Application of Physical Habitat Simulation 

in the Evaluation of Physical Habitat 

Suitability

By Robert T. Milhous

Chapter E21 of

Integrated Investigations of Environmental Effects of Historical 

Mining in the Animas River Watershed, San Juan County, Colorado

Edited by Stanley E. Church, Paul von Guerard, and Susan E. Finger

Professional Paper 1651

U.S. Department of the Interior

U.S. Geological Survey
Contents

Abstract .......................................................................................................................................................877

Introduction.................................................................................................................................................877

Purpose and Scope ..........................................................................................................................877

Methods of Study .......................................................................................................................................878

Results and Discussion .............................................................................................................................878

Physical Aquatic Habitat .................................................................................................................878

High Streamflow Conditions ..................................................................................................878

Low Streamflow Conditions ...................................................................................................881

Sediment Considerations in Habitat Analysis ..............................................................................883

Bed Material Characteristics ................................................................................................883

Pore Water Characteristics ...................................................................................................884

Sediment and Physical Habitat .............................................................................................885

Changes in Substrate ..............................................................................................................886

Conclusions.................................................................................................................................................888

References Cited........................................................................................................................................888

Figures

 1. Map showing locations of sample sites and stream gauges on principal 

streams in Animas River watershed study area ..................................................................879

 2. Graph showing daily streamflows from State of Colorado streamflow gauge 

at Howardsville during 1996 and relation between habitat and discharge 

for trout and for total benthic invertebrate biomass in Animas River ..............................880

 3. Graph showing habitat criteria for adult trout in Animas River ........................................881

 4. Diagram showing yearly fluctuation of a calculated Fish Stress Index for 

trout in Animas River ................................................................................................................881

 5. Graph showing effective habitat versus population density relations for juvenile 

brown and rainbow trout in upper Gunnison River, Colo. ....................................................882

 6. Diagram showing annual range in winter physical habitat in Animas River 

near Howardsville between 1 December and 28 February ...............................................883

 7. Graph showing particle size distribution of armor material in Animas River 

upstream and downstream from Howardsville ...................................................................884

 8. Graph showing particle size distribution of subsurface material in Animas River 

upstream and downstream from Howardsville .....................................................................887

 9. Diagram showing annual flood-plain and channel mobilization index for Animas 

River at Howardsville................................................................................................................887
Tables

 1. Spawning and incubation flows, rainbow trout fry habitat, and juvenile rainbow 

trout densities at the Duncan/Ute Trail site on the Gunnison River, Colo. ......................882

 2. Physical habitat as related to discharge, for low-flow (winter) discharges 

of the Animas River at Howardsville .....................................................................................883

 3. Spawning and incubation flows in the Gunnison River as measured downstream 

from the diversion tunnel, brown trout fry habitat, and juvenile brown trout 

densities at the Duncan/Ute Trail site downstream ............................................................883

 4. Specific weight, specific gravity, and porosity of bed material of three 

unregulated rivers ....................................................................................................................884

 5. Concentration of selected metals in surface water and pore water from 

a sand bar in the Animas River downstream from Silverton .............................................885

 6. Concentration of selected metals in surface water and pore water of the 

Animas River upstream from Howardsville ..........................................................................885

 7. Concentrations of selected metals in pore water at three locations in the 

Animas River watershed .........................................................................................................885

 8. Comparison of the sizes of armor material from the streambed of the Animas 

River upstream and downstream from Howardsville .........................................................886

Abstract

The suitability of physical habitat in the Animas River 

watershed for supporting trout populations was evaluated by 

analysis of field-collected data and historical information from 

U.S. Geological Survey and State of Colorado streamflowgauging stations. A physical habitat suitability simulation 

model based on stream velocity, channel depth, discharge, and 

substrate character was used to evaluate the data. Results indicated that suitable habitat is limited during winter. Although 

low velocities required for suitable trout habitat may exist, 

the stream depths are too shallow to offer good habitat. The 

overall availability of suitable trout habitat in the river is low 

and adversely affects the probability of survival of adult fish. 

In addition, comparison of the Animas River conditions to 

data from a similar river system suggested that high snowmelt 

runoff events in the spring could impair reproductive success 

by scouring the redds (fish nests) during incubation, thus 

preventing emergence of juvenile fish. Effects of this high 

flow might be mitigated by the presence of cobble, boulders, 

or other types of cover occurring in the river. This reconnaissance study demonstrated that factors other than those related 

to mining practices could limit the success of a trout fishery.

Introduction

The Animas River in southwestern Colorado flows south 

to join the San Juan River near Farmington, N. Mex. The 

watershed study area of this volume is defined as the drainage 

areas of Mineral and Cement Creeks and the Animas River 

upstream from Silverton, Colo. (von Guerard and others, this 

volume, Chapter B). Typical of mountainous regions, the winters are cold with considerable snowfall and little snowmelt. 

Streamflows during the winter months remain low and reasonably stable; then from April through June snowmelt, runoff 

dominates streamflow.

Historically, only a few native fishes—including Colorado 

River cutthroat trout (Oncorhynchus clarki pleuriticus) and 

possibly mottled sculpin (Cottus bairdi)—occurred in the 

Animas River watershed study area. By the early 19th century, 

non-native species, including brook trout (Salvelinus fontinalis), rainbow trout (Oncorhynchus mykiss), and brown trout 

(Salmo trutta), had been introduced (Besser and others, this 

volume, Chapter D). Currently, fish distribution within the 

watershed is patchy, but brook trout are the most widespread 

species. Although contamination of water and aquatic sediment creates toxic conditions in many areas of the watershed 

(Besser and others, this volume; Besser and Leib, this volume, 

Chapter E19), the presence or absence of fish is also influenced 

by the quality and quantity of physical habitat in the stream.

Purpose and Scope

The availability of suitable physical habitat is a major 

factor influencing the success of a fishery in any aquatic 

environment. Habitat requirements for trout vary seasonally 

and may also be species specific. Traditionally, the assessment of physical habitat in a riverine environment requires 

exhaustive sampling of stream reaches during multiple 

seasons. The development of an effective reconnaissancelevel approach for physical habitat evaluation would be useful 

for understanding population level responses in a watershed. 

Therefore, a reconnaissance study was designed to determine 

the suitability of trout habitat in the Animas River watershed. In this study, physical aquatic habitat, including stream 

velocities, depths, and the nature of the bed material, was 

evaluated at select locations in the Animas River watershed 

study area.

The two principal objectives of this study were:

• To improve understanding of the influence of miningderived sediment on aquatic physical habitat, and

• To determine the utility of a reconnaissance-level 

physical habitat suitability model in assessment of the 

impacts of mining on the aquatic ecosystem.

Chapter E21

Application of Physical Habitat Simulation 

in the Evaluation of Physical Habitat Suitability

By Robert T. Milhous
Methods of Study

Fourteen sample sites were selected throughout the study 

area to characterize physical habitat (fig. 1). Samples of bed 

material were collected at each site; these included samples of 

the armor (defined as the space between and under rocks on the 

streambed surface where trout can take cover), the substrate, 

and the sand-sized and finer particulates deposited on the 

substrate surface. At selected sites, the stream morphology was 

also measured. These measurements included from one to three 

cross sections, the stream discharge, and the water surface 

elevations (depths). Discharge information generated at four 

U.S. Geological Survey discharge-gauging stations (sites 2–5, 

fig. 1) and one gauging station near Howardsville operated by 

the State of Colorado (site 1, fig. 1) was entered into a physical habitat simulation system (PHABSIM; Milhous and others, 

1989). This model was developed to predict the habitat conditions in rivers as a function of discharge and to determine the 

relative suitability of those predicted conditions for aquatic life. 

The two basic components of PHABSIM are the hydraulic and 

habitat simulations of a stream reach using defined hydraulic 

parameters and habitat suitability criteria. Hydraulic simulation 

is used to describe the area of a stream having various combinations of depth, velocity, and channel index as a function of 

flow. Simulation of physical habitat is accomplished using the 

physical structure of the stream and discharge. This information is used to calculate a habitat measure called Weighted 

Usable Area for the stream segment from suitability information based on field sampling of the various aquatic species of 

interest. PHABSIM consists of four major steps. The first is 

to simulate water depths, the second is to simulate velocities, 

the third is to simulate the physical habitat versus discharge 

relationship, and the fourth is to simulate the physical habitat 

when combinations of flows are involved.

As used in this chapter, physical aquatic habitat is defined 

as the relationships between velocities, depths, and the nature 

of the bed material, weighted by the life history requirements 

of selected aquatic species. The equation relating the physical 

habitat area (HA) in a stream to discharge is:

HA = ∫ f(v, d, ci) da (1)

where

HA is the physical habitat area,

v is the velocity,

d is the depth,

ci is an index to the physical characteristics of 

the stream channel,

and

da is the incremental area.

The integration is over the area of a reach of stream. In most 

applications of PHABSIM, the function f( ) is divided into independent functions of velocity, depth, and the channel index.

The function used in this equation is then:

 f(v, d, ci) = h(v)*g(d)*j(ci) (2)

where h(v), g(d), and j(ci) are independent functions among 

velocity, depth, and the channel characteristics, respectively.

The physical habitat areas calculated are the habitats available 

for a life stage and species of aquatic animal weighted by how 

well the area meets the needs of the species. Examples of life 

stages are spawning, fry, juveniles, and adults. Factors other 

than physical habitat may limit aquatic populations; therefore, 

physical habitat alone is not always a good predictor of population size or strength. However, a self-sustaining population 

cannot exist in the absence of suitable physical aquatic habitat.

Results and Discussion

Physical Aquatic Habitat

The physical habitat criteria for different life stages of 

trout used in the PHABSIM analysis were developed during 

previous studies (Culp and Homa, 1991). However, the criteria for trout have been modified to include both brook and 

brown trout. The acceptable velocities for suitable habitat are 

about 0.15 m/s greater than in the original trout habitat criteria. 

Similar physical habitat criteria are available for benthic habitat 

suitability. For these criteria, benthic biomass area relates to the 

ability of the habitat conditions to support benthic invertebrates.

The physical habitat for trout and benthic invertebrates 

was related to annual discharge and the daily discharge at the 

gauge (site 1, fig. 1) during water year 1996 in the Animas 

River near Howardsville (fig. 2). The discharge data from 

Howardsville for water year 1996 were used in this figure 

because the median discharge (2.92 m3

/s) for the period of 

record (1936–1996) was similar to the average annual discharge for water year 1996 (2.89 m3

/s).

There are two periods during which trout may experience habitat stress resulting from habitat conditions being less 

than optimal. One of these periods occurs during high-flow 

conditions in the spring, and the second results from low-flow 

conditions in the winter.

High Streamflow Conditions

High velocities limit the availability of trout habitat during spring runoff (fig. 3). An index describing the stress on 

the trout population during the spring runoff period has been 

used to investigate the variation in stress from year to year. 

The conceptual basis of the stress index is that high velocities 

reduce the quality of the physical habitat, and that the more 

days the velocities exceed some critical value, the greater is 

878 Environmental Effects of Historical Mining, Animas River Watershed, Colorado
Physical Habitat Simulation and Habitat Suitability 879

Figure 1. Locations of sample sites and stream gauges on principal streams in Animas River watershed study area. Locations (solid 

triangles) are designated numerically as follows: 1, Howardsville; 2, Silverton; 3, Cement Creek; 4, Mineral Creek; 5, Downstream from 

Silverton. Substrate samples were collected near the five gauges and at sites A–I.

1

2 3

4

5

EXPLANATION

Sample locality A

5 Stream gauge, 

 with sample locality

former

Lake

Emma

Elk Park

Mineral Creek

Animas

River

Cement Creek

Chattanooga

Eureka

Silverton

Animas

Forks

Howardsville

Animas River

watershed 

study area

C O L O R A D O

Durango

0

0 1

1 2 MILES

2 KILOMETERS

107o50'30" 107o45' 107o37'30" 107o30'

37o

52'

30"

37o

45'

37o

58'

A

B

C

E D

F

G H

I
the stress on the trout population in the stream. The equation 

used to calculate the stress on the trout population caused by 

high velocities is:

 FSI = Σ((Qd – Qcrt)/Qref) (3)

where

 FSI is the Fish Stress Index for a selected time 

period (usually a year),

Qd is the daily discharge,

Qcrt is the critical discharge above which the stress 

on fi sh is signifi cant,

and

Qref is an arbitrary reference discharge used to 

make the index dimensionless.

The summation is for a water year.

The discharge–habitat quality weighting function was 

used to determine the critical velocity. The assumption is that 

a suitability of 0.1 or less introduces stress to trout populations 

that could limit the size (either biomass or numbers) of the 

populations. A relation between the mean channel velocity and 

the discharge was determined using least absolute deviation 

regression. The equation is:

vARNH = 0.376(QARNH))*0.556 (4)

where the velocity, v, is in m/s; the discharge, Q, is in m3/s; 

and ARNH means Animas River Near Howardsville. From this 

relation the discharge at an average channel velocity of 1.1 m/s 

(suitability weight of 0.1) was determined to be 5.26 m3

/s and 

is the critical discharge (Qcrt) in equation 3. The reference 

discharge (Qref) selected for the calculations of the fish stress 

index was 3.0 m3

/s. The equation for fish stress index (FSI) 

is then:

 FSI = Σ(Qd – 5.26)/3.0 (5)

where the daily discharge, Qd, is in m3

/s and the summation is for a water year. Fish stress fluctuated greatly during 

the period of record (1936–1996) at the Howardsville gauge 

(fig. 4). Not included in the analysis is the reduction in stress 

on the trout population resulting from the presence of velocity 

cover (usually cobbles and boulders). The velocity cover provides areas of locally low velocity where the fish are sheltered 

from the overall high channel velocities.

Few fish population data are available for the Animas 

River. However, some data are available for the Gunnison 

River to the north of our study area. In the Gunnison River 

basin (fig. 5; table 1), the limiting factor on the production of 

juvenile trout is the fry habitat during the months just following the emergence of the fry from the gravels the previous year 

(Nehring and Miller, 1987). Rainbow trout spawn in the spring 

and incubate during the spring runoff; the fry emerge towards 

the end of the spring runoff. Flow conditions between spawning and emergence may play a critical role, as high flows can 

effectively scour the redds (nests) and reduce juvenile survival.

An example of the effect of flow conditions on trout 

production comes from a comparison of data from table 1 and 

regression lines in figure 5 (p. 882), which shows that in 1983 

the expected production of fry (fig. 5) was five juveniles per 

hectare; instead, the measured production (table 1) was one. 

The lower than expected production may have resulted when 

the relatively low discharge during spawning was followed 

by a relatively high discharge during incubation, resulting in 

scoured-out redds.

Analysis of fry and juvenile habitat and conditions during 

incubation in the Animas River watershed has not been done. 

The spring conditions in the upper Animas River are sufficiently similar to those of the Gunnison River to warrant such 

a comparison.

Figure 2. Daily streamflows from State of Colorado streamflow gauge at Howardsville during 1996 and 

the relation between habitat and discharge for trout and for total benthic invertebrate biomass in Animas 

River. (The Colorado State Engineer has operated this gauge since 1983; USGS operated it 1936–1982.)

EXPLANATION

Discharge

Benthic

Trout

0 5 10 15 20 25

0

50

100

150

200

250

300

350

400

0

2

4

6

8

10

12

DAY IN WATER YEAR

DISCHARGE, IN CUBIC FEET PER SECOND

HABITAT AREA, IN SQUARE

METERS PER METER

880 Environmental Effects of Historical Mining, Animas River Watershed, Colorado
Physical Habitat Simulation and Habitat Suitability 881

Figure 3. Habitat criteria for adult trout in Animas River.

Figure 4. Yearly fluctuation of a calculated Fish Stress Index for trout in Animas River. Horizontal 

dashed line is median index for the 63 years of record.

Low Streamflow Conditions

The adult trout habitat criteria for winter are not the same 

as for the rest of the year. The velocity criteria for physical 

habitat at winter low flow require a lower velocity for the same 

level of habitat suitability than during other times of the year. 

During winter, when the velocities are low enough for reasonable habitat, the depths are too shallow. The winter habitat time 

series presented in figure 6 was calculated using the measured 

minimum 2-day and maximum 2-day discharges in the period 

1 December through 28 February for each water year (fig. 6). 

The winter physical habitat is stable with reasonably small 

variation. The data in figure 6 and table 2 clearly show just 

how limiting winter conditions are in the upper Animas River. 

The result is that little winter trout physical habitat exists in 

the Animas River.

The reduction in winter habitat shown in table 2 is a 

result of the velocities being too high for trout habitat. Winter 

conditions similarly limited the reproduction of brown trout in 

the Gunnison River (table 3). Brown trout production is further 

WATER YEAR

FISH STRESS INDEX

1936 1946 1956 1966 1976 1986 1996

0

50

100

150

200

250

300

2.5

2.0

1.5

1.0

0.5

0.0

0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

0.0

SUITABILITY FACTOR

VELOCITY, IN METERS PER SECOND

DEPTH, IN METERS

Depth

Velocity

EXPLANATION
limited in the Gunnison River by the conditions of spring 

runoff when fry emerge from the spawning gravels. (A significant winter difference is that the Gunnison River is regulated, 

which means winter flows are not as limiting as in the upper 

Animas River—but the overall process is similar (Milhous, 

1995).) Two data points for brown trout in figure 5 are outliers. The likely cause of the outliers is the incubation conditions before emergence of the fry in the spring. The brown 

trout spawning period used in the following analysis is from 

1 October to 15 November and the incubation period from 

1 November to 15 April. Winters in the Gunnison River basin 

can range from cold and dry (low winter runoff) to relatively 

warm and wet (high winter runoff). If the streamflows during 

the fall are high, more fish will tend to spawn successfully. 

If the streamflows during the incubation period are relatively 

high, more of the redds will produce fry. In contrast, if flows 

during the incubation period are low, fewer of the redds will 

yield fry. Good spawning flows followed by good incubation 

(high) flows should give a point to the left of the regression 

line (fig. 5), but if the incubation flows are low, the predicted 

reproductive success should be to the right. The outlier to the 

right in figure 5 occurred in 1981 and the one to the left in 

1985. The spawning flows were good in 1981, but the incubation flows were much reduced. This was followed by good 

fry habitat, but by that time poor incubation conditions had 

reduced the fry that could emerge. A comparison of data from 

1981 to 1982 shows the incubation discharge to be slightly 

reduced, but because the spawning flows were also low, a 

reduction in fry production probably did not occur. In 1985, 

the spawning and incubation flows were similar in magnitude 

and the expected result was a larger than average production 

of fry, causing a larger than expected production of juveniles a 

year later. The differences in winter flows in the Animas River 

watershed study area are not usually as large as those typical 

for the Gunnison River, but the range is probably adequate to 

limit the production of fall spawning fish such as brown trout 

and brook trout.

Table 1. Spawning and incubation flows, rainbow trout fry 

habitat, and juvenile rainbow trout densities at the Duncan/

Ute Trail site on the Gunnison River, Colo.

[Juvenile population and weighted usable area data from Nehring and Miller 

(1987); m3/s, cubic meters per second; m2/m, square meters per meter]

Water

year

Spawning

discharge

(m3

/s )

Incubation

discharge

(m3/s )

Fry

habitat

(m2/m)

Juveniles

(number/

hectare)

1980 57 72 589 32

1981 7 8 542 35

1982 12 32 255 18

1983 45 257 89 1

1984 151 274 16 1

1985 92 135 144 12

Figure 5. Effective habitat versus population density relations for juvenile brown and rainbow trout 

in upper Gunnison River, Colo. (data from Nehring and Miller, 1987).

0

20

40

60

80

100

120

ANNUAL FRY HABITAT, IN SQUARE METERS PER KILOMETER

EXPLANATION

NUMBER OF JUVENILE TROUT PER HECTARE

0 100 200 300 400 500 600

Rainbow

Brown

882 Environmental Effects of Historical Mining, Animas River Watershed, Colorado
Physical Habitat Simulation and Habitat Suitability 883

Sediment Considerations in Habitat Analysis

Winter habitat is associated with cover such as large 

rocks and loose gravels into which fish can burrow (Meyer and 

Griffith, 1997). These factors are not adequately represented 

in the PHABSIM model used to calculate the physical habitat 

presented in figure 6 and table 2. Both factors are related to the 

sediment in the streambed. In addition, the habitats that fish 

use to avoid high velocities during the spring high discharge 

period are also related to the characteristics of the streambed 

material. Fish in the Animas River use the voids within the 

streambed as places to burrow during the winter and as habitat 

for redds for spawning.

Bed Material Characteristics

The particle size of the substrate downstream from the 

armor is an important aspect of the physical habitat for fish 

and benthic invertebrates. Particle size distributions of armor 

from samples collected upstream (site B) and downstream from 

Howardsville (site 1) during August discharge ranged in size 

(fig. 7). The low gradient reach upstream from Howardsville 

has few large particles in the armor; in contrast, the reach 

downstream from Howardsville has large particles. The large 

particles at site 1 are associated with mass movement into the 

river. The river is not actively transporting the larger particles. 

All the armor at the other three locations is river-transported 

sediment.

The specific weight and porosity for the sample from the 

exposed bar (one of two at site B) upstream of Howardsville 

and from the sample downstream of Silverton (site 5) were 

Table 2. Physical habitat as related to discharge, for low-flow 

(winter) discharges of the Animas River at Howardsville.

[m3/s, cubic meters per second; m2/m, square meters per meter]

Discharge

(m3

/s )

Surface

area

(m2

/m)

Adult

trout

(m2/m)

Winter

trout

(m2/m)

Benthic

biomass

(m2/m)

0.23 7.6 6.4 0.28 3.9

0.47 8.6 8.0 0.33 5.4

2.07 11.1 6.4 0.11 10.5

3.67 12.2 4.2 0.00 4.0

Table 3. Spawning and incubation flows in the Gunnison River 

as measured downstream from the diversion tunnel, brown trout 

fry habitat, and the juvenile brown trout densities at the Duncan/

Ute Trail site downstream.

[Juvenile population was measured the following year; juvenile population 

and weighted usable area data are from Nehring and Miller (1987); m3/s, cubic 

meters per second; m2

/m, square meters per meter]

Water

year

Spawning

discharge

(m3

/s)

Incubation

discharge

(m3/s)

Fry

habitat

(m2/m)

Juveniles

(number/

hectare)

1980 22.4 14.0 314 105

1981 34.6 4.9 366 59

1982 11.6 4.1 160 40

1983 38.1 20.4 63 13

1984 33.7 15.4 14 6

1985 47.3 38.7 95 57

Figure 6. Annual range in the winter physical habitat in the Animas River near Howardsville. The physical 

habitat was calculated from minimum and maximum 2-day discharge between 1 December and 28 February.

0.00

0.05

0.10

0.15

0.20

0.25

Maximum

Minimum

EXPLANATION

1936 1946 1956 1966 1976 1986 1996

WATER YEAR

WINTER HABITAT AREA , 

IN SQUARE METERS PER METER
determined and the results compared to those for samples 

from rivers in Oregon and Wyoming (table 4). The samples 

collected from these other two rivers have more fine material than the sample from downstream from Howardsville. 

This difference in particle size may explain the lower porosity 

found for the Animas River at Howardsville in comparison to 

the other two rivers.

Pore Water Characteristics

For the reach of the Animas River upstream from 

Howardsville, another aspect of the sediment related to physical habitat is that metal concentrations in the pore water of 

the substrate may be higher than in the surface water. Two 

methods were used to sample the pore water. Nimmo and others (1998) dug a hole in a sand bar near the river and assumed 

that the water obtained from the hole had the same concentration of metals as the pore water. The results they obtained for 

a bar just upstream of the gauging station downstream from 

Silverton (site 5, fig. 1; table 5) show that the pore water has 

higher concentrations of metals than the surface water and 

that they can have a significant impact on the quality of the 

substrate for aquatic biota.

The second approach was to place an aquarium air stone 

in the substrate with a tube to the surface that was sealed. The 

air stone and attached tube were left in the substrate for at 

least 2 days before the pore water was sampled. Two samples 

were analyzed from each site. Selected results from the study 

are given in tables 6 and 7. As was obtained from the dug hole, 

these results show that the pore water can be of significantly 

different quality than the stream water.

Benthic invertebrates, small fish, and eggs deposited in 

the trout redds use the substrate as habitat at least part of the 

year. Metals found in the pore water of the substrate may be 

at higher concentrations than in the surface water. This is the 

situation for the site upstream from Howardsville (tables 6 and 

7). Thus, the substrate may not be acceptable habitat because 

of toxic components in the sediment even when the surface 

water is not toxic.

Figure 7. Particle size distribution of armor material in Animas River upstream (B) and downstream 

(C and 1) from Howardsville.

Site C

Site B

Site B

Site 1

EXPLANATION

0

10

20

30

40

50

60

70

80

90

100

0 50 100 150 200 250 300 350 400 450

PERCENT CUMULATIVE DISTRIBUTION

PARTICLE SIZE, IN MILLIMETERS

Table 4. Specific weight, specific gravity, and porosity of bed 

material of three unregulated rivers.

[kg/m, kilograms per meter; g/cm3, grams per cubic centimeter; porosity 

expressed as fraction of void space]

Stream

Specific 

weight

(kg/m3

)

Specific 

gravity

(g/cm3)

Porosity

Percent 

of sample

<3 mm

Oak Creek, Oregon 1,680 2.85 0.41 13

Soda Butte Creek, 

Wyoming and 

Montana.

1,700 2.65 0.36 25

Animas River upstream 

from Howardsville 

(site B).

2,160 2.80 0.22 20

Animas River 

downstream from 

Silverton (site 5).

1,764 2.70 0.35 3

884 Environmental Effects of Historical Mining, Animas River Watershed, Colorado
Physical Habitat Simulation and Habitat Suitability 885

Table 5. Concentration of selected metals in surface water and 

pore water from a sand bar in the Animas River downstream from 

Silverton.

[Samples collected at site 5 were filtered through a 0.45 micrometer filter and 

acidified (Nimmo and others, 1998); μg/L, micrograms per liter]

Constituent Surface water

(μg/L)

Pore water

(μg/L)

Iron 20 75

Manganese 390 145

Aluminum <100 250

Copper 3.5 235

Zinc 100 465

Table 6. Concentration of selected metals in surface water 

and pore water of the Animas River upstream from Howardsville.

[Pore water samples from site B are the first and third samples removed 

from the substrate; samples collected in August 1999 were filtered through 

a 0.45 micrometer filter and then acidified; μg/L; micrograms per liter]

Constituent Surface water

(μg/L)

Pore water

(μg/L)

Sample 1 Sample 2

Calcium 22,500 21,300 20,500

Iron 68 4,400 1,100

Manganese 366 2,760 845

Copper 9.6 84.5 25.0

Zinc 276 777 395

Cadmium 1.1 3.4 1.6

Arsenic 0.33 5.30 1.6

Table 7. Concentrations of selected metals in pore water at three 

locations in the Animas River watershed.

[Samples were collected using the air stone method, filtered through a 0.45-

micrometer filter, and acidified; mg/L, milligrams per liter; μg/L, micrograms 

per liter]

Calcium 

(mg/L)

Copper 

(μg/L)

Zinc 

(μg/L)

Cadmium 

(μg/L)

Arsenic 

(μg/L)

South Fork Mineral Creek (site G)

Stream water 20.3 1.6 17.4 0.1 0.38

Pore water 1 25.2 23.4 994 1.4 9.27

Pore water 2 21.5 8.4 324 0.49 3.64

Animas River downstream from Silverton (site 5)

Stream water 27.9 19.5 214 1.3 1.11

Pore water 1 27.0 319 1,140 3.4 14.60

Pore water 2 23.9 46.4 360 1.4 5.3

Animas River upstream from Minnie Gulch (site A)

Stream water 21.0 17.9 374 1.78 0.45

Pore water 1 18.6 119 1,140 4.21 10.6

Pore water 2 19.1 41.4 374 2.15 3.26

Habitat Evaluations Procedures developed by the 

U.S. Fish and Wildlife Service indicate that good trout cover 

exists when there are reasonable amounts of particles larger 

than 100 mm in the stream armor (Raleigh, 1982). Based on 

this criterion, the upstream locations near Howardsville have 

less cover than the downstream locations (table 8).

The specific weight information (table 4) shows that the 

upstream location near Howardsville (site B) may not provide 

good substrate habitat because the substrate is relatively dense 

and the voids are small. The lower percentage of sands in the 

substrate downstream from Howardsville (site C; fig. 8) suggests that there may be better winter habitat conditions within 

the substrate downstream because trout may be better able to 

burrow into the substrate.

The sizes of the particles in the armor are also larger 

downstream than upstream (table 8). The river downstream 

has large particles that are scattered across the surface; the 

upstream location does not. Also, the larger ratio between 

the particle size at which 90 percent are smaller (d90) and the 

median sizes suggest the presence of more voids within the 

armor that could be used by fish as winter cover.

Overall, the numbers and sizes of the fish are expected to 

be larger downstream from Howardsville than upstream from 

Howardsville, if velocity cover is the only factor limiting fish 

populations. The only trout found in the reach of the Animas 

River upstream of Howardsville are brook trout; in contrast, 

downstream from Howardsville both brook trout and rainbow trout are found (State of Colorado, unpublished records 

of a biological survey of the Animas River, 1992). Because 

brook trout tend to be smaller than the other trout, the addition of rainbow trout downstream of Howardsville will tend 

to skew the calculated biomass. The number of trout collected 

at a location near the site where the substrate samples were 

Sediment and Physical Habitat

Meyer and Griffith (1997) indicated that a primary 

type of winter cover for rainbow trout is the space between 

and under rocks on the streambed surface (the armor). 

Another type of cover used as winter habitat by rainbow 

trout is within the gravel substrate, provided that the substrate 

is coarse enough and loose enough for the fish to burrow. 

These two factors suggest that winter trout habitat in the 

Animas River near Howardsville might be better than the habitat values in table 2 calculated using velocity and depth alone. 

In both spring and winter, boulders and cobbles are important 

in providing velocity cover to trout.

Two cover types of river sediment are important in 

defining habitat considerations: (1) the size of the sediment 

on the surface of the streambed (armor) and (2) the characteristics of the substrate (provides cover for trout and habitat 

for benthic invertebrates). The presence of each of these 

cover types was investigated for the Animas River considering the size distribution and pore water data presented 

previously.
obtained upstream from Howardsville was 41 brook trout in 

91 meters of stream with a biomass density of 18.3 kg per 

hectare. Near the downstream sample site, the number of 

brook trout was 13 in 116 meters (7.0 kg/hectare) along with 

14 rainbow trout (31.5 kg/hectare); the total trout biomass 

was 38.5 kg/hectare.

Changes in Substrate

An analysis presented in Milhous (2000) showed that 

two substrate-related factors are important in the evaluation 

of river restoration alternatives in watersheds with significant effects from historical or abandoned mines and mills. 

The two factors are (1) potential changes in the size distribution and specific weights of the substrate, and (2) potential changes in quality of the pore water, caused by metals 

associated with the tailings in the substrate. These factors are 

also important in understanding the dynamics of the physical 

habitat in rivers.

Vincent and Elliott (this volume, Chapter E22) obtained 

samples of the material from a trench dug across the river flood 

plain upstream from Minnie Gulch. Their analysis showed 

that 75 percent of the fines in the upper portion of the sediment across the flood plain were mill tailings. Based on similar 

assumptions, the sample collected upstream from Howardsville 

showed the sand and fine sediment in the substrate to be about 

17 percent.

The specific weights of the substrate at two locations 

in the Animas River are compared to the specific weights 

measured for two other streams and are presented in table 

4. The Oak Creek watershed in Oregon has been little disturbed. The Soda Butte Creek sites in Wyoming and Montana 

are on a stream with less upstream mining impact than has 

occurred in the upper Animas River basin. A tailings dam 

failed on Soda Butte Creek, but sufficient periods of high 

flows have occurred following the failure to remove tailings 

from the stream gravels but not from the flood plain.

Large quantities of tailings may increase the specific 

weight of the substrate and reduce interstitial space available 

to over-wintering small fish and to benthic invertebrates. The 

conclusion is based on the high specific weight of the sample 

obtained upstream from Howardsville compared to the results 

from the other rivers. The lower specific weight (and higher 

porosity) in samples downstream from Silverton is probably 

a result of the lower fraction of the substrate that is less than 

3 mm.

The studies by Vincent and Elliott (this volume) 

also demonstrate that considerable quantities of the tailings are available for transport in the flood-plain sediment 

downstream of the mill site. If 75 percent of the sand and 

fine sediment is tailings, and the sand and fines in the sample 

obtained upstream from Minnie Gulch are the same, then no 

more than 10 percent of the active river substrate is tailings upstream from Minnie Gulch. Recent decades’ floods 

have remobilized fine-grained mill tailings downstream 

from Eureka and deposited these tailings on the braided plain 

and on the willow-covered flood plains downstream (Vincent 

and Elliott, this volume).

At the beginning of the study, one objective was to 

determine whether the amount of sediment, sand sized and 

finer, found in the substrate of rivers in historical mining 

districts differs from that found in rivers not affected by 

mining. Milhous (2000) showed that the percent fines in 

the Animas River downstream from the tailings from the 

Sunnyside Eureka Mill (site # 164, Church, Mast, and others, 

this volume, Chapter E5) averaged 13 percent, compared to 

6 percent in South Fork Mineral Creek (few mines and mills 

in the watershed). This is a relatively small impact even if all 

the difference (7 percent) was caused by the addition of mill 

tailings.

A river will remove fine particulates and sand from 

the substrate if the delivery of fine silt and sand is less than 

the capacity of the river to move this fine-grained sediment. 

When tailings are available on the flood plain, the river will 

move sediment to the river only during floods. An index of 

the ability of the river to move tailings from the flood plain 

to the river was presented in Milhous (2000) and is shown 

in figure 9. The river has the capacity to remove sand and 

fine silt from the channel during almost all of the years (the 

capacity to clean the river substrate is zero for only 2 of 

the 63 years (Milhouse, 2000)). In contrast, the capacity to 

mobilize sediment from the flood plain and channel margins 

occurs in about 15 percent of the years. From the physical 

habitat viewpoint this means that the characteristics of the 

substrate are not a constant, but a variable dependent on the 

time pattern of streamflow.

Table 8. Comparison of the sizes of armor material from the 

streambed of the Animas River upstream and downstream from 

Howardsville.

[d90, grain size of 90th percentile expressed in millimeters]

Location Median

(mm)

d90

(mm)

Ratio

(d90/median)

Percent

of sample

>100 mm

Armor

Site 1 134.6 203.3 1.51 78

Site B 100.3 137.5 1.37 52

Site B 53.2 66.0 1.24 6

Site C 209.7 404.4 1.93 94

Substrate

Site 1 30.4 95.7 3.15 not

Site B 20.2 72.7 3.61 applicable

Site B 20.6 68.5 3.33

886 Environmental Effects of Historical Mining, Animas River Watershed, Colorado
Physical Habitat Simulation and Habitat Suitability 887

Figure 8. Particle size distribution of subsurface material in Animas River upstream (B) and 

downstream (C) from Howardsville.

Figure 9. Annual flood-plain and channel mobilization index (FPMI) for Animas River at Howardsville 

(Milhous, 2000). Prior to 1936 there were major floods with significantly more capacity to move 

sediment than in that time period.

1936 1956 1966 1976 1986 1996 1946

WATER YEAR

FLOOD PLAIN MOVEMENT INDEX

60

50

40

30

20

10

0

PARTICLE SIZE, IN MILLIMETERS

PERCENT CUMULATIVE DISTRIBUTION

0

10

20

30

40

50

60

70

80

90

100

0.01 0.1 1 10 100 1,000

Site C

Site B

Site B

EXPLANATION
Conclusions

Sediment from historical mining activity has two possible 

impacts on the physical habitat. The first is on the size of the 

sediment in the substrate, and the second is on the suitability 

of sediment as physical habitat. In the upper Animas River, the 

effects of the sediment from historical mining on the particle 

size distribution of sediment in the streams appear to be minor 

(fig. 8 and table 4). This may be because the last discharge 

of sediment to the stream from mills was more than 50 years 

before the study (Jones, this volume, Chapter C).

However, the impact of sediment quality on the suitability of the substrate may be important because of the potential 

toxicological effect of metals in the substrate and associated 

pore water (tables 5–7). In some locations, and at some times, 

the surface water may be of adequate quality for trout but the 

pore water may be of poor quality. The quality of the pore 

water is most likely poor because metal-containing fines from 

mining are still in the substrate.

In the Animas River watershed study area, this 

reconnaissance-level study of the physical habitat shows that 

suitable habitat for trout survival is limited by winter streamflows and that fall-spawning fish commonly do not have 

adequate streamflow conditions for spawning success. The 

analysis also showed that trout populations are limited in some 

years because of high stream velocities at critical times. Overall, the use of reconnaissance-level studies of physical habitat 

suitability can be useful because this approach identifies limits 

on the quality of a fishery that may result from factors other 

than the effects of mining.

References Cited

Culp, T.R., and Homa, J., Jr., 1991, Fish and macroinvertebrate 

habitat suitability index curves: Lansing, N.Y., Ichthyological Associates, Report to Niagara Mohawk Power Corporation, 86 p.

Meyer, K.A., and Griffith, J.S., 1997, Effects of cobbleboulder substrate on winter residency of juvenile rainbow 

trout: North American Journal of Fisheries Management, 

v. 17, p. 77–84.

Milhous, R.T., 1995, Changes in sediment transport capacity in the Lower Gunnison River, Colorado, U.S.A., in

Petts, Geoffrey, ed., Man’s influence on freshwater ecosystems and water use: Wallingford, Oxfordshire, International 

Association of Hydrological Sciences, IAHS Publication 230, 

p. 275–280.

Milhous, R.T., 2000, Changes in the substrate of rivers in 

historic mining districts, in Hotchkiss, R.H., and Glade, 

M., eds., Building partnerships—Conference on water 

resources engineering and water resources planning and 

management: American Society of Civil Engineers, 

10 p.

Milhous, R.T., Updike, M.A., and Schneider, D.M., 1989, 

Physical habitat simulation system reference manual, 

Version II: U.S. Fish and Wildlife Service Biological 

Report 89(16), Instream Flow Information Paper 26, 

537 p.

Nehring, R.B., and Miller, D.D., 1987, The influence of 

spring discharge levels on rainbow and brown trout 

recruitment and survival, Black Canyon of the Gunnison 

River, Colorado: Proceedings of the Annual Conference 

of Western Associations of Fish and Wildlife Agencies, 

July 13–15, 1987, Salt Lake City, Utah.

Nimmo, D.R., Castle, C.J., and Besser, J.M., 1998, A toxicological reconnaissance of the upper Animas River watershed 

near Silverton, Colorado, in Nimick, D.A., and von Guerard, 

Paul, eds., Science for watershed decisions on abandoned 

mine lands—Review of preliminary results, Denver, 

Colo., February 4–5, 1998: U.S. Geological Survey OpenFile Report 98-297, p. 19 (http://amli.usgs.gov/reports/

ofr98_297/nimmo.html).

Raleigh, R.F., 1982, Habitat suitability index models; 

brook trout: U.S. Fish and Wildlife Service Report 

FWS/OBS–82/10.24, Washington, D.C., 42 p.

888 Environmental Effects of Historical Mining, Animas River Watershed, Colorado