integrates these multiple datasets to 

develop a detailed conceptual model of the geologic controls 

on metal transport in ground water. 

Field Investigations

Bedrock in Prospect Gulch is composed of volcanic rocks 

that have been hydrothermally altered (fig. 2). As a result of 

this alteration, these rocks contain pyrite, which oxidizes and 

produces acidic ground water that can have high concentrations 

of iron and sulfate. A combination of impurities in the pyrite, 

oxidation of other sulfide minerals, and dissolution of buffering 

minerals also provides a source of other metals, such as copper, 

zinc, and aluminum (which are all toxic to fish at low concentrations). Sulfide oxidation occurs naturally in the mountain block 

(acid-rock drainage, fig. 3) and can be enhanced by mining activities through underground shafts and adits and the placement of 

sulfide-rich waste rock at the surface (acid-mine drainage, fig. 3). 

To monitor the resulting metal transport processes in Prospect 

Gulch, an intensive field investigation was initiated. 

Multilevel ground-water monitoring wells with sampling 

points at several depths were drilled in three locations (fig. 2) 

to determine (1) ground-water quality, (2) ground-water flow 

conditions, and (3) geology/mineralogy with depth. Bedrock 

cores were collected to a depth of 150 to 200 feet below land 

surface. Pyrite content up to 20 weight percent was measured 

in these cores (Bove and others, 2007a), indicating a large 

capacity for acid-rock drainage and an existing natural source of 

acidity and metals. The monitoring wells were located at upper, 

middle, and lower elevations (fig. 2) to capture ground water 

above, near, and below the mining-affected areas, which are 

in the middle elevations of Prospect Gulch. Water levels in the 

monitoring wells were measured year-round, when accessible. 

Additional geochemistry data were provided from sampling 

springs and the installation of shallow ground-water sampling 

points. Detailed sampling of surface-water quantity and quality 

using stream-tracer dilution studies provided companion data to 

the ground-water sampling. The complete details on methods 

and data collected during this project are summarized in three 

U.S. Geological Survey (USGS) Open-File Reports (Johnson 

and Yager, 2006; Johnson and others, 2007; and Bove and others, 

2007a). Additional data collected before this project as part of 

the USGS Abandoned Mine Lands Initiative (Church and others, 

2007) were also used as needed to assist in interpretations.

Improved three-dimensional stratigraphy was determined 

using geophysical techniques as companion data to bedrock 

cores collected during drilling. Core data provided a ground 

truth that allowed for a more unique interpretation of the 

geophysics. Companion geophysical profiles from seismic 

and ground-conductivity methods (fig. 4) were collected at 

several locations (McDougal, 2006). Interpretations from the 

Figure 2. Map of altered bedrock in Prospect Gulch with the 

location of three ground-water monitoring wells.

Figure 3. View of Prospect Gulch, looking north, with abandoned 

mines (acid-mine drainage) and areas with altered bedrock (acidrock drainage).

end

Acid sulfate (AS)

EXPLANATION

Quartz-sericite-pyrite

Propylitic

Unconsolidated

Ground-water monitoring wellIncreasing

Alteration

Lower

Upper

LARK MINE

Middle

Altered

bedrock

Mine shafts

Lark mine

waste rock
Chapter G

38 Understanding Contaminants Associated with Mineral Deposits

geophysical data were confirmed and (or) enhanced by data 

from cores and multilevel ground-water sampling in companion monitoring wells. Data from the middle well indicate a 

perched water table based on water levels within the monitoring well, the seismic profile indicates the depth to bedrock, 

and the conductivity profile highlights conductive groundwater plumes near the Lark Mine with high concentrations 

of dissolved solids and metals (fig. 4).

Conceptual Model

Data from the geophysics, monitoring well installations, 

and hydraulic and geochemical testing were used to develop 

a conceptual model of the hydrogeology at Prospect Gulch. A 

conceptual cross section from the top of Red Mountain #3 to the 

base of Prospect Gulch, with an elevation drop of 2,500 feet, is 

shown in figure 5. The conceptual model of the ground-water 

flow is characterized by shallow, intermediate, and deep groundwater flow lines. These ground-water flow paths have longer 

residence times with depth as confirmed by helium/tritium 

age dating (Johnson and others, 2007). The interaction of the 

ground-water flow with the geology produces distinct zones of 

geochemistry (fig. 5). The shallow ground water is highlighted 

by zone A, which has low pH, elevated copper (Cu) concentrations, and low iron (Fe) concentrations. Zone B represents an 

intermediate flow path with little geochemical difference from 

the shallower zone, except for slightly higher Fe concentrations. In zones A and B, sulfide oxidation is releasing iron and 

copper, but the oxygenated system allows for the precipitation 

of iron oxyhydroxides, whereas the copper remains in solution. 

As ground water moves with depth (zone C), sulfide oxidation 

continues to release iron and copper and consume oxygen. The 

consumption of oxygen allows for iron to remain in solution, 

but copper is precipitated. These oxidation-reduction controls 

are also seen with other metal concentrations (Johnson and 

others, 2007). The ground-water geochemistry created by mine 

waste rock is characterized by distinct plumes with even lower 

pH and very high concentrations of iron, copper, and other 

metals (exceeding background) that generally occur only in the 

shallow ground water (zone D).

Figure 4. Companion geophysical profiles near the middle well. Triangles indicate the top of the shallow (on 

seismic profile) and deep (on conductivity profile) water tables. Note that the seismic profile is not as deep as 

the conductivity profile. Black circles indicate depth of sampling point within the multilevel monitoring well.

Middle well

INTERVAL VELOCITY,

IN METERS

PER SECOND

0 1,000 2,000 3,000 4,000 5,000 6,000

CONDUCTIVITY,

IN MILLISIEMENS

PER METER

EXPLANATION

EXPLANATION

Seismic Profile

Conductivity Profile

LINE DISTANCE, IN METERS

3,420

3,410

3,400

3,430

80 100 120 140 160 180 200 220

ELEVATION,

IN METERS

Middle well

Middle well

East

West East

Bedrock

Colluvium

ELEVATION, 

IN METERS

80 100 120 140 160 180 200 220

LINE DISTANCE, IN METERS

0 20 40 60

3,410

3,430

3,390

West

Plumes of

conductive

ground

water

86420 10 12 14 1816 363432302826242220
Chapter G

Chapter G: Geologic Controls on Metal Transport in Ground Water Within an Alpine Watershed Affected by Mining 39

Figure 5. Conceptual cross section with geochemical zones. 

μg/L, micrograms per liter; mg/L, milligrams per liter.

Red

Mountain #3

LARK

MINE

pH Iron

(mg/L)

Cement

Creek

Copper

(μg/L)

3.7

3.9

4.0

3.0

0.7

2.0

50

200 7,000

0.5

280

A 250

A

D D

B

C

C

B

?

?

? ?

?

The mine-affected waters result in iron and copper loading to Prospect Gulch near the Lark mine. Downstream 

from the central portion of Prospect Gulch, the shallow and 

intermediate depth ground water discharges to the stream 

with low iron and high copper concentration; hence, the 

dilution of iron and maintenance of high copper concentrations within the stream. At the base of Prospect Gulch and 

in Cement Creek downstream from the confluence with 

Prospect Gulch, the discharge of the deep ground water to 

surface water substantially increases iron and decreases 

copper concentrations.

The results of stream monitoring at the mouth of 

Prospect Gulch indicate how the shallow and deep ground 

water affects the seasonal surface-water geochemistry 

(fig. 7). After recharge events, such as spring snowmelt 

or late summer rains, the larger contribution of shallow 

ground water creates a higher concentration of copper at 

the mouth of Prospect Gulch. In contrast, during the winter 

months when streamflow is supported by deep groundwater discharge, the highest iron concentrations and lowest 

copper concentrations occur. Surface-water data provide 

a valuable tool in understanding the seasonal and spatial 

complexity of ground-water flow and geochemistry within 

Prospect Gulch.

Figure 6. Downstream variation of dissolved copper and iron. μg/L, micrograms per liter.

Discharge of ground water to the surface creates distinct geochemistry in stream water. A snapshot of surfacewater geochemistry is shown in figure 6, where samples 

representing detailed geochemistry of the stream water 

were collected at low-flow conditions (October 2004). This 

figure highlights the deep and shallow ground-water flow 

and the effects of mine-affected, shallow ground waters. 

#*#* ##* #* #*#* ###*#

#*

58–71

72–148

149–180

181–196

197–210

211–219

220–258

259–345

346–366

367–398

LARK MINE

Prospect

Gulch

Cement

Creek

Iron, in μg/L

EXPLANATION

EXPLANATION

Copper, in μg/L

218–957

958–2,910

2,911–4,410

4,411–4,780

4,781–5,110

5,111–5,820

5,821–6,520

7,621–13,300

6,521–7,620

13,301–16,500
Chapter G

40 Understanding Contaminants Associated with Mineral Deposits

Figure 7. Temporal stream flow and concentrations of dissolved copper and iron measured 

at the mouth of Prospect Gulch. ft3/s, cubic feet per second; μg/L, micrograms per liter; mg/L, 

milligrams per liter; Cu, copper; Fe, iron.

Figure 8. Simulated hydraulic head contours for conceptual 

model with decreasing hydraulic head with depth and structural 

control. Hydraulic barriers are in red, and the redirected flow path 

is in white arrow.

Ground-Water Flow Modeling

Three steady-state ground-water flow simulations were 

created for the area surrounding Prospect Gulch by using 

MODFLOW-2000 (Harbaugh and others, 2000) to evaluate the conceptual model of deep ground-water flow. These 

simulations considered steady-state conditions for the deep 

ground water and expand upon simulations completed 

before the field investigations were initiated, where sensitivity analyses were performed to guide field-data collection 

(Johnson, 2007). The three simulations all have the same 

boundary conditions and calibration data (streamflow and 

hydraulic head) but evaluate the following three conceptual models: (1) homogeneous hydraulic conductivity with 

depth, (2) decreasing hydraulic conductivity with depth, and 

(3) decreasing hydraulic conductivity with depth with the 

addition of structural controls. Structural control was provided 

by using a horizontal flow barrier that followed alignments 

similar to mapped veins and faults and boundaries provided 

by airborne magnetic data. Decreasing hydraulic conductivity with depth provides a large improvement in matching the 

observed hydraulic heads when compared to a homogeneous 

simulation but does not improve the match to streamflow. 

The additional structural control (fig. 8) improves the match 

to the observed streamflows. This structural control drains 

an upper portion of the model domain across a surfacewater divide, directing ground water to the base of Prospect 

Gulch instead of the upper reaches of Cement Creek. This 

improvement in calibration demonstrates the need for some 

structural control in the fractured bedrock, but the use of 

hydraulic barriers is not a unique solution, as other conceptual models of structural features may also give reasonable 

calibration results.

Conclusions

In Prospect Gulch, an interdisciplinary approach has 

demonstrated the occurrence of shallow and deep ground-water 

flow with distinct pathways, residence times, and geochemistry 

and has provided a conceptual model of ground-water flow and 

metal transport. The distinct geochemistry of the ground water 

is created by changing redox conditions, local geology, and 

mining effects. The discharge of ground water to nearby streams 

affects the concentrations of metals observed in the surface 

water in spatial and temporal patterns. These patterns highlight 

Date

FLOW, IN CUBIC

FEET PER SECOND

1

10

100

0.1

1.0

10

100

CONCENTRATION

1,000

DATE

8/1/2004

9/1/2004

10/1/2004

11/1/2004

12/1/2004

1/1/2005

2/1/2005

3/1/2005

4/1/2005

5/1/2005

6/1/2005

7/1/2005

8/1/2005

9/1/2005

Flow (ft3/s)

Fe (mg/L)

Cu (μg/L)
Chapter G

Chapter G: Geologic Controls on Metal Transport in Ground Water Within an Alpine Watershed Affected by Mining 41

the discharge of shallow, deep, and mine-affected ground water 

because of their unique geochemical signatures. Ground-water 

flow modeling identifies areas where surface-water and groundwater recharge and discharge zones may differ, with ground water 

crossing a surface-water divide. The combined use of geochemical data, conceptual model development, and ground-water flow 

modeling has delineated distinct ground-water flow pathways and 

identified the presence of structural control, all of which demonstrate effects on metal transport in ground water within Prospect 

Gulch. This framework and modeling approach can be used in 

Prospect Gulch and other areas in a predictive mode to determine 

how possible remedial scenarios may affect the discharge of 

metals to surrounding streams. This approach can provide stakeholders and land managers with a scientific-based conceptual 

model that can be used as a decisionmaking tool in proceeding 

with the remediation of abandoned mine lands.

Acknowledgments

As an integrated-science project, this research is a 

compilation of work completed by many, through data collection and assistance in figure preparation. Geophysical 

research was completed by Michael Powers, Bethany Burton, 

and Robert McDougal. Geologic research was completed 

by Dana Bove and Douglas Yager, and the stream tracerdilution research was completed by Laurie Wirt, David Fey, 

and Kenneth Leib. Funding for this research was provided 

by the USGS Mendenhall Postdoctoral Research Program, 

the USGS Mineral Resources Team, and the Bureau of 

Land Management.

References Cited

Besser, J.M., Finger, S.E., and Church, S.E., 2007, Impacts 

of historical mining on aquatic ecosystems—An ecological 

risk assessment, in Church, S.E., von Guerard, Paul, and 

Finger, S.E., eds., Integrated investigations of environmental 

effects of historical mining in the Animas River watershed, 

San Juan County, Colorado: U.S. Geological Survey Professional Paper 1651.

Bove, D.J., and Johnson, R.H., and Yager, D.B, 2007a, Mineralogy from cores in Prospect Gulch, San Juan County, Colorado: U.S. Geological Survey Open-File Report 2007–1095 

http://pubs.usgs.gov/of/2007/1095/

Bove, D.J., Mast, M.A., Dalton, J.B., Wright, W.G., and 

Yager, D.B, 2007b, Major styles of mineralization and 

hydrothermal alteration and related solid- and aqueous-phase 

geochemical signatures, in Church, S.E., von Guerard, Paul, 

and Finger, S.E., eds., Integrated investigations of environmental effects of historical mining in the Animas River Watershed, 

San Juan County, Colorado: U.S. Geological Survey Professional Paper 1651, 1096 p., 2 volumes.

Church, S.E., von Guerard, Paul, and Finger, S.E., eds., 

2007, Integrated investigations of environmental effects of 

historical mining in the Animas River Watershed, San Juan 

County, Colorado: U.S. Geological Survey Professional 

Paper 1651, 1096 p., 6 plates, 1 DVD.

Harbaugh, A.W., Banta, E.R., Hill, M.C., and McDonald, 

M.G., 2000, MODFLOW-2000, the U.S. Geological Survey 

modular ground-water model—User guide to modularization concepts and the ground-water flow process: 

U.S. Geological Survey Open-File Report 2000–92, 121 p.

Johnson, R.H., 2007, Ground water flow modeling with sensitivity analyses to guide field data collection in a mountain 

watershed: Ground Water Monitoring and Remediation, 

v. 27, no. 1, p. 75–83.

Johnson, R.H., Wirt, L., Manning, A.H., Leib, K.J., Fey, 

D.L., and Yager, D.B., 2007, Geochemistry of surface and 

ground water in Cement Creek from Gladstone to Georgia 

Gulch and in Prospect Gulch, San Juan County, Colorado: 

U.S. Geological Survey Open-File Report 2007–1004, 140 p. 

http://pubs.usgs.gov/of/2007/1004/

Johnson, R.H., and Yager, D.B., 2006, Completion reports, 

core logs, and hydrogeologic data from wells and piezometers in Prospect Gulch, San Juan County, Colorado: 

U.S. Geological Survey Open-File Report 2006–1030, 

32 p. http://pubs.usgs.gov/of/2006/1030/

Kimball, B.A., Runkel, R.L., Walton-Day, Katherine, and 

Bencala, K.E., 2002, Assessment of metal loads in watersheds affected by acid mine drainage by using tracer 

injection and synoptic sampling—Cement Creek, Colorado, 

USA: Applied Geochemistry, v. 17, p. 1183–1207.

Kimball, B.A., Walton-Day, Katherine, and Runkel, R.L., 

2007, Quantification of metal loading by tracer injection and synoptic sampling, 1996–2000, in Church, S.E., 

von Guerard, Paul, and Finger, S.E., eds., Integrated investigations of environmental effects of historical mining in 

the Animas River Watershed, San Juan County, Colorado: 

U.S. Geological Survey Professional Paper 1651, 1096 p., 

2 volumes.

McDougal, R.R., 2006, Electrical resistivity surveys in Prospect Gulch, San Juan County, Colorado: U.S. Geological 

Survey Open-File Report 2006–1171 http://pubs.usgs.gov/

of/2006/1171/

Paschke, S.S., Kimball, B.A., and Runkel, R.L., 2005, Quantification and simulation of metal loading to the upper Animas River, Eureka to Silverton, San Juan County, Colorado, 

September 1997 and August 1998: U.S. Geological Survey 

Scientific Investigations Report 2005–5054, 73 p.

Wirt, Laurie, Leib, K.J., Bove, D.J., and Melick, R., 

2001, Metal loading assessment of point and non-point 

sources in a small alpine sub-basin characterized by 

acid drainage—Prospect Gulch, upper Animas River 

watershed, Colorado: U.S. Geological Survey Open-File 

Report 2001–0258.
42 Chapter H: Electrical Geophysical Characterization of a MiningAffected Subbasin, Prospect Gulch, Colorado

Introduction

As a tributary of the upper Animas River in southwestern 

Colorado, Prospect Gulch is a major source of naturally occurring 

and mining-related metals to Cement Creek. In this highly mineralized subbasin it has been shown that the presence of sulfate, 

aluminum, iron, zinc, copper, and other metals associated with 

historical mining is substantial but relatively insignificant compared to contributions from areas of natural weathering of highly 

altered, pyritic rock (Wirt and others, 2001). While many of the 

streams in the area have low pH and elevated metal loads caused 

by acid-rock weathering, acid-mine drainage from historical 

mining has contributed to the degradation of ground and surface 

water (Church and others, 2007). Efforts to improve water quality 

in the watershed have focused on Prospect Gulch because many 

of its abandoned mines and waste-rock piles are located on land 

managed by the Bureau of Land Management (BLM). Information on sources and pathways of metals and related ground-water 

flow will be useful to the BLM to help develop and prioritize 

by Robert R. McDougal

Overview

Prospect Gulch is a major source of naturally 

occurring and mining-related metals to Cement Creek, 

a tributary of the upper Animas River in southwestern 

Colorado. Efforts to improve water quality in the watershed have focused on Prospect Gulch because many 

of its abandoned mines are located on Federal lands. 

Information on sources and pathways of metals and 

related ground-water flow will be useful to help prioritize and develop remediation strategies. It has been 

shown that the occurrence of sulfate, aluminum, iron, 

zinc, and other metals associated with historical mining 

and the natural weathering of pyritic rock is substantial. In this study, direct current resistivity surveys were 

conducted to determine the subsurface resistivity distribution and to identify faults and fractures that may 

act as ground-water conduits or barriers to flow. Five 

profiles of resistivity data were collected in the vicinity of Prospect Gulch, and cross-section profiles were 

constructed from the field data using a two-dimensional 

inversion algorithm. The conductive anomalies in the 

profiles are most likely caused by wet or saturated rocks 

and sediments, clay-rich deposits, or ground water 

with high concentrations of dissolved solids. Resistive 

anomalies are likely bedrock, dry surficial and subsurface deposits, or deposits of ferricrete.

remediation strategies. Several mine adits and large waste dumps 

are located on BLM property in the drainage. These are associated with the Lark, Henrietta, and Joe and John mines. Other 

notable historical mines include the Hercules and Galena Queen 

mines (fig. 1).

The direct current (dc) resistivity method is a geophysical 

technique that measures subsurface electrical resistivity to help 

characterize subsurface features related to geologic structure 

and ground-water geochemistry. The dc resistivity surveys presented in this study were conducted to determine the subsurface resistivity distribution and to identify faults and fractures 

that may act as conduits or barriers to ground-water flow. The 

results of the electrical geophysical surveys presented here are 

part of an integrated effort, including seismic surveys, drilled 

core and monitoring wells, stream-tracer injection studies, and 

geochemical analyses, to characterize and model ground-water 

flow in Prospect Gulch.

Geology and Physical Setting of Prospect Gulch

Prospect Gulch is located on the margin of the historic Red Mountain mining district, near the northwest 

structural margins of the San Juan and Silverton calderas. 

Rocks in Prospect Gulch formed following formation of the 

28.2-million-year-old San Juan Caldera and are coincident 

with and (or) postdate formation of the 27.8-million-yearold Silverton caldera (Yager and Bove, 2002). The igneous 

sequence, referred to as the Silverton Volcanics, formed from 

lavas and volcaniclastic sediment that infilled the San Juan 

caldera over an area of 14 km2

 to a thickness of nearly a kilometer (Lipman and others, 1973). Following caldera formation, and simultaneous with Silverton Volcanics deposition, 

regional alteration occurred throughout much of the study 

area. Several small-volume plugs and dikes intruded along the 

structural margins of the calderas long after caldera activity ceased. Based on the isotopic ages of the intrusions near 

Prospect Gulch, the intrusions formed several million years 

after the eruption of the Silverton Volcanics lavas during the 

Miocene Epoch (Lipman and others, 1973). The intrusions are 

thought to have provided the heat source for the hydrothermal 

alteration and mineralization of the Red Mountain mining 

district (Lipman and others, 1976; Bove and others, 2001).

A number of alteration types are found in Prospect Gulch 

and vary substantially from north to south across the subbasin 

(Bove and others, 2007a; Bove and others, 2007b). Near Red 

Mountain No. 3 (fig. 1), acid sulfate mineralization is exposed 

and is associated with pervasive silicification that formed 

resistant ridges. The acid sulfate mineralization is characterized 

by high sulfate content and includes the mineral assemblage 

of quartz, alunite, pyrophyllite (qap), and pyrite. More easily 
43

an elevation change of 800 m along its 2.4-km length. Much 

of Prospect Gulch is above tree line, which is approximately 

3,500 m at this latitude. Nonforested areas primarily consist of 

alpine vegetation, poorly developed soils, talus, and exposures 

of bedrock. 

Electrical Properties of Earth Materials

Electrical resistivity, which can be expressed inversely 

as electrical conductivity, is a fundamental property of all earth 

materials. The degree of resistance or conductance varies with 

rock or sediment type, porosity, clay mineral type and content, 

and the quantity and quality of water. Poorer quality ground 

water (that is, water with higher concentrations of dissolved 

solids) or sediments with higher clay content are usually more 

weathered argillic alteration occurs on the margins of the 

qap assemblage. The most abundant alteration assemblage in 

Prospect Gulch is the quartz-sericite-pyrite (qsp), locally containing 10 to 20 volume percent pyrite. In the lower part of the 

subbasin, regional propylitic alteration is dominant.

Structural interpretation of mapped veins in the subbasin 

indicates that general trends of northwest, north, and northeast 

are predominant. Evidence suggests that these veins may have 

formed coincident with mineralization along structural zones 

of weakness. East-west-trending veins, although uncommon, 

do occur in Prospect Gulch (Bove and others, 2007a; Bove and 

others, 2007b).

Prospect Gulch is a steep-gradient alpine to subalpine 

mountain subbasin that drains the southern flank of Red 

Mountain No. 3 (fig. 1). The stream in Prospect Gulch has 

Figure 1. Location map of the Prospect Gulch study area in the upper Animas River watershed.

Ì Ì

Ì

Ì

Ì

×

×

×

×

×

×

×

×

×

Animas R

S Fork Cement Cr

Cement

Cr

Mineral Cr

Prospect Gulch

study area

JOE AND

JOHN MINE

LARK

MINE

GALENA

QUEEN

MINE

HERCULES

MINE

Whitehead Peak

Kendall

Peak

Macomber

Peak

Storm

Ohio Peak

Peak

0 6 KILOMETERS

0 6 MILES

Sultan

Mtn

COLORADO

Grand

Junction

Upper Animas

River Basin

Red Mountain

Number 3

Prospect Creek

Emery

Peak

Silverton

Hazelton

Mtn

Anvil Mtn

107°45' 107°40' 107°35'

37°55'

37°50'

37°45'

Howardsville

HENRIETTA

MINE

Denver
Chapter H

44 Understanding Contaminants Associated with Mineral Deposits

conductive than “clean” water (Zohdy and others, 1974). The 

presence of electrically conductive minerals such as metallic 

sulfides can also result in higher conductivity values. 

Resistivity units are ohm-meters. Often, in geophysical studies associated with ground-water characterization, it 

is useful to convert values of resistivity to conductivity to identify or emphasize conductive anomalies or zones. To convert 

resistivity to conductivity, the following formula is used:

1,000/ohm-meters → millisiemens/meter

Because of the many factors that affect terrain conductivity, interpretation of geophysical surveys can often result in a 

nonunique explanation for a conductive or resistive anomaly. 

Therefore, in this study, the availability of information from 

drilled core samples (Johnson and Yager, 2006) aided in the 

interpretation of the resistivity data.

Collection of Resistivity Data

Five resistivity profiles were collected on and downgradient 

from the alluvial fan at the base of Prospect Gulch (fig. 2). 

Profile 1, paralleling Cement Creek Road, starts at the north end 

of the Prospect Gulch alluvial fan, crosses Prospect Creek, and 

ends at the southern extent of the fan. Profiles 2 and 3 coincide 

with the location of two seismic profiles collected contemporaneously with the resistivity. Profile 4 extends from the southern 

extent of the alluvial fan past an iron bog adjacent to Cement 

Creek. Profile 5 was located below the Lark mine on an old road 

grade composed of waste rock from the Henrietta mine (fig. 2).

The dc resistivity equipment used in this study records 

lateral and vertical resistivity variations in the subsurface. 

This multielectrode system has the capability of recording 

many channels of data simultaneously and allows for the collection of very dense dc resistivity data in a relatively short 

amount of time. The electrode array consisted of 76 dual mode 

switches in contact with the ground using stainless-steel stakes 

driven into the ground along a relatively straight profile. The 

dual mode electrodes are automatically switched to allow 

each to operate as either current or potential electrodes in the 

array. Equidistant spacing between each electrode was varied, 

depending upon the desired line length, depth of investigation, 

and data resolution.

The data collected in the field indicated the apparent 

resistivity of the subsurface. These data were then converted 

to true resistivity as a function of depth using a numerical 

inversion method (Advanced Geosciences, Inc., 2006). The 

result of the inversion process is a true resistivity cross section 

corrected for changes in topography along the profile by using 

elevation and position data.

Results

The inverted data were used to construct profiles of 

subsurface resistivity profiles of the Prospect Gulch alluvial 

fan, the area along the Cement Creek road from Prospect 

Gulch to Georgia Gulch, and the waste rock below the Lark 

mine (fig. 2). Resistivity values in ohm-meters obtained from 

the inversion program were converted to conductivity values 

in millisiemens per meter to emphasize conductive anomalies as previously described. Data grids were calculated using 

the minimum curvature gridding method and plotted as contoured profile maps ranging in value from 0 to 37 millisiemens 

per meter. 

The conductive anomalies in these profiles are most 

likely caused by wet or saturated rocks, clay-rich sediments, 

or ground water with high concentrations of dissolved solids. 

Resistive anomalies are likely bedrock, dry surficial and 

subsurface deposits, or deposits of ferricrete. Identification of 

these conductive and resistive zones is important to help characterize ground-water flow in the subbasin and help constrain 

ground-water modeling efforts.

Profile 1 (fig. 3) was positioned to identify conductive 

anomalies that are possibly related to ground water discharging to Cement Creek from Prospect Gulch. The highest conductivity values are interpreted as wet or saturated alluvium 

when recorded near the surface, and wet or saturated bedrock 

when recorded at depth, although the alluvium/bedrock 

interface is not well defined. Conductive anomalies occurring 

in bedrock may be associated with fracture-controlled groundwater flow, and conductive anomalies in the alluvium may be 

associated with increased clay content. A well-core log from 

an exploration well drilled near Profile 1 shows that bedrock 

(Silverton Volcanics) in this area is highly fractured and 

hydrothermally altered (Johnson and Yager, 2006).

The location of Profile 2 (fig. 4) was selected to correspond with the position of a contemporaneous seismic survey 

profile. As with Profile 1, Profile 2 is characterized by high 

resistivity at the surface, which is the result of dry surficial 

deposits and ferricrete. In some areas near the center of the 

profile, ferricrete was exposed at the surface. The very hard 

nature of the ferricrete made placement of the electrodes difficult and resulted in very high contact resistance and degraded 

signal quality.

The location of Profile 3 (fig. 5) was also coincident 

with a seismic survey profile. The relative depth of conductive features in this profile indicates that the saturated alluvial 

zone is deeper near the bottom of the alluvial fan and may also 

indicate the changing depth of clay-rich sediments. The conductive zone at the surface is near an area of saturated ground 

observed to be associated with an iron bog. The thin, resistive 

layer beneath this conductive zone is interpreted as a ferricrete 

confined unit between the conductive shallow ground water 

and the deeper conductive ground water.

Profile 4 (fig. 6) was positioned to identify conductive zones downgradient from Prospect Gulch that might be 

associated with an iron bog along Cement Creek. The profile 

is generally resistive at the surface along its length, resulting 

from ferricrete and dry soil and surficial deposits. The highly 

resistive surface layer at the northeast end of the profile coincides with the resistivity high at the southwest end of Profile 1 

and results from ferricrete and dry surficial deposits.
Chapter H

Chapter H: Electrical Geophysical Characterization of a Mining-Affected Subbasin, Prospect Gulch, Colorado 45

Figure 2. Location of resistivity survey lines and boreholes within the study area (digital orthophoto quad base image).

264000 264500 265000 265500

4195500 4196000 4196500 4197000

107°41'W 107°41'30”W 107°40'W

37°

53'

30”N

37°

53'N

1/4 MILE

0 0.5 KILOMETER

0

Universe Transverse Mercator, Zone 13N

North American Data of 1927

Line 1

Line 2

Line 3

Line 4

Line 5

LARK MINE

Prospect Gulch

Upper Bog Cement Creek

Georgia Gulch

Lower Borehole

Middle Borehole
Chapter H

46 Understanding Contaminants Associated with Mineral Deposits

Figure 4. Conductivity Profile 2. m, meters.

Figure 3. Conductivity Profile 1. m, meters.

CONDUCTIVITY,

IN MILLISIEMENS

PER METER

Northeast

265532.17E

4196093.83N

Southwest

265415.45E

4195882.72N

Prospect

Creek

Intersection

with line 3

Prospect Gulch Profile 1

3,100

3,120

0 20 40 60 80 100 120 140 160 180 200 220 240

LINE DISTANCE, IN METERS

0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36

ELEVATION, 

IN METERS

EXPLANATION

0 20 40 60 80 100 120 140 160 180

LINE DISTANCE, IN METERS

ELEVATION, 

IN METERS 3,120

3,120

Prospect Gulch Profile 2

Intersection with

Profile 3 (lower borehole)

Southwest

265410.17E

4195927.83N

Northeast

265492.50E

4196089.83N

86420 3028262422201816141210 32 3634

EXPLANATION

CONDUCTIVITY,

IN MILLISIEMENS

PER METER
Chapter H

Chapter H: Electrical Geophysical Characterization of a Mining-Affected Subbasin, Prospect Gulch, Colorado 47

Figure 5. Conductivity Profile 3. m, meters.

The shallow conductive layer extending from 260 to 

430 m is interpreted as wet clay and alluvium eroded off the 

ridge between Prospect Gulch and Georgia Gulch. The resistive zone below this layer is likely bedrock that becomes more 

conductive downgradient to the southwest.

We conclude that deep circulating ground-water flow is 

likely influenced by the resistive structure near the Upper Iron 

Bog and that the near-surface layer of ferricrete acts as a confining layer. The highly conductive anomaly between 40 and 

110 m is interpreted as the result of ground water with high 

concentrations of dissolved solids that is mantled and confined 

by the ferricrete. This zone could also contain clay-rich sediments, but this alternate interpretation cannot be confirmed 

without direct core data.

0 20 40 60 80 100 120 140

0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36

CONDUCTIVITY,

IN MILLISIEMENS

PER METER

Northwest

265341.50E

4196024.50N

Southeast

265475.00E

4195959.50N

Intersection with

line 2 (lower borehole)

Prospect Gulch Profile 3

3,120

3,140

LINE DISTANCE, IN METERS

ELEVATION, IN METERS

EXPLANATION

Profile 5 (fig. 7) was positioned to intersect ground water 

draining from the tailings and waste rock associated with the 

Lark mine to record preremediation subsurface conditions. Several seeps and springs were observed below the embankment to 

the north of the profile, some having orange-colored water with 

iron precipitate.

The near-surface conductive anomaly between 155 

and 200 m along the profile is coincident with seeps and

 saturated surface soils. This zone is interpreted as a 

plume of conductive shallow ground water draining from the 

Lark mine waste rock. The sharp interface between conductive 

and resistive zones suggests that ground water at 200 m along 

the profile is perched on a resistive surface of ferricrete and 

(or) bedrock.
Chapter H

48 Understanding Contaminants Associated with Mineral Deposits

Figure 6. Conductivity Profile 4. m, meters.

Figure 7. Conductivity Profile 5. m, meters.

CONDUCTIVITY,

IN MILLISIEMENS

PER METER

Northeast

265422.50E

4195900.50N

Southwest

265187.50E

4195508.00N

Upper Bog

(near road)

Prospect Gulch Profile 4

3,040

3,060

3,080

3,100

3,120

LINE DISTANCE, IN METERS

ELEVATION, IN METERS

EXPLANATION

0 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440

0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36

0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36

CONDUCTIVITY,

IN MILLISIEMENS

PER METER

East

264336.50E

4197014.50N

West

264135.17E

4197002.83N

3,360

3,380

3,400

3,420

LINE DISTANCE, IN METERS

ELEVATION, IN METERS

EXPLANATION

0 20 40 60 80 100 120 140 160 180 200 220

Prospect Gulch Profile 5
Chapter H

Chapter H: Electrical Geophysical Characterization of a Mining-Affected Subbasin, Prospect Gulch, Colorado 49

Conclusions

The conductivity profiles presented in this study generally identify zones of varying near-surface geology (for 

example, clay-rich sediments and ferricrete) as well as zones 

of conductive ground water. Conductive zones at depth 

indicate the presence of ground water that is either in saturated layers of clay and alluvium or in faults and fractures 

in bedrock. Where ground water is associated with mine 

waste, the subsurface conductivity is generally high, suggesting poor water quality.

This study illustrates the utility of combining geophysical investigations with available well-core logs to expand the 

interpretation and understanding of the ground-water and 

geologic systems in complex mountainous terrains. By correlating well and piezometer data with the conductivity profiles, 

the often nonunique interpretation of the geophysical data can 

be improved.

References Cited

Advanced Geosciences, Inc., 2006, EarthImager 2D, ver. 2.1.8 

(build 507): Austin, Texas.

Bove, D.J., Hon, Ken, Budding, K.E., Slack, J.F., Snee, L.W., 

and Yeoman, R.A., 2001, Geochronology and geology

 of late Oligocene through Miocene volcanism and 

mineralization in the western San Juan Mountains, 

Colorado: U.S. Geological Survey Professional Paper 1642, 

30 p.

Bove, D.J., Mast, M.A., Dalton, J.B., Wright, W.G., and 

Yager, D.B., 2007a, Major styles of mineralization and

 hydrothermal alteration and related solid- and aqueousphase geochemical signatures, in Church, S.E., 

von Guerard, Paul, and Finger, S.E., eds., Integrated investigations of environmental effects of historical mining in 

the Animas River Watershed, San Juan County, Colorado: 

U.S. Geological Survey Professional Paper 1651, 

1096 p.

Bove, D.J., Yager, D.B., Mast, M.A., and Dalton, J.B., 2007b, 

Alteration map showing major faults and veins and associated water-quality signatures of the Animas River watershed 

headwaters near Silverton, southwest Colorado: U.S. Geological Survey Scientific Investigations Map 2976, 18-p. 

pamphlet, 1 plate, scale 1:24,000.

Church, S.E., Mast, M.A., Martin, E.P., and Rich, C.L., 2007, 

Mine inventory and compilation of mine-adit chemistry 

data, Chapter E5 in Church, S.E., von Guerard, Paul, and 

Finger, S.E., eds., Integrated investigations of environmental 

effects of historical mining in the Animas River Watershed, 

San Juan County, Colorado: U.S. Geological Survey Professional Paper 1651, 1096 p.

Johnson, R.H., and Yager, D.B., 2006, Completion reports, core 

logs, and hydrogeologic data from wells and piezometers in 

Prospect Gulch, San Juan County, Colorado: U.S. Geological 

Survey Open-File Report 2006–1030, 32 p.

Lipman, P.W., Steven, T.A., Luedke, R.G., and Burbank, W.S., 

1973, Revised volcanic history of the San Juan, Uncompahgre, Silverton, and Lake City calderas in the western 

San Juan Mountains, Colorado: U.S. Geological Survey 

Journal of Research, v. 1, 627–642.

Lipman, P.W., Fisher, F.S., Mehnert, H.H., Naeser, C.W., 

Luedke, R.G., and Steven, T.A., 1976, Multiple ages of midTertiary mineralization and alteration in the western San Juan 

Mountains, Colorado: Economic Geology, v. 71, 571–588.

Wirt, Laurie, Leib, J.L., Melick, Roger, and Bove, D.J., 2001, 

Metal loading assessment of a small mountainous sub-basin 

characterized by acid drainage—Prospect Gulch, Upper 

Animas River Watershed, Colorado: U.S. Geological Survey 

Open-File Report 2001–0258, 36 p.

Yager, D.B., and Bove, D.J., 2002, Generalized geologic map 

of part of the upper Animas River watershed and vicinity, 

Silverton, Colorado: U.S. Geological Survey Miscellaneous 

Field Studies Map MF–2377, 1:48.000.

Zohdy, A.A.R., Eaton, G.P., and Mabey, D.R., 1974, Application of surface geophysics to ground-water investigations: 

U.S. Geological Survey Techniques of Water-Resources 

Investigations, book 2, chap. D1, 116 p.
50 Chapter I: U.S. Geological Survey Research in Handcart Gulch, 

Colorado—An Alpine Watershed Affected by Metalliferous 

Hydrothermal Alteration

Overview

Handcart Gulch is an alpine watershed along the 

Continental Divide. It contains an unmined mineral 

occurrence composed primarily of pyrite with trace 

metals including copper and molybdenum. Although 

the geology of Handcart Gulch is typical of many 

hydrothermal mineral deposits in the intermountain 

West, the area is unique because of a set of deep and 

shallow wells used to conduct an integrated study of 

the processes involved with the liberation, transport, 

and fate of naturally occurring acid-rock drainage 

in a mountain watershed. Commonly, mountainous 

watersheds are underlain by complexly deformed 

crystalline rocks where the occurrence, storage, 

and flow of ground water are poorly understood. 

These environments also are characterized by high 

to extreme hydraulic gradients and heterogeneous 

networks of fractures and faults that control the 

ground-water flow system and contaminant transport. 

Integrating geological, hydrological, geochemical, and 

geophysical data in a series of numerical flow models, we find that ground-water flow at the watershed 

scale can be conceptualized using a relatively simple 

equivalent porous media approach. We also find that 

ground water accounts for a significant component 

of discharge to the trunk stream, about 37 percent of 

the total annual streamflow. The work to date (2008) 

suggests that, in spite of low bulk permeability and 

various geologic complexities, hydrologic contributions 

from fractured crystalline bedrock rock should be 

carefully considered when evaluating alpine groundwater flow systems.

by Jonathan Saul Caine, Andrew H. Manning, Philip L. Verplanck, Dana J. Bove, Katherine Gurley Kahn, 

and Shemin Ge

Introduction

Handcart Gulch provides a unique opportunity to study 

how a variety of complex geological characteristics control the 

hydrology in an alpine watershed containing an unmined, metallic mineral occurrence. The occurrence can be characterized 

as a copper-molybdenum porphyry system in which pyrite is 

the most abundant metallic mineral. Although pyrite is of little 

economic value, it has had a major effect on the Handcart Gulch 

watershed. The study arose out of the need to better understand 

the liberation, transport, and fate of natural contaminants related 

to the weathering of pyrite in mountain watersheds, especially 

the function of ground water in transporting these contaminants 

to the surface-water system. The study area is unique because 

there is a network of shallow and deep boreholes that the USGS 

has converted to ground-water research and monitoring wells. 

Such wells exist in few alpine environments worldwide and, 

as such, provide the opportunity to more fully understand the 

hydrogeological system as a whole.

The motivation to complete an integrated study of the 

geology and hydrology of Handcart Gulch is multifold and 

was a collaborative effort between the U.S. Geological Survey 

Geologic and Water Resources Disciplines as well as the 

Mendenhall Program, the University of Colorado, and the 

Colorado Geological Survey. There is growing recognition 

that mountains occupy a critical place in the hydrologic cycle 

in many parts of the world. They capture precipitation by 

orographic effect, store water in snowpack and in mountain 

aquifers, are a primary source of surface water in arid regions, 

and serve as recharge zones for local and regional aquifers. 

Rapidly increasing population in mountainous areas has led 

to a greater utilization of mountain aquifers and a need to 

better understand their production capacity and vulnerability 

to contamination. Mineral deposits are common in mountain 

environments and are the source of natural and mining-related 

acid and trace-metal loading to alpine surface and ground 

waters. However, identifying transport pathways and specific 

local sources of contamination has remained a challenge 

(for example, Runnells and others, 1992; Kimball and others, 2002; Mast and others, 2007). The growing demand 

to improve water quality in affected mountain streams and 

develop scientifically based remediation strategies for affected 

waters has created a need to better understand the groundwater systems feeding mountain streams. Additionally, the 

potential for hydraulic gradients in mountainous terrain to 

drive ground-water flow to considerable depth within the 

Earth’s upper crust is poorly understood. Such deep flow 

likely contributes significantly to the formation of mineral 

deposits, seismicity, and other geologic processes. Mountains 

commonly exist in environments underlain by complex geology, and important questions regarding the potential effects of 

geology on ground-water flow in mountainous settings include 

the following:

(1) To what degree do discrete fracture networks and (or) 

fault zones control preferred ground-water flow paths, 

and at what scale might the bulk permeability structure be 

treated as a continuum?

(2) Is the bulk permeability of fractured bedrock sufficiently 

low, as is commonly assumed, to ignore contributions 

of bedrock-hosted ground water to streams? If not, 

is this component of flow typically high enough to 

demand the inclusion of bedrock waters in watershed 

hydrologic models?
51

(3) How does bedrock permeability vary spatially, and does 

this type of heterogeneity need to be incorporated in 

numerical ground-water flow models?

(4) What geologic factors control the concentrations and fluxes 

of acid and metals in mountain ground-water flow systems?

This chapter provides an overview of U.S. Geological 

Survey research in Handcart Gulch and a brief synopsis of 

preliminary results from the site. More detailed information can 

be found in the following publications: Caine and others (2006), 

Manning and Caine (2007), Kahn and others (2007), Verplanck 

and others (2007), and Verplanck and others (in press).

Overview of Handcart Gulch Research

Geology, Mineral Deposit, Hydrothermal 

Alteration, and Contaminant Sources

Handcart Gulch is located in central Colorado within the 

Colorado Mineral Belt (figs. 1 and 2; Tweto and Sims, 1963). 

The mineral occurrence in Handcart is hosted within complexly folded and fractured Precambrian metamorphic bedrock. The bedrock consists of gneisses, schists, amphibolites, 

and granites that have been intruded by small, Tertiary-age, 

porphyritic igneous stocks that likely account for the metallic 

mineralization (figs. 2 and 3). T.S. Lovering originally mapped 

the area in 1935 and identified what he called “iron bog” 

along the bed of the trunk stream along most of its course. 

This material is ferricrete, iron-hydroxide-cemented alluvium 

and colluvium. Another geological unit in the watershed with 

hydrological significance is a rock glacier (figs. 2 and 3).

The Montezuma mining district, to the north of Handcart 

Gulch, has a long mining history starting with an initial 

discovery of silver in 1864 (fig. 1; Lovering, 1935). Metals 

mined in the district include silver, lead, zinc, copper, and 

molybdenum (Botinelly, 1979). As in Handcart Gulch, these 

metals are associated with disseminated and veinlet-hosted 

pyrite (FeS2

) in large zones of hydrothermal alteration related 

to Tertiary intrusions (figs. 2 and 3). Pyrite at the near surface 

of the Earth is unstable in the presence of oxygenated waters 

and thus breaks down into its principal chemical components 

by weathering processes. The primary components include 

iron and any trace metals such as copper that commonly 

occur with pyrite, as well as sulfur, usually in the form of 

sulfuric acid. Acidified and metal-laden waters are transported 

from zones of oxidation by infiltrating precipitation into the 

ground-water flow system or by runoff and (or) ground-water 

Figure 1. Location of Handcart Gulch with major physiographic province boundaries and the location of the study area within 

the Colorado Mineral Belt and Montezuma Mining District, which is characteristic of many such districts in the Mineral Belt. Also 

shown is a visible satellite image draped on a tilted digital elevation model. The image shows the extreme topographic relief (over 

800 meters with a gradient of about 0.1) and the red-orange weathering of the unmined mineral occurrence. The study area (red) 

and numerical ground-water flow model domains (red and green) are also shown. Webster Pass and Red Cone Mountain are 

shown for reference.
Red

Cone

WP3 WP4

Chapter I

52 Understanding Contaminants Associated with Mineral Deposits

Figure 2. Red Cone, altitude 3,900 meters, in the upper reaches 

of Handcart Gulch in Colorado. Note the red staining from the 

oxidation of pyrite at concentrations of nearly 8 percent of the 

rock mass. This is the primary and natural source of low-pH water 

in the watershed. The locations of the mineral exploration holes 

WP3 and WP4 are shown as purple ovals.

base-flow discharge into stream channels or other surfacewater bodies. These processes cause the Handcart Gulch trunk 

stream to be naturally acidic (pH 2.6–4.6) with elevated metal 

concentrations. Because no mining has occurred in Handcart 

Gulch, the watershed also provides a unique opportunity to 

evaluate and monitor a natural acid-rock-drainage system 

and associated processes that liberate, transport, and deposit 

contaminants.

Wells and Field Data

In the summers of 2001 and 2002 a private mineral 

exploration company (Mineral Systems, Inc.) drilled and cored 

four deep, mineral exploration boreholes in Handcart Gulch 

(deep wells; fig. 3). The wells are located in the upper part of the 

watershed, the highest one at Webster Pass on the Continental 

Divide at an altitude of 3,690 meters, and range in depth from 

366 to 1,067 meters (fig. 3). Mineral Systems, Inc., donated the 

boreholes to the U.S. Geological Survey, who reconditioned them 

for use as research and monitoring wells. The deep wells were 

supplemented with nine new shallow wells (3 to 52 meters deep) 

located in five well nests adjacent to the trunk stream (shallow 

wells; fig. 3; Caine and others, 2006).

During the field seasons of 2003 to 2005, a variety of 

data were collected in the boreholes and from the watershed, 

including (1) basic geologic, fracture network, and fault data 

as well as rock samples for alteration mineralogy, elemental 

geochemistry, and thin-sectioning; (2) a tracer-dilution study 

in the trunk stream; (3) continuous hourly stream discharge 

and temperature data from the trunk stream for water year 

2005; (4) geophysical borehole-logging data (caliper, optical 

and acoustic imaging, heat-pulse flow metering, temperature, 

water conductivity, gamma, specific potential, and magnetic 

susceptibility); and (6) single-well, aquifer hydraulic test 

data. Ground- and surface-water samples were collected and 

analyzed for major and trace elements, multiple isotopes (Sr, 

S, O, and H), dissolved noble gases (including 3

He), tritium, 

chlorofluorocarbons, and 13C and 14C—the latter three for water 

age determinations.

Preliminary Results and Discussion

Research is ongoing in Handcart Gulch, and the site, 

wells, and installed instrumentation are intended for long-term 

monitoring. The following is a list of results and a sample of 

associated publications to date.

(1) Outcrop and well-log data indicate that the bedrock is 

complexly deformed and primarily consists of tightly folded 

felsic and mafic Precambrian metamorphic rocks (figs. 3 and 

7). Geologic structures include the Montezuma ductile shear 

zone (fig. 4), cut by a few brittle, small-displacement faults, 

and high-intensity joint networks. Down-hole televiewer and 

flow-meter data indicate that the high intensity, open-joint 

networks persist to depth. However, the percentage of fractures that are hydraulically conductive is small (fig. 7). There 

also are a few discrete, polymetallic veins in the watershed. 

Of all these structures, only the open-joint networks have a 

significant function in ground-water processes.

The dominant hydrothermal alteration assemblage is 

quartz-sericite-pyrite (qsp) commonly found in felsic lithologies with an average concentration of about 8 weight-percent 

fine-grained, disseminated pyrite and quartz-pyrite veinlets. 

These are the primary source rocks for natural contamination 

to surface and ground waters. The intensity of hydrothermal 

alteration decreases away from Webster Pass and Red Cone 

and transitions outward from qsp, to propylitic alteration 

(particularly in mafic amphibolites), to relatively unaltered 

rocks (figs. 2, 3, and 4).

The pervasive hydrothermal qsp alteration extends 

to as much as 1,000-m depth from the ground surface. 

Beneath this depth, rocks are generally more weakly to propylitically altered, particularly in amphibolitic lithologies. 

On the basis of the four WP and four HC bedrock wells, 

zones of pyrite oxidation related to infiltrating ground water 

appear to generally reflect a fracture-controlled unsaturated 

zone, ranging in depth from about 100 m below surface at 

higher elevations to just a few meters near the base of the 

study area (Caine and others, 2006).

(2) A tracer-dilution study (Kimball and others, 2002) was 

conducted in the upper 2 kilometers of the Handcart 

Gulch trunk stream to quantify stream discharge and to 

delineate locations of metal loading. Data indicated that 

discharge, acidity, and loading of zinc and copper increase 

in the downstream direction, and zinc and copper concentrations exceed aquatic-life standards (fig. 5).
Chapter I

Chapter I: U.S. Geological Survey Research in Hardcart Gulch, Colorado 53

Figure 3. Simplified geologic map (modified from Lovering, 1935), block diagram, and cross section of the Handcart 

Gulch study area draped on a digital elevation model showing the location of the research wells. Also shown is a 

geological conceptual model in cross section depicting the major features that might control the ground-water flow 

system and associated contaminant sources.

(3) Ground-water samples from Handcart Gulch are 

Ca-SO4 type and range in pH from 2.5 to 6.8. Most 

samples (75 percent) have pH values between 3.3 

and 4.3 (Verplanck and others, 2007). Surface-water 

samples are also Ca-SO4

 type and have a narrower 

range in pH (2.7 to 4.0). Ground- and surfacewater samples vary from relatively dilute (specific 

conductance of 68 μS/cm) to concentrated (2,000 μS/cm). 

Compared to other unmined, porphyry-mineralized 

areas in the Southern Rocky Mountains, dissolved 

copper concentrations in Handcart Gulch ground and 

surface waters are relatively high and dissolved zinc 

concentrations are relatively low (fig. 6; Verplanck and 

others, in press).
2.5

3.0

3.5

4.0

4.5

pH, IN STANDARD UNITS

COPPER, IN MICROGRAMS PER LITER ZINC, IN MICROGRAMS PER LITER 100

200

300

400

500

0

0

200

400

600

800

1,000

1,200

DISTANCE DOWNSTREAM, IN METERS

0 500 1,000 1,500 2,000

0 500 1,000 1,500 2,000

0 500 1,000 1,500 2,000

BW1 BW2 BW3 BW4

FW5

DISTANCE DOWNSTREAM, IN METERS

DISTANCE DOWNSTREAM, IN METERS

FW5

BW1 BW2 BW4BW3

FW5

BW1 BW3BW2 BW4

(2350)

CO aquatic

life Std.

(5 μg/L)

CO aquatic

life Std.

(50 μg/L)

Stream

Inflows

Bedrock wells

Colorado Aquatic Life Standard

EXPLANATION

Chapter I

54 Understanding Contaminants Associated with Mineral Deposits

Figure 5. Examples of pH and dissolved constituent load data for zinc (Zn) and copper (Cu) as a function of downstream distance 

along the trunk stream in Handcart Gulch. Constituent concentrations for springs (inflows) and bedrock wells (BW) are also shown.

Figure 4. Hydrothermal alteration and geologic structure map draped on a digital elevation model as shown in figure 3. 

Note: Webster Pass is at the headwaters of Handcart Gulch and the northwest edge of the study area for reference.
Chapter I

Chapter I: U.S. Geological Survey Research in Hardcart Gulch, Colorado 55

(4) Up to 13 meters of well-indurated ferricrete forms a confining unit, resulting in artesian conditions in the bedrock 

near the trunk stream. Measured static water levels in the 

bedrock under the stream were as much as 3 meters above 

ground surface. Sustained or seasonal artesian flow occurs 

in many of the bedrock wells adjacent to the trunk stream 

(with a maximum flow of 76 liters or about 20 gallons per 

minute, Caine and others, 2006). Because the ferricrete 

impedes ground-water discharge to the stream, much of 

the bedrock ground water may flow down-drainage underneath the stream, making its discharge location uncertain.

(5) Temperature-depth profiles from the deep wells become 

nearly linear at depths greater than about 100 meters 

below the water table (greater than about 200 meters 

below ground surface), suggesting that active ground-water 

circulation does not exceed these depths (see Manning and 

Caine, Chapter J, this volume).

(6) Tritium/helium (3H/3He) ground-water age results indicate increasing ground-water age with depth (Manning 

and Caine, 2007, and chap. J, this volume). Mean ages 

from integrated bedrock ground-water samples collected 

near the trunk stream are very similar. These data are 

consistent with a relatively simple representation of the 

flow system in which recharge and circulation depth are 

constant throughout the drainage (see Manning and Caine, 

Chapter J, this volume, for details). This in turn supports a 

conceptual model where the watershed aquifer system can 

be represented as equivalent porous media in spite of the 

complexities in the geology and fracture networks. 

(7) Seasonal water-table fluctuations in the upper part of the 

watershed are very large (up to about 45 meters) indicating significant seasonal cycles of saturation and oxygenation in the thick unsaturated zone in the upper reaches 

of the watershed. This may be an important mechanism 

controlling pyrite oxidation and the liberation of acidity 

and metals to ground and surface waters.

(8) Geological, geophysical, hydrological, water age, and 

thermal data were used as input for constructing a series 

of numerical ground-water flow models and a water 

budget (Kahn and others, 2007). Single-well aquifer-test 

data were numerically modeled with MODFLOW-2000 

(Harbaugh and others, 2000) to estimate hydraulic conductivities (K) and specific storage values (S) for the surface deposits and bedrock. Model-derived K and S values 

for the surficial deposits are about 10–6 to 10–5 m/s and 

about 10–4 to 10–3 per meter, respectively, and values for 

the bedrock are about 10–9 to 10–6 m/s and about 10–5 to 

10–4 per meter, respectively. These results indicate groundwater flow rates through fracture networks can be high 

in the bedrock aquifer, particularly near the trunk stream. 

Therefore, bedrock ground water is a nontrivial component of the hydrologic system.

Figure 6. Variation in pH and dissolved copper (A) and zinc 

(B) concentration of ground and surface waters from five porphyry 

mineralized areas. HCG = Handcart Gulch waters are indicated in red.

EXPLANATION

COPPER, IN MILLIGRAMS 

PER LITER

102

101

100

10–1

10–2

10–3

ZINC, IN MILLIGRAMS 

PER LITER

pH, IN STANDARD UNITS

pH, IN STANDARD UNITS

Handcart waters

102

101

100

10–1

10–2

10–3

Animas

Mt Emmons

HCG surface

HCG wells

E. Alpine G.

Red River surface

Red River wells

2 3 4 5 6 7 8 9

2 3 4 5 6 7 8 9

Handcart waters

B

A
Figure 7. An example of composite geophysical and lithological logs from Handcart Gulch wells. Optical televiewer image (OBI) shows surface depositssinusoidal traces of open fractures in WP4 (all other logs from shallow HCBW1 next to the trunk stream). Fracture orientations derived from the acoustic tplotted on an equal area projection are consistent with outcrop and regional fracture orientations. Heat-pulse flow meter (HPFM data shown as FLOW) inmagnitude in the well and does not correlate with fracture orientation or fracture intensity. Inflow does correlate with temperature and conductivity. Lithoalteration log data are also shown for HCBW1 shallow bedrock well (red layered material is ferricrete, green diagonal pattern is amphibolite; P = propylitisericite-pyrite or argillic alteration). See Caine and others (2006 ) for details. gpm, gallons per minute; μS/cm, microsiemens per centimeter; frac/ft, fracturCelsius; m, meter.
Chapter I

Chapter I: U.S. Geological Survey Research in Hardcart Gulch, Colorado 57

A coupled heat, mass, and fluid-transport finite-element 

model of the watershed incorporates the water-age and 

temperature-depth data. Successful calibration to observed 

heads and temperatures required specifying permeabilities similar to those derived from the aquifer-test data, decreasing permeability with depth, applying a recharge rate of 10–20 cm/yr 

to the bedrock aquifer, and using relatively high flow velocities 

under the stream in the downstream direction (Manning and 

Caine, 2007).

A MODFLOW-2000 watershed-scale finite-difference model was also constructed using stream discharge, 

precipitation, and other climate data from an adjacent 

watershed to estimate a water budget for Handcart Gulch. 

During water year 2005, precipitation in the watershed was 

2.16 × 10–3 km3

 and total stream discharge was 1.28 × 10–3 km3

of which base flow accounted for about 4.73 × 10–4 km3

(Kahn and others, 2007). Estimated base flow for the year 

equates to about 1.25 × 108

 gallons of water, about 22 percent 

of precipitation, and about 37 percent of total stream discharge. Modeling components of the water budget suggest 

that, under normal climatic conditions, water is available to recharge the ground-water flow system (Kahn and 

others, 2007).

Acknowledgments

This work would not have been possible without the 

generosity of Dr. Charles S. Robinson of Mineral Systems, 

Inc., who donated the deep boreholes in the study area for 

research purposes. Cooperation with the USDA Forest Service 

and the Colorado Geological Survey is much appreciated. 

Numerous field partners whose time and efforts we greatly 

appreciate conducted and assisted with various types of field 

work: Briant Kimball, Katherine Walton-Day, Robert Runkel, 

Richard Wanty, Greg O’Neill, and others. We thank Cliff Taylor 

and Carma San Juan of the USGS for constructive reviews 

of this report. This work was funded by the U.S. Geological 

Survey’s Mineral Resources and Mendenhall Postdoctoral 

Fellowship Programs.

References Cited

Botinelly, Theodore, 1979, Mineralogy as a guide for exploration in the Montezuma District, central Colorado: 

U.S. Geological Survey Open-File Report 79–1177, 18 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 

Handcart Gulch, Colorado—An alpine watershed affected by 

metalliferous hydrothermal alteration: U.S. Geological Survey 

Open-File Report 2006–1189, 14 p. http://pubs.usgs.gov/

of/2006/1189/

Harbaugh, A.W., Banta, E.R., Hill, M.C., and McDonald, 

M.G., 2000, MODFLOW-2000, the U.S. Geological Survey 

modular ground-water model—User guide to modularization concepts and the ground-water flow process: 

U.S. Geological Survey Open-File Report 2000–92, 121 p.

Kahn, K.G., Ge, S., Caine, J.S., and Manning, A.H., 2007, 

Characterization of the shallow groundwater system in an 

alpine watershed, Handcart Gulch, Colorado: Journal of 

Hydrogeology: DOI: 10.1007/s10040–007–0225–6.

Kimball, B.A., Runkel, R.L., Walton-Day, K., and Bencala, 

K.E., 2002, Assessment of metal loads in watersheds 

affected by acid mine drainage by using tracer injection synoptic sampling—Cement Creek, Colorado, USA: Applied 

Geochemistry, v. 17, p. 1183–1207.

Lovering, T.S., 1935, Geology and ore deposits of the Montezuma quadrangle, Colorado: U.S. Geological Survey 

Professional Paper 178, 119 p.

Manning, A.H., and Caine, J.S., 2007, Groundwater 

noble gas, age, and temperature signatures in an alpine 

watershed—Valuable tools in conceptual model development: Water Resources Research, v. 43, W04404, DOI: 

10.1029/2006WR005349.

Mast, M.A., Verplanck, P.L., Wright, W.G., and Bove, D.J., 

2007, Characterization of background water quality in the 

upper Animas River watershed, Chapter E7 in Church, 

S.E., von Guerard, Paul, and Finger, S.E., eds. Integrated 

investigations of environmental effects of historical mining 

in the Animas River watershed, San Juan County, Colorado: 

U.S. Geological Survey Professional Paper 1651, 1096 p., 

p. 347–386.

Runnells, D.D., Shepherd, T.A., and Angino, E.E., 1992, Metals in water-determining natural background concentrations 

in mineralized areas: Environmental Science and Technology, v. 26, p. 2316–2323.

Tweto, Ogden, and Sims, P.K., 1963, Precambrian ancestry of 

the Colorado Mineral Belt: Geological Society of America 

Bulletin, v. 74, p. 991–1014.

Verplanck, P.L., Manning, A.H., Kimball, B.A., McCleskey, 

R.B., Runkel, R.L., Caine, J.S., Adams, M., Gemery-Hill, 

P.A., and Fey, D.L., 2007, Ground- and surface-water 

chemistry of Handcart Gulch, Park County, Colorado, 2003–2006: U.S. Geological Survey Open-File 

Report 2007–1020.

Verplanck, P.L., Nordstrom, D.K., Bove, D.J., Plumlee, 

G.S., and Runkel, R.L., in press, Naturally acidic surface 

and ground waters draining porphyry-related mineralized 

areas of the southern Rocky Mountains, Colorado and 

New Mexico: Applied Geochemistry.
58 Chapter J: Developing a Conceptual Model of Ground-Water Flow 

in an Alpine Watershed

by Andrew H. Manning and Jonathan Saul Caine

Introduction

Many acid-rock and acid-mine drainage sites are located 

in mountainous terrain. A growing number of studies indicate 

that ground-water inputs exert a major influence on streamwater chemistry in mountain watersheds (Soulsby and others, 

2000; Kimball and others, 2001, 2002; Liu and others, 2004); 

ground water may compose a substantial fraction of the total 

annual streamflow (20–50 percent; Tiedeman and others, 

1998; Uhlenbrook and others, 2002; Kosugi and others, 2006) 

and commonly has considerably higher concentrations of 

dissolved constituents than precipitation returned rapidly to 

the stream as surface runoff. Therefore, understanding how 

streams become contaminated by low-pH, metal-rich water 

in many cases requires understanding the ground-water flow 

system feeding the stream.

The transport of dissolved constituents in ground water 

is best represented by a coupled numerical ground-water flow 

and solute-transport model. Building such a numerical model 

requires first developing a conceptual model of the groundwater flow system that includes its most fundamental characteristics, such as the location of its boundaries, the location of 

recharge and discharge, and the distribution of zones of similar 

hydraulic conductivity (hydrogeologic framework). Unfortunately, in all but the rarest cases, ground-water data from 

mountain watersheds are insufficient to develop a defensible 

Overview

Understanding how ground water transports 

metals and acid to mountain streams is critical in order 

to effectively manage mountain watersheds affected 

by acid-rock and acid-mine drainage. The transport of 

dissolved constituents in ground water is best represented by a coupled numerical ground-water flow and 

solute-transport model. Building such a numerical 

model requires first developing a conceptual model of 

the ground-water flow system that includes its most 

fundamental characteristics. This chapter describes the 

development of a conceptual model of ground-water 

flow in Handcart Gulch, an alpine watershed in the 

Front Range of Colorado affected by acid-rock drainage. New applications of ground-water age and temperature data that utilize the site’s unique monitoringwell network were essential in this process and resulted 

in a conceptual model considerably more accurate and 

defensible than what could have been developed using 

standard hydrologic and chemical data alone.

conceptual model, let alone to construct and calibrate a 

numerical model with any real confidence. Data from monitoring wells in mountain watersheds are particularly scarce, 

especially near the uppermost parts of watersheds. Thus, 

mountain ground-water flow systems remain poorly understood. Conceptual models of these systems that rely upon 

simple assumptions are dubious because these systems are 

potentially highly complex; they commonly involve structurally complex rocks, extreme head gradients (ground-slope 

angles of 10–40°), and extremely fluctuating recharge due to 

seasonal snowmelt.

A primary motivation for developing the Handcart Gulch 

study site was to obtain sufficient ground-water data to build 

a numerical ground-water flow and solute-transport model 

of an alpine watershed affected by acid-rock drainage (Caine 

and others, Chapter I, this volume). Wells with depths ranging 

from 3 to 342 m were installed along the trunk stream and in 

upper parts of the watershed, the highest well being located 

directly on the Continental Divide at 3,688 meters above sea 

level (fig. 1). This chapter describes the development of a 

conceptual model of ground-water flow in the watershed, the 

first critical step in building a numerical flow and transport 

model. New applications of ground-water age and temperature 

data were essential in this process and resulted in a conceptual 

model that is considerably more defensible than what could 

have been developed using standard hydrologic data alone.

Methods

Detailed descriptions of the physiography, geology, climate, and general hydrology of Handcart Gulch are provided 

in Caine and others (Chapter I, this volume) and Manning and 

Caine (2007). Hydraulic head measurements, aquifer tests, 

core logging, outcrop mapping, borehole geophysical logging, 

and other data types from the site reveal several important 

general aspects of the ground-water flow system (Caine and 

others, 2006; Kahn and others, 2008). The two fundamental 

characteristics addressed specifically in this chapter include 

(1) the depth to which ground-water flow actively occurs 

(aquifer thickness); and (2) the degree to which aquifer thickness, recharge rate (probably controlled in part by permeability), and porosity vary throughout the watershed. The latter is 

particularly uncertain given the limited well coverage. These 

two pieces of information are essential components of any 

conceptual model of a ground-water flow system and had to 

be attained using nontraditional applications of ground-water 

temperature and age data.

We determined aquifer thickness (envisioned as a 

watershed-scale average thickness) using temperature-depth 

profiles from borings that transect the entire thickness of 

the aquifer. The concept that bedrock ground-water flow in 

mountains dominantly occurs in a shallow, higher permeability 
59

Profiles were measured in 2004 by using a standard downhole 

temperature/conductivity logging tool following procedures 

detailed in Manning and Caine (2007).

We evaluated potential watershed-scale variations in 

aquifer thickness, recharge rate, and porosity by comparing the 

mean age of ground water discharging to the stream at different locations along the stream. Haitjema (1995) demonstrated 

that the mean age of ground water discharging to a stream 

should be constant throughout a watershed if aquifer thickness 

(z), recharge rate (R), and porosity (n) are constant throughout 

that watershed (fig. 2A). Therefore, if ground-water samples 

can be collected at multiple locations along a stream such that 

each sample integrates all ground water discharging to the 

stream at that location (flow-weighted sample), then the mean 

age of these different flow-weighted samples should reflect 

watershed-scale variation in z, R, and n. More specifically, if 

z, R, and n are constant, then the mean age of flow-weighted 

samples should be constant (fig. 2A). Conversely, if z, R, and 

n vary significantly on a watershed scale due to geological 

complexities such as major fault zones intersecting the stream 

and lithologic variations, then the mean age of flow-weighted 

samples should also vary significantly (fig. 2B). Herein, the 

former case is referred to as a “uniform flow system” and 

the latter case as a “complex flow system.” Observing uniform mean ages of flow-weighted samples along a stream, of 

course, does not prove the presence of a uniform flow system. 

Nonetheless, such uniform mean ages still serve as supporting 

evidence that these parameters either are relatively constant 

or vary in a systematic way on a watershed 

scale and that a relatively simple equivalent 

porous-media model (which represents the 

system as a continuum without discrete features) might represent the ground-water flow 

system sufficiently well to provide useful 

information about watershed-scale flow and 

transport processes.

Ground-water age was determined using 

the tritium/helium-3 method (see Solomon 

and Cook [2000] for a comprehensive review). 

Tritium (3

H) is a radioactive isotope of hydrogen 

that occurs in water and decays to 3He (a dissolved noble gas) with a half-life of 12.32 years. 

The age of a ground-water sample is determined 

by measuring both 3

H and tritium-derived 

zone (active zone) that overlies a deeper, lower permeability 

zone hosting little flow (inactive zone) has been described 

by several workers (Snow, 1973; Robinson and others, 1974; 

Mayo and others, 2003). Higher permeability at shallower 

depth is generally attributed to a greater degree of weathering and (or) smaller overburden loads allowing more fractures 

to remain open. Temperature-depth profiles serve as a direct 

and continuous measure of the change in flow rate with depth 

because ground temperatures are sensitive to ground-water 

flow rates. The transition between linear temperature-depth 

profiles with gradients similar to the local conductive geothermal gradient (conductive profiles) and nonlinear temperaturedepth profiles associated with advective heat transport from 

ground-water flow (disturbed profiles) should occur at Darcy 

flow velocities of roughly 1 cm/yr in mountain watersheds 

(Domenico and Palciauskas, 1973; Forster and Smith, 1989). 

Estimated recharge rates in alpine watersheds are typically 

tens of centimeters per year (Hely and others, 1971; Wasiolek, 

1995). Therefore, flow velocities in the active zone generally should be high enough to result in disturbed profiles, and 

flow velocities in the inactive zone generally should be low 

enough (less than 10 percent of the recharge rate) to result in 

conductive profiles.

Temperature-depth profiles presented here were measured in wells WP1 and WP2 (fig. 1), which are located in the 

upper part of the watershed and have total depths of 336 m and 

236 m, respectively (Caine and others, Chapter I, this volume). 

Figure 1. Topographic map of Handcart Gulch 

study area showing locations of deep wells 

(WP1–4, in red), bedrock wells near trunk stream 

(HCBW1–4 and HCFW5, in yellow), and springs 

(S1–10, in white). Base map from U.S. Geological 

Survey Montezuma quadrangle, 1:24,000 (1958).

105°52'33''W

39°

31'

49''N

0 3000 FEET

Study Area

and

Watershed

Boundary

WP1

WP2 WP4

WP3

S7

S10

S6

S5

HCBW1

S4

S9

S1

HCBW2 HCBW3

HCBW4

S2

S8 S3

HCFW5

0

1500

400 800 METERS

N
Chapter J

60 Understanding Contaminants Associated with Mineral Deposits

(tritiogenic) 3He concentrations and then using their ratio along 

with the radioactive decay equation to compute the time elapsed 

since the sampled water entered the saturated zone. The method 

can be used to date water less than 50 years old.

Samples discussed here were collected from 10 springs 

and 5 bedrock wells in late summer and fall of 2003 and 

were analyzed for dissolved gases and tritium. Details regarding sampling procedures, analytical techniques, and 3

H/3He 

age calculations are available in Manning and Caine (2007). 

All sampled springs and wells are located next to the stream 

except HCBW4, which is set back 60 m from the stream. 

Wells HCBW1–4 (fig. 1) are completed exclusively in bedrock 

and have total depths of 30–52 m. Well HCFW5 (total depth 

of 7 m) is completed in both bedrock and overlying ferricrete 

but is considered a bedrock well because significant artesian 

flow was encountered when the bedrock was penetrated during drilling. All five bedrock wells are open throughout the 

bedrock interval. Additional well information is provided by 

Caine and others (2006).

Two types of samples were collected from the bedrock wells: discrete and integrated. Discrete samples were 

collected from near the bottom of the well in order to 

characterize ground water at deeper levels of the bedrock 

aquifer. Integrated samples were collected from above the 

well screen. Four of the five bedrock wells are artesian, 

HCBW4 being the exception. The artesian flow means that 

the integrated samples should integrate a broad spectrum 

of flow paths in the bedrock en route to the stream, thereby 

approximating a flow-weighted sample. The integrated sample 

from HCBW4 was collected using a submersible pump and 

pumping at a high flow rate. Given the well’s long screen 

(29 m) and relatively close proximity to the stream, the 

integrated sample from HCBW4 should also approximate a 

flow-weighted sample.

Results

Temperature-depth profiles from WP1 and WP2 are 

relatively smooth and do not suggest the presence of large, 

discrete inflows and outflows (fig. 3). Both profiles have an 

upper curved segment and a lower linear segment. Curved 

segments are concave upward, indicative of downward flow 

(recharge) and (or) lateral flow from higher elevations. Linear 

segments in WP1 and WP2 have slopes of 21°C/km and 

28°C/km, respectively, consistent with expected conductive 

geotherms for the Front Range (20–25°C/km; Birch, 1950; 

Decker, 1969). In WP1, the profile becomes conductive at a 

depth of about 210 m, or about 100 m below the water table. 

In WP2, the profile becomes conductive at a depth of about 

130 m, or about 110 m below the water table. Therefore, 

profiles from WP1 and WP2 are consistent with diffuse flow 

in the active zone associated with pervasive fractures and suggest a maximum circulation depth of about 200 m, or about 

100 m below the water table. A maximum active zone thickness of about 200 m is consistent with estimates by Robinson 

and others (1974) and by Snow (1968) for nearby areas of the 

Front Range and with most estimates (100–200 m) for bedrock 

aquifers in other mountainous areas (Tiedeman and others, 

1998; Desbarats, 2002; Mayo and others, 2003).

Figure 2. Schematic diagrams illustrating two different conceptual 

models of ground-water flow in an alpine watershed underlain 

by fractured crystalline rock. (A) Uniform flow system in which 

aquifer thickness, z, recharge rate, R, and porosity, n, are relatively 

uniform throughout the watershed. Mean residence times, τ, of 

samples from wells along the creek that integrate all flow paths to 

the creek (flow-weighted samples) are uniform and equal to zn/R 

(Haitjema,1995). (B) Complex flow system in which z, R, and n vary 

throughout the watershed, resulting in variations in τ along the 

creek. K, hydraulic conductivity.

v v v vv v

z

z

z

R

R

R

R

Well

Stream

Active

zone

Inactive

zone 2

3

1

2

3

4

4

1

v v v vv v

z

z

Large z

Small R

R

R

B Complex flow system

A Uniform flow system

Well

Low-K

intrusive rock Fault

zone

High-n

hydrothermally

altered rock

Active

zone

Inactive

zone

1

zzzz zn

R

1

xxxx
Chapter J

Chapter J: Developing a Conceptual Model of Ground-Water Flow in an Alpine Watershed 61

Computed 3

H/3He ages are plotted relative to distance 

down the stream in figure 4. The ages range from 0.1 to 

35.9 years and generally have an uncertainty of 0.5–2.0 years. 

The integrated well samples presumably contain a mixture of 

waters of varying age. Therefore, the ages shown in figure 4 

for these samples are mean ages computed from the 3

H and 3He 

measurements, assuming that the samples contain an exponential age distribution (Vogel, 1967; Cook and Böhlke, 2000).

The 3

H/3He ages indicate that ground-water age in the 

vicinity of the stream increases with depth, as expected in a 

uniform flow system. Spring samples collected at the surface 

are the youngest (mainly less than 3 years old), discrete well 

samples collected from the bottom of the wells are the oldest 

(19–36 years), and integrated well samples containing water 

from a range of intermediate depths are of intermediate age.

The ages of the integrated well samples from HCBW2 

downstream to HCFW5 are remarkably uniform, ranging from 

8 to 11 years (fig. 4). The similarity in the age of these flowweighted samples is consistent with a uniform flow system 

downstream from HCBW2, which includes most of the study 

area. The 3

H/3He ages of both discrete and integrated well samples collected from HCBW1 indicate that bedrock ground water 

is older at this location than at other locations in the watershed. Ground-water temperatures at depths greater than 10 m 

(below the zone of seasonal oscillation) are warmer in HCBW1 

(3.6°–3.9°C) than in the other bedrock wells (2.3°–3.1°C), 

which also is consistent with water in HCBW1 being anomalously old. The reason for the older water at HCBW1 is not 

clear and requires further investigation.

Figure 3. Temperature-depth profiles from WP wells. Both 

start at the water table. Dashed line is conductive geothermal 

gradient inferred from the lower linear portion of the profile. 

km, kilometers; °C, degrees Celsius.

Figure 4. Distance downstream relative to 3

H/3He age for springs 

and bedrock well samples. BW1–4 and FW5 along top axis 

indicate well locations. Samples collected from springs are the 

youngest. Discrete well samples, collected from the bottom of the 

well screen, are the oldest. Integrated well samples, collected 

from the entire well screen, are of intermediate age. Dashed lines 

indicate the relatively narrow zone of variation of mean ages for 

integrated well samples (HCBW1 excepted). One sigma error bars 

are displayed on symbols. 

0 100 200 300 400 500 600 700 0

5

10

15

20

25

30

35

40

BW1 BW2 BW3 BW4 FW5

Spring

Well - Discrete

Well - Integrated

DISTANCE DOWNSTREAM, IN METERS

TRITIUM/HELIUM-3 AGE, IN YEARS

0

50

100

150

200

250

300

350

400

0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0

DEPTH, IN METERS

WP1

WP2

28°C/km

21°C/km

TEMPERATURE, IN DEGREES CELSIUS

Active zone

Inactive zone

Active zone

Inactive zone
Chapter J

62 Understanding Contaminants Associated with Mineral Deposits

Conclusions

Temperature-depth profiles indicate active ground-water 

circulation to a maximum depth (aquifer thickness) of about 

200 m, or about 100 m below the water table in the study area. 

Borehole temperature logging is a reliable method of identifying aquifer thickness in alpine watersheds underlain by 

fractured crystalline rock because linear profiles with slopes 

similar to the conductive geothermal gradient are reliable indicators of very low flow velocities characteristic of the underlying inactive zone.

The ages of integrated bedrock samples, assumed to be 

approximately flow weighted due to artesian flow, are remarkably consistent along the stream, four of five being from 8 to 

11 years old. This result, in combination with other hydrologic 

and geologic data, supports a simple watershed-scale conceptual model of ground-water flow in which permeability 

is primarily a function of depth, and where recharge, aquifer 

thickness, and porosity are relatively uniform throughout most 

of the watershed. The conceptual model’s simplicity is surprising given the geological complexity of the study area. A flow 

system of this sort could be reasonably well represented with 

an equivalent porous-media model calibrated with limited 

data, and such a model may be used to simulate solute transport and to explore chemical mass balance and fluxes within 

the watershed.

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information, lithologic logs, water-level data, and overview of research in Handcart Gulch, Colorado—An alpine 

watershed affected by metalliferous hydrothermal alteration: 

U.S. Geological Survey Open-File Report 2006–1189, 14 p.

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for groundwater flow and solute transport, in Cook, P.G., 

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hydrology: New York, Kluwer Academic Publishers, p. 1–30.

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ground-water flow: Geological Society of America Bulletin, 

v. 84, p. 3803–3814.

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groundwater flow on thermal regimes in mountainous 

terrain—A model study: Journal of Geophysical Research, 

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Hely, A.G., Mower, R.W., and Harr, C.A., 1971, Water 

resources of Salt Lake County, Utah: Utah Department 

of Natural Resources Technical Publication 31, 192 p.

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in an alpine watershed—Handcart Gulch, Colorado: Hydrogeology Journal, v. 16, p. 103–121.

Kimball, B.A., Runkel, R.L., and Gerner, L.J., 2001, Quantification of mine drainage inflows to Little Cottonwood Creek, 

Utah, using a tracer-injection and synoptic-sampling study: 

Environmental Science and Technology, v. 40, p. 1390–1404.

Kimball, B.A., Runkel, R.L., Walton-Day, Katherine, and 

Bencala, K.E., 2002, Assessment of metal loads in watersheds 

affected by acid mine drainage by using tracer injection and 

synoptic sampling, Cement Creek, Colorado, USA: Applied 

Geochemistry, v. 17, p. 1183–1207.

Kosugi, Ken’ichirou, Katsura, Shin’ya, Katsuyama, Masanori, 

and Mizuyama, Takahisa, 2006, Water flow processes in 

weathered granitic bedrock and their effects on runoff generation in a small headwater catchment: Water Resources 

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noble gas, age, and temperature signatures in an alpine 

watershed—Valuable tools in conceptual model development: Water Resources Research, v. 43, W04404, 

doi:10.1029/2006WR005349.
Chapter J

Chapter J: Developing a Conceptual Model of Ground-Water Flow in an Alpine Watershed 63

Mayo, A.L., Morris, T.H., Peltier, Steven, Petersen, E.C., 

Payne, Kelly, Holman, L.S., Tingey, David, Fogel, Tamara, 

Black, B.J., and Gibbs, T.D., 2003, Active and inactive 

groundwater flow systems—Evidence from a stratified, 

mountainous terrain: Geological Society of America Bulletin, v. 115, p. 1456–1472.

Robinson, C.S., Lee, F.T., Scott, J.H., Carroll, R.D., Hurr, 

R.T., Richards, D.B., Mattei, F.A., Hartmann, B.E., and 

Abel, J.F., 1974, Engineering geologic, geophysical, hydrologic and rock-mechanics investigations of the Straight 

Creek Tunnel site and pilot bore, Colorado: U.S. Geological 

Survey Professional Paper 815, 158 p.

Snow, D.T., 1968, Hydraulic character of fractured metamorphic rocks of the Front Range and implications to the Rocky 

Mountain Arsenal well: Golden, Colorado School of Mines 

Quarterly, v. 63, p. 167–199.

Snow, D.T., 1973, Mountain groundwater supplies: The 

Mountain Geologist, v. 10, p. 19–24.

Solomon, D.K., and Cook, P.G., 2000, 3

H and 3He, in Cook, 

P.G., and Herczeg, A.L., eds., Environmental tracers in subsurface hydrology: New York, Kluwer Academic Publishers, p. 397–424.

Soulsby, Chris, Malcolm, Rob, and Malcolm, I.A., 2000, 

Groundwater in headwaters—Hydrological and ecological significance: Geological Society Special Publication, 

no. 182, p. 19–34.

Tiedeman, C.R., Goode, D.J., and Hsieh, P.A., 1998, 

Characterizing a ground water basin in a New England 

mountain and valley terrain: Ground Water, v. 36, 

p. 611–620.

Uhlenbrook, Stefan, Frey, Markus, Leibundgut, Christian, 

and Maloszewski, Piotr, 2002, Hydrograph separations 

in a mesoscale mountainous basin at event and seasonal 

timescales: Water Resources Research, v. 38, no. 6, 

doi:10.1029/2001WR000938.

Vogel, J.C., 1967, Investigation of groundwater flow with 

radiocarbon, in Isotopes in hydrology, IAEA–SM–83/7: 

Vienna, International Atomic Energy Agency, 

p. 355–369.

Wasiolek, Maryann, 1995, Subsurface recharge to the Tesuque 

aquifer system from selected drainage basins along the western side of the Sangre de Cristo Mountains near Santa Fe, 

New Mexico: U.S. Geological Survey Water-Resources 

Investigations Report 94–4072, 72 p.
64 

that have been essentially abandoned by previous mine owners. 

Many of these abandoned mines are affected by acid drainage that is caused by weathering of acid-generating minerals; 

principal among these minerals is pyrite (FeS2

). In the presence 

of oxygen and water, pyrite and other sulfide minerals react to 

yield sulfuric acid (H2

SO4), which can lower stream pH, leach 

toxic metals, and substantially degrade water quality (fig. 1). 

Weathering of mine waste and consequent acid drainage has 

overwhelmed the acid-neutralizing capacity (ANC) of some 

streams already affected by natural weathering of pyritic country rocks (Yager and others, 2000; Mast and others, 2007).

Country rocks that host mineralization provide clues as 

to possible reclamation strategies that might be used to alleviate acid-mine drainage issues. This is due to the presence of 

acid-neutralizing minerals, such as calcite (CaCO3

), that form 

in some altered igneous country rocks. Limestone is nearly 

pure calcite and is commonly transported from long distances 

to reclamation sites that require a substance that can effectively 

neutralize acidity. If a local source of acid-neutralizing country 

rock can be identified, this could lessen the need to haul limestone to mine sites, thus reducing reclamation costs and perhaps 

providing a potential source of jobs for communities that are in 

transition from a mining-based economy once mining ceases. 

The purpose of this study was, therefore, to identify the local 

source rocks that can aid in mine-waste cleanup.

A map and database that identify the acid-neutralizing 

capacity (ANC) for 59 samples were generated as a result of 

this study (fig. 2). This map and accompanying data (Yager 

and others, 2005, 2008) can guide local land managers to outcrops with a high net acid production (NAP) and to high-ANC 

rocks suitable for remediation of acid drainage.

Methods Used to Determine 

Environmental Rock Properties

Two important environmental rock properties of igneous 

country rocks that can be measured and quantified are NAP 

and ANC. A field sampling effort was completed to collect 

representative examples from all igneous rock types in the 

study area; NAP and ANC were subsequently determined 

for all samples. In addition, rocks were analyzed for majorand trace-element chemical compositions, CO2

, carbon from 

carbonate, quantitative mineralogy, and physical properties 

(magnetic susceptibility and resistivity) (Yager and others, 

2005, 2008). NAP and ANC are correlated with rock chemical composition and mineralogy; therefore, it was useful to 

quantify these rock characteristics. In addition, rock physical 

properties were determined as ground-truth verification of 

airborne geophysical datasets (Yager and others, 2005, 2008). 

Chapter K: Environmental Rock Properties at Abandoned Mine 

Lands that Generate or Neutralize Acid Drainage, Silverton, Colorado

Overview

Land managers are interested in the environmental rock properties, net acid production (NAP), and 

acid-neutralizing capacity (ANC) of local bedrocks 

that are host to base- and precious-metal mineralization. This study addresses these properties for igneous 

rocks near Silverton, Colorado, and has identified 

volcanic units that are currently used by land managers to help mitigate the effects of acid drainage at mine 

sites. This work has implications for reducing hauling 

costs if local ANC rocks could be used in combination 

with or in place of limestone, the rock type traditionally transported to mine sites to neutralize acid drainage. Detailed studies including field work, mineralogy, geochemical analyses, rock physical properties 

(magnetic susceptibility), and laboratory investigations 

(acid titration experiments) aid in understanding the 

characteristic rock properties that contribute to generating or neutralizing acid drainage.

Introduction

This study is focused on the historical mining area of 

Silverton, Colorado, in the western San Juan Mountains, a 

region affected by two caldera-forming events that occurred 

about 28 million years ago. The calderas (collapsed volcanoes) were infilled by a nearly 1-km-thick accumulation of 

lava flows that were subsequently hydrothermally altered and 

locally mineralized with base metals (copper-lead-zinc) and 

precious metals (gold-silver). Acid water that formed from 

natural weathering processes emanated from hydrothermally 

altered and mineralized rocks in the Silverton area long before 

any mining activity. Historical observations in the region by 

Spanish expeditions in 1776 describe springs that “flowed red 

in color” and were “hot and ill-tasting” (Vélez de Escalante, 

1792). The Hayden expedition in 1874 documented poor water 

quality in the study area, referring to Mineral Creek as “so 

strongly impregnated with mineral ingredients as to be quite 

unfit to drink” (Rhoda, 1876). These explorers’ descriptions 

indicate there was some natural acid drainage in the area prior 

to mining. Since the 1870s when mining began, large volumes 

of mine-waste rock containing acid-generating minerals were 

concentrated at the surface, adding to the acid and metal burden 

to streams already affected by natural weathering processes.

Today, Federal and State land managers and private 

stakeholders throughout the Western United States are actively 

involved in the cleanup of watersheds affected by metal mines 

by Douglas B. Yager
65

This was done to determine whether correlations among 

physical and environmental properties of rock could enable 

regional mapping of outcrops with varying NAP and ANC by 

using airborne geophysical datasets (McCafferty and others 

this volume, Chapter L). The following sections define acidity, 

discuss how acid can be neutralized, and relate how NAP and 

ANC are measured.

Acidity and How It Is Neutralized

Acidity is a function of the concentration of H+ in solution. Acidity is measured with a pH probe that detects and 

records the exponential quantity of H+

 ions. A one-unit change 

in pH is 10 times different than the previous whole unit. It 

is recorded on a logarithmic scale between pH 1 (acid) and 

pH 14 (alkaline) with pH 7 being neither acid nor alkaline 

but neutral. Drinking water is commonly pH 7.

The concentration of H+

 needs to be reduced to decrease 

acidity and increase pH. One way to increase pH is to expose 

acid solutions to rocks that contain acid-neutralizing minerals that consume H+

. Minerals in Silverton-area igneous 

rocks that react with H+

 are calcite and chlorite [(Mg, Fe, 

Al)6

(Si, Al)4O10(OH)8] and to a lesser extent epidote [Ca2(Al, 

Fe)3

(SiO4)

3

(OH)]. Calcite reacts with H+ to eventually form free 

calcium and carbonic acid (H2

CO3). Carbonic acid is a weak 

acid, and it is only slightly acid under normal atmospheric conditions. The negatively charged hydroxyl group (OH–

) in chlorite reacts with the positively charged hydrogen ion in an acid 

solution to form water. Chlorite reactions are slow compared 

to calcite reactions. However, this could be beneficial from a 

remediation standpoint as it appears that chlorite may be able to 

decrease acidity long after calcite has been consumed. We are 

currently (2008) investigating the utility of using rocks containing both calcite and chlorite in remediation projects.

Measuring Net Acid Production (NAP)

NAP tests were done with a method described by 

Lapakko and Lawrence (1993) that uses a titration procedure 

to determine the amount of sodium hydroxide (NaOH), a 

strong alkaline base that would be required to neutralize acid 

generated by rocks. The test uses boiling hydrogen peroxide 

(H2

O2) to dissolve all sulfides in the sample available for 

sulfuric acid production. Once a powdered rock sample is 

dissolved in the hydrogen pyroxide solution, NaOH solution is 

added to the sample—the larger the volume of NaOH needed 

to raise the pH to neutral, the more the sample has the capacity to generate acid due to the quantity of dissolved sulfides. 

The amount of base added is calculated as calcium carbonate 

(CaCO3

) equivalents measured in kilograms per ton. Calcium 

Figure 1. (A) U.S. Geological Survey scientist measuring the acidity 

(pH) of a ground-water seep on the bank of Cement Creek near 

Prospect Gulch. Such acidic seeps and acidic surface water are 

toxic to aquatic life. No fish live in Cement Creek. (B) Abandoned mine 

southwest of Silverton, Colorado, along Mineral Creek.

A

B
Chapter K

66 Understanding Contaminants Associated with Mineral Deposits

Figure 2. Map showing 59 ANC sites. Vertical bars are proportionate to acid-neutralizing capacity in kilograms per ton calcium 

carbonate equivalent. Note that some vertical bar symbols are obscured by topography. Alteration assemblages (Bove and others, 2007) 

are draped on USGS DEM hillshade image (2 X vertical exaggeration). Green areas represent the propylitic alteration assemblage that 

affects most of the study area; rocks portrayed in red, brown, and yellow represent areas of late-stage intense alteration containing 

abundant pyrite and other sulfides that locally obliterate the acid-neutralizing capacity supplied by the propylitic assemblage.

carbonate equivalents are calculated because mine-waste 

remediation projects commonly use limestone to neutralize 

acidity. This test is a useful screening tool to eliminate highNAP samples from further ANC study and to determine those 

samples that are acid producers.

Measuring Acid-Neutralizing Capacity (ANC)

Laboratory experiments were also used to determine the 

ANC of igneous rocks. These experiments involved combining crushed (<2 mm) samples with deionized water in a glass 

beaker (fig. 3). The rock/water mixture is titrated by adding small 

amounts of sulfuric acid (the main acid in mine drainage) to the 

rock/water mixture to quantify the amount of acid added to reach 

the titration endpoint (pH 2). The calcium carbonate equivalent 

(in kilograms per ton) is calculated and recorded as “instantaneous ANC” (see Yager and others, 2005, for details of this 

calculation). The term instantaneous ANC is used because ANC 

reactions in this study occur over a duration of hours and not 

weeks, or in the case of remediation projects, years (Gustavson 

Figure 3. Laboratory ANC test apparatus. 

Glass beaker contains water and rock fragments 

(gray). Acid is added to the sample through the 

red tube; probe (center of beaker) monitors pH.

Cement Ck

M

.

ineral Ck.

Animas River

N

Acid neutralizing

 kilograms/ton 

 calcium carbonate

98–145

44–98

24–44

9–24

0–9

Silverton

COLORADO

Study

area

EXPLANATION

0 1 MILE

0 1 KILOMETER
Chapter K

Chapter K: Environmental Rock Properties at Abandoned Mine Lands that Generate or Neutralize Acid Drainage 67

others, 2007). Rocks that contain the mineral mixtures calcite and 

chlorite with ANC properties can neutralize or sequester greater 

amounts of acid and have a greater acid-remediation potential 

compared to those rocks that lack these minerals.

Application to the Silverton Study Area

Several of the Silverton ANC igneous rock units (for 

example, the San Juan Formation, Eureka Member of the 

Sapinero Mesa Tuff, and pyroxene andesite member of the 

Silverton Volcanics have pervasive calcite and chlorite that 

make these units ideal for neutralizing acid drainage (fig. 4). 

In contrast to the highly altered red, yellow, and bleachedwhite mineralized rocks in figure 5, volcanic rocks with high 

ANC properties range in hue from pale grey, to green, to 

nearly black in outcrop (fig. 6). Outcrop color is an indicator 

of the types of ANC minerals present (calcite, chlorite, epidote) that formed during a regional propylitic alteration event 

(Bove and others, 2007). Propylitic alteration in the study 

area is thought to have formed during the period 28.2 Ma to 

about 27.6 Ma, as the nearly 1-kilometer sequence of Silverton 

Volcanics lavas that infilled the San Juan caldera cooled, 

and in the process of cooling, degassed volatile constituents. 

Large quantities of carbon dioxide (CO2

), perhaps the primary 

rock-altering volatile component, among others such as water 

(H2

O) and sulfur dioxide (SO2), were released during cooling, altering the original minerals and matrix of the country 

rock (Burbank, 1960; Bove and others, 2007).Where rocks are 

overprinted by more intense, higher temperature alteration, 

the greenish hue of the propylitic assemblage is obliterated, 

bleached to white, and replaced with NAP minerals.

The current use of local ANC igneous rocks in Bureau 

of Land Management and USDA Forest Service remediation 

projects, such as at the Brooklyn mine in Browns Gulch north 

of Silverton, and at the U.S. Environmental Protection Agency’s 

Idarado mine-tailings Superfund site near Red Mountain Pass, 

north of the study area, has helped to alleviate the need to haul 

limestone from distant quarries, reducing both material and 

hauling costs, and has helped create local, low environmentalimpact mining jobs. Identification of high-ANC rocks prior 

to mining will allow reclamation managers to develop plans 

that layer or mix ANC material with NAP mine wastes as they 

accumulate, to minimize or eliminate acid mine drainage, and 

to decrease the cost of postmining remediation. Data presented 

here help support mine cleanup efforts and permit land managers and stakeholders to identify rocks that (1) confound minecleanup efforts by generating acidity or (2) are beneficial minewaste materials that can neutralize acid mine drainage.

Figure 4. High-ANC samples: A, Eureka Member of the Sapinero 

Mesa Tuff; Ch is chlorite-filled pumice, red areas are calcite (Ca) 

that has been stained with “alizarin red,” B, pyroxene andesite 

member of the Silverton volcanics with alizarin red-stained calcite 

in veinlets and replaced crystals; matrix has abundant chlorite 

that imparts a greenish hue.

Ch

Ca

A

B
Chapter K

68 Understanding Contaminants Associated with Mineral Deposits

Figure 6. Greenish-gray ANC rocks southeast of Silverton. The greenish-gray hue is caused by the minerals 

chlorite and epidote. Inset is a sample (6 centimeters across) of the Burns Member of Silverton Volcanics.

Figure. 5. Hydrothermally altered and mineralized igneous bedrock north of 

Silverton, Colorado; red-yellow and brown hues are caused by oxidation of pyrite and 

other sulfide minerals that produce acid rock drainage.
Chapter K

Chapter K: Environmental Rock Properties at Abandoned Mine Lands that Generate or Neutralize Acid Drainage 69

References Cited

Bove, D.J., Yager, D.B., Mast, M.A., and Dalton, J.B., 2007, 

Alteration map showing major faults and veins and associated water-quality signatures of the Animas River watershed 

headwaters near Silverton, southwest Colorado: U.S. Geological Survey Scientific Investigations Map 2976, 18-page 

pamphlet, 1 plate, scale 1:24,000.

Burbank, W.S., 1960, Pre-ore propylization, Silverton 

Caldera, Colorado, in Geological Survey Research 1960: 

U.S. Geological Survey Professional Paper 400–B, article 6, 

p. B12–B13.

Gustavson, K.E., Barnthouse, L.W., Brierley, C.L., Clark, 

E.H. II, and Ward, C.H., 2007, Superfund and mining 

megasites: Environmental Science and Technology, v. 41, 

p. 2667–2672. 

Lapakko, Kim, and Lawrence, R.W., 1993, Modification of the net acid production (NAP) test, in Proceedings of the Seventeenth Annual British Columbia Mine 

Reclamation Symposium, May 4–7, 1993: Port Hardy, 

British Columbia, p. 145–159.

Mast, M.A., Verplanck, P.L., Wright, W.G., and Bove, D.J., 

2007, Characterization of background water quality, Chapter E7 in Church, S.E., von Guerard, Paul, and Finger, S.E., 

eds., Integrated investigations of environmental effects of 

historical mining in the Animas River watershed, San Juan 

County, Colorado: U.S. Geological Survey Professional 

Paper 1651, p. 351–386.

Rhoda, F., 1876, Report on the topography of the San Juan 

country, in, Hayden, F.V., annual report of the United States 

Geological Survey of the territories, embracing Colorado 

and parts of adjacent territories; being a report of progress 

of the exploration for the year 1874: 515 p.

Vélez de Escalante, Silvestre, 1792, The Dominguez—

Escalante journal—Their expedition through Colorado, 

Utah, Arizona, and New Mexico in 1776: translated by Fray 

Angelico Chavez, edited by Ted J. Warner, 1995, Salt Lake 

City, University of Utah Press, 153 p.

Yager, D.B., Choate, LaDonna, and Stanton, M.R., 2008, 

Net acid production, acid neutralizing capacity, and associated mineralogical and geochemical characteristics of 

Animas River watershed igneous rocks near Silverton, 

Colorado: U.S. Geological Survey Scientific Investigations 

Report 2008–5063, 63 p. 

Yager, D.B., Mast, M.A., Verplanck, P.L., Bove, D.J., Wright, 

W.G., and Hageman, P.L., 2000, Natural versus miningrelated water quality degradation to tributaries draining 

Mount Moly, Silverton, Colorado: Proceedings of the Fifth 

International Conference on Acid Rock Drainage, Littleton, 

Colorado Society for Mining, Metallurgy, and Exploration, 

Inc., May 21–24, 2000, v. 1, p. 535–547.

Yager, D.B., McCafferty, A.E., Stanton, M.R., Diehl, S.F., 

Driscoll, R.L., Fey, D.L., and Sutley, S.J., 2005, Net acid 

production, acid neutralizing capacity, and associated 

geophysical, mineralogical, and geochemical characteristics 

of Animas River watershed rocks near Silverton, Colorado: 

U.S. Geological Survey Open-File Report 2005–1433, 75 p.
70 Chapter L: Connecting Airborne Geophysical Data to Geologic 

Structures in the Upper Animas River Watershed, Silverton, Colorado

spacing for the western one-half of the watershed and every 

400 m for the eastern one-half. The electromagnetic response 

of the Earth was measured with three frequencies that included 

984, 4,310, and 33,000 Hz. Data were collected at approximately 30 m above the ground surface, and measurements 

were taken every 3 m along the flight lines. Values of apparent 

resistivity were subsequently computed for each measurement 

point. A comprehensive discussion of the geophysical data 

acquisition and processing is in Smith and others (2007). The 

geophysical interpretations presented here were produced from 

grids of the magnetic and electromagnetic data.

In order to relate geophysical interpretations to geologic 

structure, we applied data-enhancement techniques to the 

gridded magnetic data, which transformed anomalies into 

forms that we could correlate to geologic structures. First, 

application of a reduction-to-pole (RTP) filter produced a grid 

(fig. 2A) in which magnetic anomalies are correctly positioned over their causative sources. Next, gradient trends of 

the magnetic anomalies were calculated from the RTP data 

(fig. 2B). Finally, we analyzed the gradient trends considering the mapped geologic structural trends. We increased the 

resolution of the small-scale anomalies by using a matched 

filter. Because of their high spatial frequency, these anomalies are directly related to near-surface magnetic sources. The 

high-frequency RTP magnetic data were used to determine 

the magnetic characteristics of surface geologic structures by 

using a statistical probability approach.

The midfrequency 4,310 Hz-data (fig. 3A) were used to 

investigate the resistivity characteristics of structures located 

from 0 m to between 30 to 50 m below the surface. The structures in this depth range are likely those that would be associated with shallow to mid-depth, structurally controlled vein 

deposits and geologic features controlling ground-water flow 

paths. Specifically, using data from the grid of the 4,310-Hz 

resistivity data, we applied filters to extract resistivity gradient trends so they could be related to mapped structural trends 

(fig. 3B) and to determine the electrical properties associated 

with the geologic structures.

Geophysical Gradient Trends Related 

to Shallow Crustal Geologic Structures

Geophysical gradient trends are defined as distinct linear 

and curvilinear elements that can be mapped from contours 

in geophysical maps. Magnetic and resistivity gradients result 

from contrasts in magnetic and electrical properties of rocks, 

respectively, and map the boundaries between rocks with dissimilar physical properties. These boundaries frequently correlate to mapped geologic structures and trends associated with 

Overview 

High-resolution magnetic and electromagnetic 

survey data collected during helicopter flights were 

used to characterize the geophysical signatures and 

directional trends of geologic structures in the upper 

Animas River watershed study area. Geologic structures include faults and mineralized and nonmineralized veins. Many of the structures have localized 

mineralization or provide connectivity for groundwater movement, or both. In some cases, faults act as 

conduits for migration of ground water or movement 

of fluids and alteration of the host-rock mineralogy. 

In other cases, faults and veins may act as barriers to 

flow, such as where they are annealed with quartz. We 

use the airborne geophysical data and their derivative 

products to provide an understanding of how physical properties of magnetization and resistivity relate 

to and typify mapped geologic structures; specifically, 

faults, fractures, and mineralized veins.

Introduction

Our investigation uses a number of approaches to define 

the magnetic and electrical characteristics of mineralized and 

nonmineralized faults and veins in the study area. We use 

the results to infer the locations of exposed and concealed 

geologic structures in the watershed. Specifically, the airborne 

geophysical survey data were enhanced and analyzed to:

•	 identify major geophysical gradient trends that correspond with mapped structures,

•	 characterize electrical and magnetic properties of 

the structures, and

•	 interpret concealed crustal structures not mapped 

at the surface.

This paper summarizes interpretation of airborne geophysical data presented in McDougal and others (2007).

Airborne Geophysical Data

Magnetic and electromagnetic (EM) data were collected 

during helicopter flights over the upper Animas River watershed study area (fig. 1) in 1996 (Smith and others, 2007). 

Data were acquired along north-south flight lines at a 200-m 

by Anne E. McCafferty and Robert R. McDougal
71

rock-unit (formational) contacts. The planimetric orientations 

of mapped structures and mineralized veins were compared to 

orientations of geophysical gradients. The orientations were 

calculated from the RTP magnetic data (fig. 2) and from the 

mid-frequency 4,310-Hz resistivity data (fig. 3) using methodology described in McDougal and others (2007). Evidence 

that many of the magnetic and resistivity gradients are related 

to geologic structures can be seen by comparing the rose 

diagrams from the geophysical data and the geologic data. 

Results show that good agreements between the orientations 

of geophysical gradients are colinear with east-west, northerly, 

and northwesterly geologic structure trends.

Figure 1. Location of airborne geophysical survey and selected geographic and geologic features in the Animas River 

watershed study area. Modified from Yager and Bove (2002). Profile A–A’ in figure 4.

Magnetic and Electrical Signature 

of Geologic Structures

Do the geologic structures within the watershed have characteristic magnetic or electrical signatures? If so, can we determine these signatures from the airborne survey data and use this 

information to locate unmapped structures? We explored these 

questions using a predictive modeling approach that objectively 

determines the statistical likelihood (probability) that a range of 

values within the magnetic or apparent resistivity data characterize geologic structures (Lee and others, 2001). Results show that:

EXPLANATION

Silverton

TOLTEC FAULT

BONITA

FAULT

ROSS BASIN

EUREKA GRABEN

SULTAN MTN

STOCK

A A'

M ni eral Cr

SUNNYSIDE FAULT

Watershed boundary

S. Fork

Cement Cr

37°

52’

30”N

107°45’W 107°37’30”W

Cement Creek

Animas River

Late Tertiary intrusive rocks

Tertiary pyroxene andesite rocks

Tertiary volcanic rocks

Fault

Silverton caldera structural margin—Dashed where concealed

Airborne geophysical survey boundary

0 5 KILOMETERS
Chapter L

72 Understanding Contaminants Associated with Mineral Deposits

Figure 2. (A) Reduced-to-pole magnetic anomaly map. Data from this map were filtered to enhance magnetic anomalies and 

gradient trends associated with shallow geologic structures. Faults and veins from Yager and Bove (2007) are overlain on the 

magnetic data map. (B) Magnetic gradient trends (A) compared to planimetric orientation of mapped faults (B) and veins (C). 

Rose diagrams of mapped structures were calculated as class percentages; rose diagrams of geophysical gradients were 

calculated as number per class.

•	 Faults and veins have characteristic magnetic and apparent 

resistivity signatures within discrete data value ranges.

•	 Magnetically, the faults and veins are mostly characterized by extremely low magnetizations that are associated with the magnetite-poor mineralogy of the silicic 

vein material.

•	 Less typically, some faults and veins are characterized 

by moderately high magnetizations.

•	 Mapped faults and veins are characterized by moderately high electrical resistivity consistent with the 

silicic mineralogy of the vein material and silica-rich 

phases within the Silverton Volcanics.

•	 The predictive models give high probability values that 

correlate accurately with many known structures; but, 

more interestingly, high probability values are also present 

that indicate areas that are devoid of structures that likely 

predict the locations of potentially unmapped structures.

2,800 1,400 0 1,400 2,800

270 90

0

Magnetic anomaly (RTP) gradient trends A Orientation of mapped mineralized veins C

90

0

270

8 7 6 5 4 3 2 1 0 1 2 3 4 5 6 7 8

–472 –357 –298 –247 –202 –161 –110 –51 57 246

Orientation of mapped faults B

270

0

90

10 8 6 4 2 2 10864

EXPLANATION

107°45’W 107°37’30”W

37°

52’

30”N

A

B

0 5 KILOMETERS

nanotesla

Cement Creek

Animas River

Mineral Creek
Chapter L

Chapter L: Connecting Airborne Geophysical Data to Geologic Structures 73

We plotted the predicted locations of geologic structures from the geophysical data in a geologic cross section 

(Luedke and Burbank, 2000), shown as profile A–A' (fig. 4). 

The geologic cross section runs from west to east, begins 

north of Middle Fork Mineral Creek, ends southwest of Storm 

Peak, and is entirely within the Silverton caldera. Probabilities associated with the predicted locations are shown 

as histogram bars beneath the magnetic or apparent resistivity profile. The variable bar heights indicate the relative 

strength of positive probabilities; therefore, the higher the bar 

height, the higher the probability that a particular geophysical 

characteristic will have a strong spatial association with a 

geologic structure. Where both magnetic and electromagnetic 

models predict structures, we consider this as very strong 

evidence that these locations identify unmapped structures. 

To highlight these occurrences, geologic structures that have a 

predicted location in both the magnetic and resistivity models 

have been projected onto the geologic cross section as blue 

dashed lines.

Both the magnetic and apparent resistivity predictive 

models show a number of predicted structures coincident with 

mapped structures and locations of predicted new structures. For 

Figure 3. (A) Map of 4,310 hertz apparent resistivity data showing lateral variations in the electrical resistivity of rocks 

from topographic surface to depths 30 to 50 meters. Data from this map were used to define the resistivity properties of 

geologic structures. Faults and veins from Yager and Bove (2007) are overlain on the resistivity map. (B) Resistivity gradient 

trends (A) compared to planimetric orientation of mapped faults (B) and veins (C). Rose diagrams of mapped structures were 

calculated as class percentages; rose diagrams of geophysical gradients were calculated as number per class.

 24 169 309 454 601 763 942 1147 1415 1847

ohm-meters

EXPLANATION

Mineral Creek

Cement Creek

Animas River

107°45’W 107°37’30”W

37°

52’

30”N

B

A

0 5 KILOMETERS

Resistivity (4,310 Hz) gradient trends

A

Orientation of mapped mineralized veins

C

90

0

270

8 7 6 5 4 3 2 1 0 1 2 3 4 5 6 7 8

Orientation of mapped faults

B

270

0

90 1,500 0 1,500 10 8 6 4 2 2 10864270 90

0
Chapter L

74 Understanding Contaminants Associated with Mineral Deposits

Figure 4. Magnetic (RTP) and apparent resistivity (4,310 hertz) over geologic cross section (Luedke and Burbank, 2000). Boxes 

on profiles ( ) map locations of mineralized veins or faults (red). Locations of predicted structures from modeling are shown as bar 

charts below the profile. Predicted structures with coincident locations in both models are shown as blue dashed lines. Modified 

from McDougal and others (2007). The airborne geophysical models predict approximately 46 percent more structures than 

are mapped. 

example, of the 14 mapped structures between the west end of 

profile A–A' and Mineral Creek, the magnetic model located 8 

(57 percent) and the resistivity model located 12 (86 percent). In 

total, 35 structures are mapped along the profile. An additional 

16 new structures are predicted from the magnetic and resistivity models, resulting in an increase of 46 percent more predicted 

than mapped. Many of the predicted, but unmapped, structures 

are located in areas of surfical deposits and may map the locations of faults or veins that would be covered.

Summary and Conclusions

This investigation was conducted to define and analyze 

the geophysical characteristics of faults and veins within the 

study area. We use this information to predict permissive areas 

for unmapped geologic structures in the watershed based on 

probability. Magnetic and electrical attributes were quantified 

for geologic structures, and the statistical method used identified target areas for further investigation. For example, the 

Profile A-A'

4,000

3,500

3,000

2,500

Surficial deposits

Tertiary extrusive rocks

Quaternary

Mineralized vein or

 fault—dashed where

 inferred or covered;

 arrows show

 direction of relative

 movement 

EXPLANATION

METERS

WEST EAST

Predicted structure

 (weights >1)

−100

−50

0

50

100

150

MAGNETICS 

(NANOTESLA)

0

500

1,000

1,500

2,000

2,500

3,000

APPARENT RESISTIVITY 

(OHM-METERS)

Predicted structures

 (weights >1 in both

 models)

Location of structure

 along magnetic or

 resistivity profile 

Eureka Member of

 Sapinero Mesa Tuff

 (Oligocene)

San Juan Formation

 (lower Oligocene)

Pyroxene andesite

 member

Burns Member

Silverton Volcanics

(Oligocene) Mineral Creek US ROUTE 550

Browns Gulch

Ohio Peak

Ohio Gulch

Cement Creek

Storm Peak

SILVERTON AND SAN JUAN CALDERAS

NO VERTICAL EXAGGERATION

0 1 KILOMETER

0 1 MILE
Chapter L

Chapter L: Connecting Airborne Geophysical Data to Geologic Structures 75

predictive models could be considered in remediation planning 

or used as an exploration tool for ground-water or mineralresource applications. The methods and approaches we used 

here can be applied to other watersheds with similar structural 

and volcanic regimes containing acid-generating historical 

mines or source rocks.

The predictive geophysical models showing high probabilities accurately locate many known structures. More interesting, the models suggest structures in areas where they had 

not been mapped. Many of the permissive areas lie in places 

of restricted access, limited outcrop, and thick alluvial soil or 

vegetation cover. 

The planimetric orientation of electrical resistivity gradients identifies a prominent east-west orientation that correlates 

with one trend of unmapped structures. In terms of structurally 

controlled ground-water flow, faults and veins of this orientation would be least likely to provide flow paths. The resistive 

geophysical signature suggests that these structures are quartz 

filled and extend to a depth of at least 50 m. In areas where 

quartz-filled structures have secondary or younger fracturing, 

secondary permeability may be considerable. Magnetically, 

the faults and veins are characterized by either extremely 

low magnetizations or moderately high magnetizations. 

Faults and veins both are associated with moderately steep 

magnetic gradients.

Buried or covered geologic structures not mapped at the 

surface are suggested by both the magnetic and electromagnetic data. Faults and veins are characterized by moderately 

high electrical resistivities and may point to more silica-rich 

phases within the Silverton Volcanics. The predictive model 

calculated from the electrical resistivity characteristics of 

structures identifies areas where faults and veins are resistive at depth and, as previously discussed, least likely to be 

structurally controlled ground-water conduits, except where 

significantly fractured. 

The predictive models presented here could be used to 

guide further geologic mapping and investigation, incorporated in hydrologic applications, or considered in remediation 

planning. The implication that significantly more mineralized and nonmineralized faults and veins, approximately 

36 percent on average (McDougal and others, 2007), may exist 

in the watershed than previously mapped might be important 

in terms of estimating fracture permeability that would be 

included in ground-water modeling efforts.

The methods and approaches used in this study can be 

applied to other watersheds with similar structural and volcanic regimes containing acid-generating historical mines or 

source rocks. Further investigations may benefit from integration of the geophysical, topographic, and mineralogical characterization of structures presented here, with geochemical and 

geologic analysis to identify discrete ground-water flow paths 

and structurally controlled inflows to streams.

References Cited

Lee, G.K., McCafferty, A.E., Alminas, H.V., Bankey, Viki, 

Frishman, David, Knepper, D.H., Jr., Kulik, D.M., Marsh, 

S.P., Phillips, J.D., Pitkin, J.A., Smith, S.M., Stoeser, D.B., 

Tysdal, R.G., and Van Gosen, B.S., 2001, Montana geoenvironmental explorer: U.S. Geological Survey Digital Data 

Release DDS–65.

Luedke, R.G., and Burbank, W.S., 2000, Geologic map of 

the Silverton and Howardsville quadrangles, southwestern 

Colorado: U.S. Geological Survey Geologic Investigations 

Map I–2681, scale 1:24,000, 11 p.

McDougal, R.R., McCafferty, A.E., Smith, B.D., and Yager, 

D.A., 2007, Topographic, geophysical, and mineralogical 

characterization of geologic structures using a statistical 

modeling approach, in Church, S.E., von Guerard, Paul, and 

Finger, S.E., eds., Integrated investigations of environmental 

effects of historical mining in the Animas River watershed, 

San Juan County, Colorado: U.S. Geological Survey Professional Paper 1651, chap. E13, p. 643–688.

Smith, B.D., McDougal, R.R., Deszcz-Pan, M., and Yager, 

D.B., 2007, Helicopter electromagnetic and magnetic surveys, in Church, S.E., von Guerard, Paul, and Finger, S.E., 

eds., Integrated investigations of environmental effects of 

historical mining in the Animas River watershed, San Juan 

County, Colorado: U.S. Geological Survey Professional 

Paper 1651, chap. E4, p. 231–254.

Yager, D.B., and Bove, D.J., 2002, Generalized geologic map 

of part of the upper Animas River watershed and vicinity, 

Silverton, Colorado: U.S. Geological Survey Miscellaneous 

Field Studies Map 2377.

Yager, D.B., and Bove, D.J., 2007, Geologic framework, in

Church, S.E., von Guerard, Paul, and Finger, S.E., eds., 

Integrated investigations of environmental effects of historical mining in the Animas River watershed, San Juan 

County, Colorado: U.S. Geological Survey Professional 

Paper 1651, chap. E1, p. 107–140.
76 Chapter M: Using a Geographic Information System (GIS) to Determine 

the Physical Factors that Affect Water Quality in the Western 

San Juan Mountains, Silverton, Colorado

Overview

A cooperative, U.S. Geological Survey–Federal 

Land Management Agency study of abandoned mine 

lands in the western San Juan Mountains, Silverton, 

Colorado, was undertaken to evaluate water quality. 

The resulting comprehensive digital data base included 

GIS layers that were analyzed in this followup study by 

using a GIS and statistical approach to determine the 

most prominent physical factors that influence water 

quality. The GIS-statistical approach identified areas of 

quartz-sericite-pyrite alteration among the most important assemblages that adversely affect water quality 

in the study area. Ground-water quantity and quality 

were addressed using detailed hydrologic and geophysical conductivity surveys that enable the identification of 

ground-water inflows. These data correspond to stream 

inflows that are useful in inferring possible metal contaminant loading that could be associated with ground 

water. These findings are important to land managers 

and local stakeholders involved in land-use decisions 

and abandoned mine cleanup.

Introduction

During 1996 to 2001, the U.S. Geological Survey along 

with multiple Federal, State, and local stakeholders, completed 

an Abandoned Mine Lands Initiative (AMLI) study of the 

Animas River watershed near Silverton, Colo. (von Guerard 

and others, 2007). These AMLI datasets are a result of one 

of the most comprehensively studied watersheds affected 

by metallic mining in the world and consist of geologic, 

geophysical, geochemical, hydrologic, biologic, remote sensing, and base cartographic digital information (Yager and 

Bove, 2007; Smith and others, 2007; Kimball and others, 

2007; Bove and others, 2007; Dalton and others, 2005). This 

region was the site of base- and precious-metal hard rock 

mining from the late 1870s to 1991. An extensive legacy of 

mining has left behind thousands of mines and prospects. 

Weathering of mine waste and hydrothermally altered bedrock, which hosts metallic mineral deposits, produces acidic 

drainage that adversely affects the environment. Federal land 

managers and the local Animas River Stakeholders Group 

are actively involved in abandoned mines cleanup in the 

study area.

The principal goal of this study is to analyze the extensive digital AMLI datasets summarized in Sole and others 

(2007) to advance understanding of the factors that control 

water quality. Our analysis of AMLI datasets combined a 

Geographical Information System (GIS) and a statistical-based 

approach to identify both mining and nonmining sources of 

metals and acidity to surface water and ground water (Yager 

and others, 2002; Yager and Caine, 2003).

Geology of the Study Area

The geology of the western San Juan Mountains study 

area is exceptional in that many diverse rock types representing every geologic era from the Proterozoic to Cenozoic are 

preserved. It is an area that was extensively glaciated during 

the Pleistocene and has high topographic relief, providing 

excellent bedrock exposures. The general stratigraphy of the 

San Juan Mountains near Silverton consists of Precambrian 

crystalline basement overlain by Paleozoic to Tertiary sedimentary rocks and a voluminous Oligocene volcanic cover 

(Yager and Bove, 2007). Two caldera-forming eruptions, 

together with subsequent postcaldera-collapse intrusive activity and volcanism affected much of the study area. Structures 

that developed during and after caldera collapse focused 

hydrothermal fluids during several episodes of alteration 

and base- with precious-metal mineralization that formed in 

the Tertiary volcanic assemblage. Today, an arcuate drainage network delineates the structural margins of each caldera 

(fig. 1). Weathering of pervasively altered igneous bedrocks 

and surficial deposits derived from them is a critical factor 

that influences water quality. Thus, much of this study has 

focused on the physical and chemical attributes of the Tertiary 

igneous sequence.

Geographic Information System (GIS) 

and Statistical Methods

GIS Overlays

While naturally altered and unmined areas have affected 

water quality, mining has concentrated acid-generating minerals and leachable metals in waste piles and in fluvial tailings 

on the surface, adding to the premining geochemical baseline metal concentrations in streams. Inspection of multiple 

GIS layers was used to qualitatively distinguish areas where 

surface water or ground water is affected by natural and (or) 

anthropogenic sources of contaminants. Prospect Gulch is a 

by Douglas B. Yager, Raymond H. Johnson, and Bruce D. Smith
77

between catchments and associated water-quality signatures. 

One physical factor important to our study is the area of acidgenerating alteration types that contain pyrite among other 

acid-generating minerals in each catchment. Pyrite in the presence of oxygen and water dissolves to produce sulfuric acid 

that degrades water quality and is toxic to aquatic life. Each of 

the 98 catchments delineated has varying proportions of acidgenerating or acid-neutralizing bedrocks (fig. 4) and associated 

water-quality signatures (fig. 5).

GIS analysis also was used to determine the nonvegetated 

areas of catchments (figs. 6 and 7). Where acid-generating 

rock types are exposed due to lack of vegetative cover, erosion 

from precipitation and surface runoff can increase and have an 

effect on water quality (Ritter and others, 1995). These types 

of analyses identified the subbasins that are most likely to be 

affected by weathering of acid-generating alteration types that 

degrade water quality.

Statistics

Linear regression analysis was used to determine correlations between areas of alteration types determined by GIS 

analysis for each catchment and the water-quality parameters 

measured in streams at the mouths of the catchments. The 

Kendall’s Tau method of regression (Kendall, 1975) was used 

to calculate the strength of correlation between the dependent and independent variables of interest, for example, area 

of quartz-sericite-pyrite (qsp), and pH determined by field 

measurement. Regression analysis results identified a correlation between catchment area of qsp alteration and pH (fig. 8), 

in addition to correlations with other water-quality variables 

such as aluminum concentration. Compared with other studyarea alteration types, qsp alteration was determined to be one 

of the most important alteration types that adversely affects 

water quality. This method can be used to rank catchments that 

have the highest potential to affect water quality and adversely 

affect riparian habitat.

Ground Water in the Study Area

The AMLI study did not specifically evaluate the effect 

of inflowing ground-water quality and quantity on surface 

water in detail. However, an extensive data set exists with the 

quantity, quality, and location of ground-water discharge to 

surrounding streams (Kimball and others, 2007). In addition, 

geophysical data can be useful in inferring the location and 

quality of ground-water discharge where drill-hole, piezometer, or other direct measurement and sampling of ground 

water are lacking.

good example that shows the combined mining and nonmining factors that affect water quality in a well-studied, heavily 

altered and mined catchment (fig. 2). These methods are especially effective for quickly and easily communicating scientific 

data to audiences with varying backgrounds and experience.

Geomorphometric Methods

Geomorphometric analysis involves extracting quantitative 

measurements for topographic surfaces as well as for hydrologic 

networks. A surface-hydrology modeling tool, the GIS Weasel 

(Viger and others, 1998), was used to analyze a 10-m-resolution 

USGS digital elevation model and extract basinwide geomorphometric data (for example, slope, aspect, flow direction, flow 

accumulation, drainage network, and Strahler stream order). 

GIS Weasel also interfaces with ArcGrid to delineate modeling response units, or subbasin hydrologic catchments, referred 

to as catchments in this study (fig. 3).

Once catchments were delineated, ArcGrid GIS 

Weasel parameterization routines were used to compile characteristics of each catchment such as areas of altered rock 

and corresponding areas of nonvegetated rock or soil. These 

physical factors were evaluated for similarities and differences 

Figure 1. Landsat thematic mapper remote sensing scene 

draped on digital terrain model of study area. Arcuate drainages 

of Mineral Creek and Animas River follow the structural margins 

of two collapsed volcanoes (calderas) that formed during 

the Oligocene.

Silverton

N

COLORADO

Study

area

M ni eral Creek

Cement Creek

Animas River

South Fork Mineral Creek
Chapter M

78 Understanding Contaminants Associated with Mineral Deposits

In stream tracer-dilution studies (Kimball and others, 

2007), all visible surface-water inflows observed along a stream 

segment are recorded and measured for flow, quantity, and 

quality. When the upstream flow plus added inflows do not sum 

to the downstream total, an unsampled ground-water discharge 

is inferred as causing the increased surface-water flow. This 

inferred ground-water discharge, in addition to sampled springs 

and seeps, provides the total amount of ground-water contribution to the stream at specified locations (fig. 9). Interpretation 

of the source, flow path, and quality of ground water required 

evaluating geologic, topographic, geochemical, hydrologic, and 

geomorphic variables. A GIS-based approach helped in evaluating the multiple variables that influence this complex system.

Initial research is aiding in understanding the complexities of the ground-water system starting with locations, quantity, 

and quality of ground-water discharge as stream inflows (fig. 9). 

Geochemical data collected from water-quality sampling sites 

(inset box, fig. 9A) indicated the ground-water discharge in this 

area has compositions that are dissimilar to surface-water quality 

in the immediate vicinity, suggesting that the ground-water 

recharge did not occur locally. Understanding the movement 

of ground water, the subsequent transport of metals, and the 

final discharge to surface water is important for water quality in 

studies of catchments in mountainous terrain (Caine and others, 

2004). Our studies, in combination to those reported in Johnson 

and others (2007) and Kimball and others (2007), identified that 

ground-water discharge in the study area occurs (1) where surface 

gradients decrease, (2) where there is an abrupt change in rock 

type, for example, near the Tertiary volcanic and Precambrian 

bedrock contact; (3) where landslides or alluvial fans with high 

clay content cause reduced ground-water flow beneath the stream; 

or (4) where geologic structures focus ground-water flow (Smith 

and others, 2007).

Geophysical conductivity profiles (Smith and others, 2007) 

constructed along stream segments with known ground-water 

discharge also provide an indication of ground-water quality. 

High conductivity can be indicative of high metal concentrations (fig. 9B). When several GIS layers such as alteration type, 

geologic structure, geophysics, and bedrock and surficial geology are combined, more detailed interpretations are possible 

that consider the quality of ground water, flow paths, source 

material (for example, surficial deposit or altered bedrock), and 

the resulting water quality.

Figure 2. Alteration types draped on shaded relief model of Prospect Gulch, and pH from water-quality 

samples collected on September 29, 1999; pick and hammer symbols represent mines and prospects. 

Note that pH is greater than 5.0 near head of basin (green circles), left center of catchment. Acidity 

increases downstream (right of image) as weathering of mine waste and alteration assemblages affects 

water quality. Acid sulfate alteration (red) and quartz-sericite-pyrite alteration (yellow). Propylitic rocks 

(green) near mouth of catchment at one sampling site may be neutralizing acidity. Alteration from Bove 

and others, 2007; pH values from Johnson and others, 2007.

LARK MINE

pH

>5.0

>4.5 <5.0

>3.5 <4.5

>3.3 <3.5

<3.3
Chapter M

Chapter M: Using a Geographic Information System (GIS) to Determine the Physical Factors that Affect Water Quality 79

Figure 3. Subbasins delineated using the GIS Weasel. The subbasins form the principal modeling response units of interest 

in this study. Quantitative data for multiple physical factors such as area of alteration types were acquired for subbasins and 

compared with water-quality “signals” at the mouths of each subbasin catchment. Labeled catchments discussed elsewhere 

are RT, Red Tributary; TG, Topeka Gulch; PG, Prospect Gulch; and BG, Boulder Gulch.

Topeka Gulch

Red Tributary

Prospect Gulch

Arrow indicates acid-

 generating assemblage

EXPLANATION

AS QSP PROP QU WSP

ALTERATION TYPE

80

70

60

50

40

30

20

10

0

PERCENT

Figure 4. Alteration types determined for three catchments (areas in percent). Alteration types: AS, acid sulfate; 

QSP, quartz-sericite-pyrite; PROP, propylitic; QU, Quaternary undifferentiated; and WSP, weak sericite-pyrite. 

Alteration types described in Bove and others (2007) and Yager and Bove (2007).

0

0 1.6 KILOMETERS

1 MILE

PG

TG BG

RT

Middle Fork

South Fork

Cement Creek

An mi as River Animas River

M ni eral Creek

N

Middle Fork
Chapter M

80 Understanding Contaminants Associated with Mineral Deposits

A

B

0

100

200

300

400

500

600

700

800

900

1,000

0

10,000

20,000

30,000

40,000

50,000

60,000

70,000

Prospect Gulch Boulder Gulch Topeka Gulch Red Tributary

Zinc

Copper

Prospect Gulch Boulder Gulch Topeka Gulch Red Tributary

Iron

Aluminum

MICROGRAMS PER LITER MICROGRAMS PER LITER

Figure 5. Surface-water-quality data for catchments in figures 4 and 7. (A) Iron (Fe) and aluminum (Al) data); (B) zinc (Zn) and copper 

(Cu) data. Data were collected during base-flow conditions during the fall after most snow had melted. Surface-water-quality data 

for Boulder Gulch (composed of over 82 percent propylitic alteration and having some acid neutralizing capacity, Yager, Chapter K, this 

volume; Yager and others, 2005) shown for comparison with other more highly altered catchments. Water-quality data from Johnson 

and others, 2007; Mast and others, 2007.

Figure 6. Red Tributary catchment located west of 

Silverton in Middle Fork Mineral Creek subbasin. Areas 

in tan indicate sparsely vegetated slopes that have 

minimal precipitation interception capacity and a high 

erosion potential. Top of digital orthophoto quadrangle 

is to the north. Subbasin outline in black; blue lines 

represent streams. Dark areas in subbasin are spruce 

forest. Area covered by image is about 4.5 kilometers 

by 3.7 kilometers.

107°45'28" 107°43'28"

37°

50'

48.5"

37°

49'

12.3"

Headwaters

Mouth
Chapter M

Chapter M: Using a Geographic Information System (GIS) to Determine the Physical Factors that Affect Water Quality 81

Figure 7. (A) Areas of sparse vegetation (in percent) determined by GIS analysis of 

AVIRIS mapping (Dalton and others, 2005), and (B) corresponding catchment areas that 

are both nonvegetated and also have corresponding areas of various alteration types 

(in percent).

Figure 8. Linear regression results showing the 

correlation between catchment area of quartzsericite-pyrite alteration and pH. Kendall’s Tau negative 

correlation of –0.7 and low “P” value indicates that 

lower pH (more acidic water quality) is correlative with 

increasing area of quartz-sericite-pyrite alteration. 

Note that Boulder Gulch has less acidic water quality 

and contains rocks with a high acid-neutralizing 

capacity (see Yager, Chapter K, this volume).

40

35

30

25

20

15

10

5

0

70

60

50

40

30

20

10

0

PERCENT PERCENT

A

B

Sparsely vegetated area (percent)

Alteration type in sparsely vegetated area (percent)

Topeka Gulch Red tributary Prospect Gulch

AS QSP PROP QU WSP

EXPLANATION

Topeka Gulch

Red tributary

Prospect Gulch

 ln pH

QUARTZ-SERICITE-PYRITE,

IN SQUARE METERS

80,000

100,000

60,000

40,000

20,000

0

1.0 1.2 1.4 1.6 1.8 2.0

Prospect

Ohio

Kendall’s Tau (–0.7)

p value (0.005)

Boulder
Chapter M

82 Understanding Contaminants Associated with Mineral Deposits

Figure 9. Ground-water inflows determined 

by tracer injection studies. Height of lines 

(A) are proportional to quantity of groundwater inflows that range from 0 to 0.9 cubic 

foot per second (yellow) to 7 cubic feet per 

second (red). White box (A) corresponds to 

the area in (B). Conductivity profiles (from 

airborne geophysics) and corresponding 

ground-water inflows shown in (B) along 

Mineral Creek. Bright colors (yellow-orangered) correlate with increasing conductivity 

along the stream. White arrows point to 

low-conductivity ground-water inflows 

(left), and higher conductivity groundwater inflows (right). Iron concentrations 

(Fe, in micrograms per liter) shown for 

corresponding surface-water and groundwater inflows.

Conclusions

Multiple anthropogenic and natural catchment physical 

factors in each catchment combine to influence water quality. A GIS and statistical approach that evaluates the correlation between percentage of areas of geologic substrate and 

water-quality signals determined at the mouths of study-area 

catchments provides an effective way to evaluate and identify 

the important factors that have the greatest influence on water 

quality. Simultaneous statistical analysis of several physical 

factors, using multiple linear regression analysis, can now be 

used to determine how combinations of factors synergistically 

affect catchment water quality.

Ground-water studies commonly are limited by few direct 

observations of the ground-water flow system; for example, 

drilling or piezometers. Data from detailed surface-water and 

ground-water sampling and geophysical conductivity profiles 

helped to infer ground-water discharge areas to streams along 

with associated water-quality changes. By combining these 

data along with other GIS, AMLI geodatasets, more detailed 

interpretations can be made regarding ground-water quality, 

quantity, and flow paths. GIS approaches such as this can 

help land managers identify and prioritize abandoned mine 

areas for cleanup that will have the greatest positive effects on 

downstream water quality.

Stream Fe = 2,390

Inflow Fe = 27,900

Stream Fe = 2,270

Inflow Fe = 105

B

A
Chapter M

Chapter M: Using a Geographic Information System (GIS) to Determine the Physical Factors that Affect Water Quality 83

References Cited

Bove, D.J., Yager, D.B., Mast, M.A., and Dalton, J.B., 2007, 

Alteration map showing major faults and veins and associated water-quality signatures of the Animas River watershed 

headwaters near Silverton, southwest Colorado: U.S. Geological Survey Scientific Investigations Map 2976, 18-page 

pamphlet, 1 plate, scale 1:24,000.

Caine, J.S., Bove, D.J., Manning, A.H., and Verplanck, P.L., 

2004, Preliminary characterization of geological controls on 

groundwater flow and solute transport in an alpine hydrothermal metal deposit—Handcart Gulch, Montezuma Mining 

district, Colorado Rocky Mountain Front Range: Geological 

Society of America Abstracts with Programs, v. 36, 

p. 539.

Dalton, J.B., Bove, D.J., and Mladinich, C.S., 2005, Remote 

sensing characterization of the Animas River watershed, 

southwestern Colorado, by AVIRIS imaging spectroscopy: U.S. Geological Survey Scientific Investigations 

Report 2004–5203, 49 p.

Johnson, R.H., Wirt, L., Manning, A.H., Leib, K.J., Fey, D.L., 

and Yager, D.B., 2007, Geochemistry of surface and ground 

water in Cement Creek from Gladstone to Georgia Gulch 

and in Prospect Gulch, San Juan County, Colorado: 

U.S. Geological Survey Open-File Report 2007–1004, 

140 p.

Kendall, M.G., 1975, Rank correlation methods, 4th edition: 

Charles Griffin, London, 202 p.

Kimball, B.A., Walton-Day, Katherine, and Runkel, R.L., 

2007, Quantification of metal loading by tracer injection 

and synoptic sampling, 1996–2000, in Church, S.E., 

von Guerard, Paul, and Finger, S.E., eds., Integrated investigations of environmental effects of historical mining in 

the Animas River watershed, San Juan County, Colorado: 

U.S. Geological Survey Professional Paper 1651, chap. E9, 

p. 417–495.

Mast, M.A., Verplanck, P.L., Wright, W.G., and Bove, D.J., 

2007, Characterization of background water quality, in

Church, S.E., von Guerard, Paul, and Finger, S.E., eds., 

Integrated investigations of environmental effects of historical mining in the Animas River watershed, San Juan 

County, Colorado: U.S. Geological Survey Professional 

Paper 1651, chap. E7, p. 347–386.

Ritter, D.F., Kochel, R.C., and Miller, J.R., 1995, Process geomorphology, 3d ed.: New York, McGraw-Hill Professional 

Publishing, 560 p.

Smith, B.D., McDougal, R.R., Deszcz-Pan, Maryla, and Yager, 

D.B., 2007, Helicopter electromagnetic and magnetic surveys, in Church, S.E., von Guerard, Paul, and Finger, S.E., 

eds., Integrated investigations of environmental effects of 

historical mining in the Animas River watershed, San Juan 

County, Colorado: U.S. Geological Survey Professional 

Paper 1651, chap. E4, p. 231–254.

Sole, T.C., Grannito, Matthew, Rich, C.L., Litke, D.W., and 

Pelltier, R.T., 2007, Digital databases and CD–ROM for 

the Animas River watershed, in Church, S.E., von Guerard, 

Paul, and Finger, S.E., eds., Integrated investigations of 

environmental effects of historical mining in the Animas 

River watershed, San Juan County, Colorado: U.S. Geological Survey Professional Paper 1651, chap. G, p. 1079–1096.

Viger, R.J., Markstrom, S.L., and Leavesley, G.H., 1998, 

The GIS Weasel—An interface for the treatment of spatial 

information used in watershed modeling and water resource 

management: Proceedings of the First Federal Interagency 

Hydrologic Modeling Conference April 19–23, 1998, 

Las Vegas, Nevada, v. II, chap. 7, p. 73–80.

von Guerard, Paul, Church, S.E., Yager, D.B., and Besser, 

J.M., 2007, The Animas River watershed, San Juan County, 

Colorado, in Church, S.E., von Guerard, Paul, and Finger, 

S.E., eds., Integrated investigations of environmental 

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San Juan County, Colorado: U.S. Geological Survey Professional Paper 1651, chap. B, p. 17–38.

Yager, D.B., and Bove, D.J., 2007, Geologic framework, in

Church, S.E., von Guerard, Paul, and Finger, S.E., eds., 

Integrated investigations of environmental effects of historical mining in the Animas River watershed, San Juan 

County, Colorado: U.S. Geological Survey Professional 

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that influence water quality: Geological Society of America 

Abstracts with Programs, v. 35, no. 5, p. 6.

Yager, D.B., Caine, J.S., Bove, D.J., Church, S.E., Smith, 

B.D., McDougal, R.R., Wirt, Laurie, Mast, M.A., Kimball, 

B.A., and Walton-Day, Katherine, 2002, A GIS data viewer 

for physical and geochemical characterization of abandoned 

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Abstracts with Programs, v. 34, no. 6, p. 145.

Yager, D.B., McCafferty, A.E., Stanton, M.R., Diehl, S.F., 

Driscoll, R.L., Fey, D.L., and Sutley, S.J., 2005, Net acid production, acid neutralizing capacity, and associated geophysical, mineralogical, and geochemical characteristics of Animas 

River watershed rocks near Silverton, Colorado: U.S. Geological Survey Open-File Report 2005–1433, 75 p.
84 Part 3—Postremediation Recovery of Stream Ecosystems

After metals and acidity have been mobilized from their sources and transported to receiving streams, determining their fate and effect on the ecosystem is important to the understanding 

the potential effects of abandoned mines and mineralized but unmined areas. The effects of metals 

and acidity on ecosystems have been closely monitored by mining companies, land managers, and 

government regulators involved in mine sites. It has been determined that different factors contribute to the movement of metals and acidic water through our environment. This section presents 

time-series data collected as part of the downstream monitoring effort at three mine sites to evaluate the changes in water chemistry that affect the recovery of the aquatic ecosystem.
85
86 Chapter N: Recovery of Aquatic Life in Surface Streams Affected 

by Mining Following Remediation

aquatic-life habitat. The terms remediation, reclamation, rehabilitation, and restoration all have differing ecological goals (Finger, 

Church, and von Guerard, 2007). Using the watershed approach 

defined in the Abandoned Mine Land Initiative (Buxton and 

others, 1997), the U.S. Geological Survey recommended to the 

Bureau of Land Management (BLM) and to the U.S. Department 

of Agriculture (USDA) Forest Service that the most cost-effective 

approach to achieving ecological goals was to focus on those sites 

within a watershed where the largest effect could be achieved 

with the remediation efforts (Nimick and others, 2004; Church, 

von Guerard, and Finger, 2007). A summary of the scientific 

methods developed, data obtained, and critical information 

developed from these different studies was presented in Kimball 

and others (2006). This summary can be used by Federal and 

State land-management agencies, private entities, and stakeholder 

groups as guidelines for evaluating the scientific information 

needed before developing a site or watershed remediation plan. At 

a recent conference, Federal land-management agencies summarized a decade of watershed remedial work (USDA Forest Service 

and Bureau of Land Management, 2007). Successful remediation (removal of contaminants and improvement of water quality 

downstream as a result of work on a site), reclamation (recontouring and reestablishing of vegetation at a site), and restoration 

(reestablishment of the ecological function of the site as shown by 

self-sustaining fish populations and a healthy riparian zone) have 

occurred on Federal lands throughout the Western United States 

(Finger and others, 2004, 2007). One of the fundamental issues 

that has been poorly documented in the scientific literature is the 

length of time necessary to achieve restoration given a set of starting conditions and the scope of remedial work undertaken.

During the course of this project, we have had the 

opportunity to evaluate remedial work undertaken by Federal 

and State agencies and by private industry at three sites: the 

Boulder River watershed in Montana, the Animas River watershed in Colorado, and in the San Carlos Reservoir on the Gila 

River downstream from the Morenci copper mine in Arizona 

(fig. 1). The necessary monitoring data to support aquatic 

recovery at other remediated sites probably exists in a fragmented state for many other remediated mine sites or watersheds, but generally these data reside in unpublished reports 

by various consultants used during the course of remediation 

and are neither available to the public nor in the scientific 

literature. In order to demonstrate the success of recovery of 

aquatic life, we need to have thorough documentation of the 

conditions prior to remediation and monitoring data collected 

during and following the remediation for a substantial period 

of time (Finger and others, 2004, 2007). Our results, discussed 

more fully in this chapter, show that recovery of aquatic life 

downstream from the remediated sites is highly dependent 

upon the geologic setting, rock types present in the watershed, 

topographic relief in the watershed and geomorphology of the 

stream reaches affected, the nature and extent of hydrothermal 

Overview

Documentation of the successful recovery of 

aquatic life downstream from remediated mine sites 

has been examined at three sites: the Animas River 

watershed in Colorado, the Boulder River watershed in Montana, and the Gila River in Arizona. 

The first two sites were studied extensively during 

the U.S. Geological Survey Abandoned Mine Lands 

Initiative (AMLI, 1997–2002). These data show that 

recovery of both the riparian habitat and aquatic life 

in the immediate downstream reach is highly dependent upon many variables: geologic setting, rock types 

present in the watershed, the topographic relief in the 

watershed and geomorphology of the stream reaches 

affected, nature and extent of hydrothermal alteration 

in the watershed, metals released and their residence 

time in various media, pH of the water in the receiving stream, and extent to which adequate financial 

resources were available for the remedial activities. 

One outcome from the AMLI studies has been the 

development of a decision tree to be used to determine 

what scientific studies are most useful in watershed 

characterization (Kimball and others, 2006). Examples 

of successful restoration activities are documented for 

the Boulder River watershed, and remediation work 

in the Animas River watershed has perhaps resulted 

in some small downstream improvement of water and 

sediment quality.

Work at the third site, downstream from the 

Morenci mine site in Arizona, has demonstrated that 

mitigation resulted in improved water and sediment 

quality. The environmental contamination resulted from 

poor management of mine-site runoff. Corrective action 

by Phelps Dodge, the operator at the time, resulted in 

immediate downstream improvement in water and sediment quality in the San Carlos Reservoir.

by Stanley E. Church

Introduction

The effect of mining on water quality has been examined 

in detail by many workers (Nimick and others, 2004; Church, 

von Guerard, and Finger, 2007, and numerous references therein). 

These studies have shown that the processes resulting in acidic 

drainage are multiple, and the remedial solutions are often quite 

complex. It is necessary to separate the effects of weathering of 

hydrothermally altered rock from the additional effects resulting 

from mining. Furthermore, it is necessary to carefully define the 

goals of any remedial work done on the watershed to improve 
87

alteration in the watershed, metals released and their residence time in various media, pH of the water in the receiving 

stream, and extent to which adequate financial resources were 

available for the remedial activities. In two of the three sites 

studied, the recovery of aquatic life downstream from these 

remediated sites appears to require more time than anticipated. 

Results from three case studies will be discussed in this report:

•	 Recovery of the Boulder River downstream from a 

small historical polymetallic vein mining district in 

west-central Montana;

•	 Recovery downstream on the Animas River in southwestern Colorado, an extensive hydrothermally altered 

and heavily mined watershed; and

•	 Recovery of the Gila River and in San Carlos Reservoir 

downstream from a point source at the Morenci porphyry copper mine in eastern Arizona.

Three additional sites were investigated in anticipation of 

future remedial activities to establish preremediation baseline 

geochemical data; however, remedial action has not been initiated. Fey and others (2002) reported baseline sediment and 

water-quality results from the Snake River watershed in central 

Colorado. This basin is being considered for remedial work 

under the U.S. Environmental Protection Agency (USEPA) 

Brownfields program (http://www.epa.gov/brownfields/). 

Church, Fey, and Marot (2005) investigated the geochemical 

Figure 1. Index map showing study areas discussed in text.

effect on stream sediment of the Red River both during 

active mining and the premining period downstream from the 

Questa porphyry molybdenum mine to provide documentation to the State of New Mexico for anticipated mine-site 

closure. Church, Kirschner, and others (2007) investigated 

the premining and background data in the Blue Creek watershed downstream from the Midnite uranium mine in Stevens 

County, Washington. Remedial action is anticipated at this site 

over the next decade.

Boulder River Watershed, Montana

Sampling of water and sediment in the Boulder River 

downstream from historical mine sites before remediation was 

documented in the U.S. Geological Survey Abandoned Mine 

Lands Initiative (AMLI) (Finger and others, 2004; Church and 

others, 2004; Nimick and Cleasby, 2004; Farag and others, 2007). 

Postremedial monitoring data are summarized in (Unruh and 

others, in press). This study shows that improvement has resulted 

immediately downstream from some, but not all, remediated 

mine sites. Overall, remedial work in the tributary basins (figs. 2 

and 3) has resulted in small changes in water and sediment 

geochemistry over a 5-year timeframe. Historical mining in the 

districts was from polymetallic vein deposits in the granitic rocks 

in the Boulder batholith (O’Neill and others, 2004). The district 

produced copper, lead, silver, and zinc with minor gold from 1868 

through 1958. An open pit at the Comet mine on High Ore Creek 

was a major source of sediment contamination (Fey and Church, 

1998; Church and others, 2004) in the Boulder River, whereas 

dissolved constituents from Cataract Creek (Nimick and Cleasby, 

2004) were the primary source of aqueous contaminants to the 

Boulder River (http://ecorestoration.montana.edu/mineland/

histories/metal/comet/default.htm). The Comet mine site was 

remediated by the State of Montana and BLM in 1998 (Gelinas 

and Tupling, 2004). Monitoring work by the USGS took place 

over the following 5-year period. Additional monitoring work is 

reported in an unpublished report prepared for the BLM, Butte, 

Mont. (J.D. Belanger-Woods, Butch Gerbrandt, and J.P. Madison, 

2003, High Ore Creek postremediation surface water sampling data summary report, 101 p.). Data from the monitoring 

work show:

•	 Temporal trends of dissolved and total concentrations 

of metals in water have changed in some stream reaches 

downstream since the remediation phase began (fig. 2).

•	 Extensive restoration by the State of Montana and the 

BLM in the High Ore Creek tributary at and downstream from the Comet mine site (Gelinas and Tupling, 

2004) has resulted in restoration of High Ore Creek as 

a viable trout fishery with an excellent riparian zone 

(fig. 3; Mike Browne, written commun., 2007).

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Chapter N

88 Understanding Contaminants Associated with Mineral Deposits

Figure 2. Temporal trends of streamflow and concentrations of dissolved (open circles) and total (closed 

circles) trace elements in water, Uncle Sam Gulch, 1996–2005, a contaminated tributary of Cataract Creek in 

the Boulder River watershed study area (Unruh and others, in press). Upstream remediation work shutting 

off surface water flowing into the Crystal mine was completed in 2002 (dashed line in figure) and resulted in 

a reduction in the amount of copper and zinc released.

Pre-cleanup Post-cleanup

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Chapter N

Chapter N: Recovery of Aquatic Life in Surface Streams Affected by Mining Following Remediation 89

•	 Removal actions have been conducted by the USDA 

Forest Service in the Basin and Cataract Creek tributaries (fig. 4), but little improvement in sediment quality 

or aquatic life has been demonstrated downstream in 

the Boulder River (Rhea and others, 2006; Unruh and 

others, in press).

•	 Stream response to remedial actions (1998–2001) was 

demonstrated in the water-quality sampling, but no 

measurable improvement is indicated by the sediment 

or biological data in the Boulder River downstream 

from the tributaries where restoration has been conducted (Unruh and others, in press).

•	 The recovery curve for biota in the Boulder River is 

projected to be a decadal response function unless contaminated sediment is removed from the Boulder River.

Animas River Watershed, Colorado

The Animas River watershed is a heavily mineralized and 

highly altered area (Church, von Guerard, and Finger, 2007). 

Fish habitat is limited; food supply is limited by high dissolved 

concentrations of cadmium and zinc, and fish are limited by 

high dissolved concentrations of copper (Besser and others, 

2001, 2007). Remediation costs in the Animas River watershed by all sources through 2004 have exceeded $20 million 

(Church, Owen, and others, 2007). Monitoring of sediment and 

water has shown very little improvement although some benthic 

macroinvertebrates have reappeared in stream reaches on lower 

Mineral Creek that were previously barren (Anderson, 2007; 

William Simon, oral commun., 2006). The following summary 

is largely from Church, Owen, and others (2007):

•	 Remediation work in the headwaters of Mineral Creek 

has lowered the dissolved loads of zinc and copper 

associated with historical mining of breccia pipe 

deposits in the Red Mountain district in the headwaters 

of Mineral Creek.

•	 Remediation work in the headwaters of Cement Creek 

has lowered the dissolved concentrations of manganese 

and sulfate.

•	 During the period from April 1996 through April 1999, 

the water-treatment plant operating at Gladstone by 

the Sunnyside Gold Corporation lowered the dissolved 

copper and zinc load in Cement Creek relative to 

preremediation conditions (Kimball and others, 2002; 

fig. 5).

•	 Extensive remediation of mill wastes disposed of in the 

Animas River has resulted in small changes in dissolved 

metal concentrations: copper and zinc have improved 

slightly, manganese concentrations have elevated substantially, and sulfate concentrations are somewhat elevated above the preremediation baseline concentrations, 

possibly because of the remediation work that disturbed 

the streambed and exposed new material (Kimball and 

others, 2007; Church, Owen, and others, 2007; fig. 6).

•	 Analysis of aerial photography from the upper 

Animas River over a 50-year period (Vincent and 

Figure 3. High Ore Creek photographs showing 

changes in the riparian zone before and after 

restoration by Bureau of Land management in 

2002. Photographs provided by Mike Browne (2007).
Chapter N

90 Understanding Contaminants Associated with Mineral Deposits

Elliott, 2007) showed a slow rate of recovery of 

willows in the riparian zone downstream from the 

Sunnyside mill. Without implementation of riparian zone restoration like that in High Ore Creek, 

recovery of the riparian habitat downstream from the 

Eureka mill will likely require many decades, if not 

centuries, to restore the riparian ecological function 

of this reach to premining conditions (Vincent and 

Elliott, 2007).

•	 Dissolved concentration data from the compliance point downstream from the confluence of the 

two major tributaries with the Animas River show 

little change over the decade of monitoring and 

ongoing remediation (fig. 6). Remediation in this 

ecosystem will be measured in several decades, 

if not centuries (Church, Owen, and others, 2007).

San Carlos Reservoir Downstream 

from the Morenci Copper Mine, Gila 

and San Francisco Rivers, Arizona

Sediment cores from the San Carlos Reservoir clearly 

document the release of copper from the Morenci porphyry copper mine site over time (fig. 7). The age of sediment in the core 

was dated using 137Cs and 210Pb methods. Core geochemistry 

was correlated with historical documentation of contamination 

at the mine site (Church, Fey, and Marot, 2005). The data show:

•	 When open-pit mining began at Morenci in the late 

1930s, the copper concentration in sediment in the 

San Carlos Reservoir was at about the crustal abundance 

concentration for copper (CACu = 68 parts per million; 

Fortescue, 1992), that is, about half of the probableeffects sediment quality guideline concentration for copper (SQGCu = 149 ppm; MacDonald and others, 2000). 

At this concentration, the SQGCu accurately predicts a 

toxic effect 90 percent or more of the time for sedimentdwelling organisms (n = 347).

•	 About the year 1957, there was a one-time release of 

copper that greatly exceeded SQG (245-cm depth, core 

04SCR112). This event was accompanied by a zinc 

release that also exceeded SQG (SQGZn = 459 ppm, 

MacDonald and others, 2000). Recovery was essentially instantaneous, but the release would have resulted 

in massive acute aquatic exposure and probably death. 

Unfortunately, no biological data are available from that 

time period.

•	 Further development at the mine site and lapse in environmental monitoring at the mine site resulted in a long 

period of elevated copper release beginning about 1967.

•	 The Morenci copper mine entered into a cease-anddesist consent decree with the USEPA in 1986 (Chase 

Creek Consent Decree, U.S. Department of Justice and 

Phelps Dodge Corporation, August 25, 1986, filed with 

the U.S. District Court in Arizona) and immediately 

instituted surface-runoff controls on the mine site. The 

result downstream was essentially instantaneous: copper 

concentrations dropped to near the SQG where they 

have remained ever since.

•	 Open-pit mining over the past 70 years has resulted in 

doubling the copper concentration in the sediment in 

the San Carlos Reservoir, near the point at which many 

aquatic organisms would be affected (fig. 7; Church 

and others, 2005).

•	 BLM has granted Freeport-McMoRan, the current 

operator, a NO-RELEASE permit to develop the 

Dos Pobres and Safford porphyry copper open-pit 

mines downstream from the Morenci copper mine, 

but upstream from the San Carlos Reservoir.

Figure 4. Buckeye mill site in the upper reaches of Basin Creek, 

showing site before and after reclamation. The mill tailings (white 

waste pile on the flood plain, top photograph) released metals 

and contaminated sediment to the stream during high-flow runoff 

(Cannon and others, 2004). Photographs from Nimick (2004).

October 7, 1999

August 27, 2002
Chapter N

Chapter N: Recovery of Aquatic Life in Surface Streams Affected by Mining Following Remediation 91

Figure 5. Time-series plots showing 12 sample moving-average concentrations of dissolved copper (A), zinc (B), manganese (C), and 

sulfate (D) in Cement Creek. Water sampled at USGS gage (09358550) on Cement Creek. Baseline monitoring data collected from 1994 

to 1996. Remediation at mine sites and period of operation of the water-treatment plant at Gladstone are shown at top of figure. See 

Church, Owen, and others (2007) for details.

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Chapter N

92 Understanding Contaminants Associated with Mineral Deposits

Figure 6. Time-series plots showing 12 sample moving-average concentrations of dissolved copper (A), zinc (B), manganese (C), and 

sulfate (D) at the compliance site downstream from the confluence of Mineral Creek with the Animas River. Water sampled at the USGS 

gage (09359020). Baseline monitoring data collected from 1991 to 1996. See Church, Owen, and others (2007) for details.

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Chapter N

Chapter N: Recovery of Aquatic Life in Surface Streams Affected by Mining Following Remediation 93

Figure 7. Variation of concentration of copper in sediment with 

depth, core 04SCR112, San Carlos Reservoir (gray line; Church, 

Choate, and others, 2005). Two large copper spikes are preserved in 

the sediment core and record uncontrolled releases that occurred 

at the Morenci copper mine. Analysis of the contaminant peaks 

was undertaken in 2007 at 1-centimeter intervals (black line). These 

new analyses confirm the instantaneous nature of the release at 

243 centimeters that took place in about the year 1957. The second 

was a prolonged release from the mine site that began in 1978 and 

lasted through 1983 (124–72 centimeter depth). The dashed line 

is the SQGCu concentration (149 parts per million; MacDonald and 

others, 2000).

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Summary

Our studies of aquatic recovery downstream from remediated mine sites show that, at active mine sites, release of metal 

contaminants to surface streams can be controlled with onsite 

engineering remedies and controls, and that the downstream 

response can be essentially immediate once those remedies are 

implemented. The Morenci copper mine is one example of such 

a success story. Comparison of the concentrations of copper, 

lead, and zinc measured in the active stream channel of the 

San Francisco and Gila Rivers downstream from the Morenci 

mine site to San Carlos Reservoir in 1990 and 2004 shows very 

similar results and does not appear to indicate that sediment in 

the active downstream channel in the Gila and San Francisco 

Rivers constitutes a long-term sink of contaminated sediment 

(fig. 7). Likewise, a spill, probably of molybdenum product at 

the Questa mine site, also showed an immediate response to the 

cleanup of the spill in sediment cored from Eagle Rock Lake on 

the Red River (Church, Fey, and Marot, 2005).

In a watershed where there is little hydrothermal alteration, 

the primary source of metals is mine-waste piles, mill tailings, 

and acidic water generated at the mine sites. In this case, the 

cleanup of the largest contributing sites in the watershed will 

result in an improvement of the water and sediment quality in 

the immediate downstream reach, but stored fluvial tailings and 

mine waste in sediment traps such as overbank deposits, stream 

meanders, and oxbow lakes must also be removed to achieve 

recovery of aquatic life and restoration of a functional riparian 

zone. Excellent results are shown by the remediation on the 

Buckeye mine site in upper Basin Creek and the Comet mine 

site in High Ore Creek (figs. 3 and 4).

In watersheds where the geology is more complex and 

hydrothermal alteration extensive (Bove and others, 2007), 

determination of premining water and sediment quality is more 

difficult (Church, Fey, and Unruh, 2007). Defining remedial 

objectives that are financially achievable may not result in 

restoration of aquatic life in the immediate downstream reach, 

but the improvement in water and sediment quality achieved 

will improve aquatic habitat to the point where aquatic life may 

return to previously dead downstream reaches. This has been 

the goal of the Federal and State land managers and the local 

stakeholders group in the Animas River watershed. It is especially important to recognize that some stream reaches in these 

watersheds may not have supported aquatic life prior to mining 

(Besser and others, 2007; Church, Fey, and Unruh, 2007).
Chapter N

94 Understanding Contaminants Associated with Mineral Deposits

References Cited

Anderson, C.R., 2007, Effects of mining on benthic macroinvertebrate communities and monitoring strategy, in Church, 

S.E., von Guerard, Paul, and Finger, S.E., eds., Integrated 

investigations of environmental effects of historical mining 

in the Animas River watershed, San Juan County, Colorado: 

U.S. Geological Survey Professional Paper 1651, p. 851–872.

Besser, J.M., Brumbaugh, W.G., May, T.W., Church. S.E., and 

Kimball, B.A., 2001, Bioavailability of metals in stream food 

webs and hazards to brook trout (Salvelinus fontinalis) in the 

upper Animas River watershed, Colorado: Archives of Environmental Contamination and Toxicology, v. 40, p. 48–59. 

Besser, J.M., Finger, S.E., and Church, S.E., 2007, Impacts 

of historical mining on aquatic ecosystems—An ecological 

risk assessment, in Church, S.E., von Guerard, Paul, and 

Finger, S.E., eds., Integrated investigations of environmental 

effects of historical mining in the Animas River watershed, 

San Juan County, Colorado: U.S. Geological Survey Professional Paper 1651, p. 87–106.

Bove, D.J., Yager, D.B., Mast, M.A., and Dalton, J.B., 2007, 

Alteration map showing major faults and veins and associated water-quality signatures of the Animas River watershed 

headwaters near Silverton, southwest Colorado: U.S. Geological Survey Scientific Investigations Map 2976, 18-page 

pamphlet, 1 plate, scale 1:24,000.

Browne, Mike, 2007, Montana abandoned mine land program 

ten-year anniversary, Presentation made at the BLM and 

Forest Service meeting, Silverton, Colo., September 27, 2007.

Buxton, H.T., Nimick, D.A., von Guerard, Paul, Church, 

S.E., Frazier, Ann, Gray, J.R., Lipin, B.R., Marsh, S.P., 

Woodward, Daniel, Kimball, Briant, Finger, Susan, 

Ischinger, Lee, Fordham, J.C., Power, M.S., Bunck, 

Christine, and Jones, J.W., 1997, A science-based, watershed strategy to support effective remediation of abandoned mine lands: Proceedings of the Fourth International 

Conference on Acid Rock Drainage, Vancouver, B.C., 

May 31–June 6, 1997, p. 1869–1880.

Cannon, M.R., Church, S.E., Fey, D.L., McDougal, R.R., 

Smith, B.D., and Nimick, D.A., 2004, Understanding traceelement sources and transport to upper Basin Creek in the 

vicinity of the Buckeye and Enterprise mines, in Nimick, 

D.A., Church, S.E., and Finger, S.E., eds., Integrated investigations of environmental effects of historical mining in the 

Basin and Boulder mining districts, Boulder River watershed, Jefferson County, Montana: U.S. Geological Survey 

Professional Paper 1652, p. 401–455.

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

Monique, 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. 

(http://pubs.usgs.gov/sir/2005/5086/)

Church, S.E., Fey, D.L., and Marot, M.E., 2005, Questa 

baseline and pre-mining ground-water quality investigation 8—Lake-sediment geochemical record from 1960 

to 2002, Eagle Rock and Fawn Lakes, Taos County, 

New Mexico: U.S. Geological Survey Scientific Investigations Report 2005–5006, 47 p. http://pubs.usgs.gov/

sir/2005/5006/

Church, S.E., Fey, D.L., and Unruh, D.M, 2007, Trace 

elements and lead isotopes in modern streambed and terrace 

sediment—Determination of current and premining geochemical baselines, in Church, S.E., von Guerard, Paul, and 

Finger, S.E., eds., Integrated investigations of environmental 

effects of historical mining in the Animas River watershed, San Juan County, Colorado: U.S. Geological Survey 

Professional Paper 1651, p. 571–642. http://pubs.usgs.gov/

pp/1651/

Church, S.E., Kirschner, F.K., Choate, L.M., Lamothe, 

P.J., Budahn, J.R., and Brown, Z.A., 2007, Geochemical 

premining background study of the Blue Creek drainage, Stevens County, Washington: U.S. Geological Survey Scientific Investigations Report 2007–5262, 177 p. 

http://pubs.usgs.gov/sir/2007/5262/

Church, S.E., Owen, J.R., von Guerard, Paul, Verplanck, 

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Publishing support provided by:

Denver Publishing Service Center, Denver, Colorado

Manuscript approved for publication, August 13, 2008

Edited by Mary A. Kidd

Graphics and layout by Joy Monson

For more information concerning this publication, contact:

Team Chief Scientist, USGS Central Mineral Resources

Box 25046, MS 973

Denver, CO 80225

(303) 236-1562

Or visit the Central Mineral Resources Team Web site at:

http://minerals.cr.usgs.gov/

This publication is available online at:

http://pubs.usgs.gov/cir/1328/
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