Animas River Fish Passage and 

Canal Entrainment Evaluation and 

Recommendations 

Animas-La Plata Project, Colorado and New Mexico

Upper Colorado Region 

U.S. Department of the Interior 

Bureau of Reclamation 

Western Colorado Area Office

Grand Junction and Durango, Colorado April 2007 
Mission Statements 

The mission of the Department of the Interior is to protect and 

provide access to our Nation’s natural and cultural heritage and 

honor our trust responsibilities to Indian Tribes and our 

commitments to island communities.

The mission of the Bureau of Reclamation is to manage, develop, 

and protect water and related resources in an environmentally and

economically sound manner in the interest of the American public. 
U.S. Department of the Interior 

Bureau of Reclamation 

Western Colorado Area Office 

Grand Junction and Durango, Colorado April 2007

Animas River Fish Passage and 

Canal Entrainment Evaluation and 

Recommendations 

Animas-La Plata Project, Colorado and New Mexico 

Upper Colorado Region 

Prepared by 

Michael S. Francis, Biologist 

Western Colorado Area Office 

Durango, Colorado 
Executive Summary 

To meet an environmental commitment in the 2000 the Animas-La Plata Project Final 

Supplemental Environmental Impact Statement (FSEIS), the Bureau of Reclamation 

(Reclamation) evaluated the significance of the City of Farmington’s Animas Pump 

Station #2 (APS) and Farmer’s Ditch Diversion (FDD) as movement barriers for 

flannelmouth suckers (Catostomus latipinnis or FMS) and bluehead suckers (C. 

discobolus discobolus or BHS) as well as the issue of small/young-of-the-year (YOY) 

native sucker entrainment losses into canals. 

A portion of both native sucker populations of sexually mature size were capable of 

ascending both diversions. Too few bluehead suckers were recaptured to allow for 

effective statistical analysis, but significantly more recaptured FMS ascended the APS 

than the FDD. The APS does not appear to be a significant barrier to fish over 400 mm in 

length while its gates are open, however the FDD is a more substantial barrier lacking inchannel gates. Both diversions are barriers to juvenile sucker movement, but to what 

degree could not be statistically determined as recaptures of smaller fish was underrepresented. There was no significant difference in the net distance moved per year by 

flannelmouth suckers in the upper and middle reaches (above FDD and between FDD 

and APS respectively) but those in the lower reach move more in an upstream direction. 

The Animas River was sampled for the presence of YOY native suckers from 2000-2002. 

The sample evaluation concluded that FMS and BHS reproduction in the upper Animas 

River was at high levels. The subsequent examination of existing data regarding current 

technologies for screening of small native sucker larvae indicate that effective methods 

for prevention of entrainment losses may have limited effectiveness and would be too 

costly in installation and maintenance. Numerous older juvenile suckers were found in 

sampling immediately below both diversions. In considering these factors together, 

Reclamation decided that loss of YOY suckers due to entrainment in canals, although 

occurring, was not a significant loss to the river’s population nor effectively manageable 

at this time. 

Reclamation recommends that the City of Farmington be contacted to attempt 

coordinating the operation of the APS gates to allow for greater native fish access to the 

upstream sections of the Animas River without negatively impacting the pump station 

operations. Reclamation further recommends the manual translocation of native suckers 

from downstream of both the APS and FDD to upstream of the FDD, emphasizing 

sexually mature and larger size class juvenile individuals, with care taken to ensure nonnative species are excluded in the translocation efforts. Reclamation also offers 

additional points to be considered in determining if these recommendations should be 

implemented. 
Acknowledgements 

Many individuals assisted in collecting field data and processing information during the 

course of the five-year study. Steve Whiteman and Ben Zimmerman with the Southern 

Ute Indian Tribe were invaluable in terms of providing logistical support and annual 

report preparation since the initiation of the study. Dr. Rich Valdez was instrumental in 

providing guidance and in developing a study design. 

Within the Bureau of Reclamation, Kirk Lashmett organized and led the study effort for

several years. This report is an expansion of an earlier draft he developed with added 

analysis and discussion. Riecky Rieck routinely provided much appreciated assistance 

during the course of conducting field fishery surveys. Also assisting over the years were 

C. Marc Wethington of the New Mexico Department of Game and Fish and the staff of 

the Southern Ute Wildlife Resource Management Division: Rich Porambo, Aran 

Johnson, Danielle McGraw, Chris Olguin and Karen Peterson. 

It is important to note that portions of the text herein are derived from the 2007 SWCA 

Environmental Consultants report to the Bureau of Reclamation entitled “Analysis of

Existing Data on Potential Animas River Diversion Effects on the Movements of Adult

Flannelmouth and Bluehead Suckers”. Their detailed analysis of the data generated by 

the study should prove invaluable for the future conservation of native suckers in the 

Animas River. 

 
Contents 

Page 

Executive Summary ................................................................................ 4

Acknowledgements................................................................................. 5

Introduction.............................................................................................. 1

Background....................................................................................................... 1 

Methods.................................................................................................... 7

Fish Barriers...................................................................................................... 7 

Sampling ..................................................................................................... 8 

Recording.................................................................................................... 8 

Analysis....................................................................................................... 9 

Fish Entrainment in Canals............................................................................... 9 

Sampling ................................................................................................... 10 

Recording.................................................................................................. 10 

Analysis..................................................................................................... 10 

Results ................................................................................................... 12

General Results............................................................................................... 12 

Species Encountered ................................................................................. 12 

Fish Barriers.................................................................................................... 12 

Recapture Rate.......................................................................................... 12 

Length/Frequency ..................................................................................... 13 

Net Annual Movement.............................................................................. 18 

Upstream Movement................................................................................. 19 

Farmer’s Ditch Diversion ................................................................... 19 

Animas Pump Station #2 .................................................................... 20 

Farmer’s Ditch Diversion Compared to Animas Pump Station #2..... 21 

Downstream Movement............................................................................ 21 

Fish Entrainment in Canals............................................................................. 22 

Discussion ............................................................................................. 24

Fish Barriers.................................................................................................... 24 

Fish Entrainment in Canals............................................................................. 25 

Recommendations ................................................................................ 28

Fish Barriers.................................................................................................... 28 

Animas Pump Station #2 .......................................................................... 28 

Farmer’s Ditch Diversion ......................................................................... 28 

Fish Entrainment in Canals............................................................................. 29 

Other Considerations ...................................................................................... 29 

Population Viability Analysis................................................................... 29 

Conservation Planning and Implementation............................................. 30 

Other Reclamation Commitments............................................................. 30 

References and Literature Consulted.................................................. 31
Fish Passage and Canal Entrainment Evaluation 

Introduction 

The Animas-La Plata Project (Project) Final Supplemental Environmental Impact 

Statement (FSEIS) was completed in July 2000 and the associated Record of 

Decision (ROD) was signed in September 2000. Reclamation is currently 

involved in implementing the environmental commitments for Refined 

Alternative 4 as defined in the FSEIS and restated in the ROD and the Project 

Environmental Commitment and Monitoring Plan. 

This report is intended to meet the requirement to provide the “...firm 

recommendation for mitigation due to the effects [of non-Project structures 

potentially compounded or alleviated by Project operations] on native fishes...” 

(Reclamation 2000 and 2004). Reclamation could not effectively meet the

original date suggested to provide this recommendation report “...no later than 

2005...” but does meet the FSEIS intent of providing the recommendations “...at 

least two years prior to project pumping from the Animas River.”

Background 

In consultation with the Fish and Wildlife Service, Reclamation acknowledged 

the difficulty in quantifying the long-term effects to native fish populations

resulting from the Animas-La Plata Project’s depletion and/or operation. This 

conclusion was based on the following facts: 

1. The flow depletions resulting from the Animas-La Plata Project are 

relatively small in relation to other [non-Project] pre-existing depletions. 

2. Very little is known of the relationship between fish habitat and flow 

levels in the Animas River. 

3. The Animas-La Plata Project will actually enhance flows above historic 

rates in the river when releases are made from Ridges Basin Dam to 

provide Project water to downstream users. 

4. Concerns exist regarding native sucker recruitment in the upper Animas 

River that might be related to fish migration barriers unrelated to the 

Project. 

Reclamation concluded that the greatest potential threats to the long-term 

conservation of the Animas River native fishery were pre-existing non-Project 

structures diverting water from the river. Reclamation further determined that not

enough specific information was available regarding these pre-existing diversions 

on the Animas River to determine if they were significant barriers to upstream

movement of adult native suckers or if the structures result in significant loss of

1 
Fish Passage and Canal Entrainment Evaluation 

small/young-of-the-year (YOY) fish from entrainment into canals as stated in 

Reclamation (2000 and 2004): 

“The potential impact [of the Animas-La Plata Project] to native fishes in the 

Animas River, especially the effects of chronic habitat reduction, may not be 

directly mitigatable1

 on the Animas River. Investigations should be initiated to 

determine whether or not fish barriers exist, whether small fish/young-of-the-year 

fish are significantly lost through entrainment in [non-Project] canals.... A firm 

recommendation for mitigation due to the effects [of non-Project structures 

potentially compounded by Project operations] on native fishes will be made by 

no later than 2005, at least two years prior to project pumping from the Animas 

River. Once this mitigation recommendation is approved and agreed to by the

Service, CDOW [Colorado Division of Wildlife], New Mexico Department of

Game and Fish (NMDGF), and perhaps the Southern Ute Indian Tribe (SUIT), its 

implementation will immediately begin.” 

Therefore, as an environmental commitment for unspecified potential impacts of 

Project operations on the native fishery of the Animas River, Reclamation 

committed to perform investigations to determine “whether or not fish barriers 

[on the Animas River] exist, whether small fish/young-of-the-year fish are 

significantly lost through entrainment in canals...”. Subsequently, a study 

proposal was prepared and a Cooperative Agreement modification was 

implemented with the SUIT via their Division of Wildlife (SUDW) under Public 

Law 92-638 to perform the needed aquatic resource studies. 

The two man-made structures identified in the study design as having the greatest 

potential to be barriers for native fish movement on the Animas River were the 

City of Farmington’s Animas Pump Station #2 (APS, Figures 1 and 2, below) and 

the Farmer’s Ditch Diversion (FDD, Figures 1 and 3, below). 

The APS is located at river mile (RM) 11.9 (as measured from the confluence 

with the San Juan River) and has been operating since 1986 (personal 

communication, S. Williams 2007). The FDD is located at RM 21.9 and has been

operating since 1892 (personal communication, R. Genauldi 2007), but not 

always in its current concrete configuration. 

The FDD also has great potential to cause significant loss of YOY fish through 

entrainment in its delivery canal. Reclamation performed additional sampling and 

analysis relative to YOY native fish in an effort to determine potential long-term 

effects of the diversions on the native fishery of the Animas River. 

 

 

1

 Spelling error. The intended word for this sentence was mitigable, the adjective form of 

mitigate, meaning able to be mitigated. 

2 
Fish Passage and Canal Entrainment Evaluation 

Figure 1: Map of Studied Diversions. 

3 
Fish Passage and Canal Entrainment Evaluation 

Figure 2: City of Farmington’s Animas Pump Station #2 (APS) with open gates. 

Figure 3: Farmer’s Ditch Diversion (FDD) at relatively low flow conditions. 

4 
Fish Passage and Canal Entrainment Evaluation 

Figures 4 and 5 below show examples of important Animas River native fish, the 

flannelmouth (Catostomus latipinnis or FMS) and bluehead suckers (C. 

discobolus discobolus or BHS) specifically evaluated in this study. 

Figure 4: Flannelmouth Sucker (FMS).

Figure 5: Bluehead Sucker (BHS).

The local importance of these native fish has changed since 112 km (69.6 miles) 

of the San Juan River were targeted for non-game fish eradication (Olson 1962 in

Ptacek 2005). Recent evidence suggests that BHS populations are in decline 

throughout its historic range and are now found in less than half of its historic 

range. (Wheeler 1997, Bezzerides and Bestgen 2002 and Weitzel 2002 in Ptacek 

et al. 2005). FMS do remain widely distributed in the San Juan River drainage 

(Holden and Stalnaker 1975 in Rees et al. 2005). However, in many areas of the

upper Colorado River basin, FMS populations are thought to be decreasing (Sigler 

and Sigler 1996 in Rees et al. 2005). 

Rees et al. (2005) and Ptacek et al. (2005) identify fish passage barriers 

(specifically including diversion dams) as one of the primary threats to FMS and 

BHS. Blockage of spawning migrations has been identified as contributing to 

possible recruitment declines in FMS in the Colorado River (Chart and Bergersen 

1992 and McKinney et al. 1999 in Paukert and Rogers 2004). 

The BHS and FMS are considered a sensitive species by the US Forest Service 

(Ptacek et al. 2005 and Rees et al. 2005) but currently have no other federal 

protection status. The BHS and FMS are ‘Species of Concern’ and of ‘Special

5 
Fish Passage and Canal Entrainment Evaluation 

Concern’ in Utah and Wyoming respectively. The FMS are also of ‘Special 

Concern’ in Colorado (UDWR 2004). BHS are listed as being of possible 

concern in the Navajo Nation Endangered Species List (NNDFWL 2001). 

The Range-Wide Conservation Agreement for Roundtail Chub Gila robusta, 

Bluehead Sucker Catostomus discobolus, and Flannelmouth Sucker Catostomus 

latipinnis (RWCA), has the goal of “...ensur[ing] the persistence of roundtail 

chub, bluehead sucker, and flannelmouth sucker populations throughout their 

ranges”. The RWCA has been signed by the state wildlife management agencies

of Arizona, Colorado, Nevada, New Mexico, Utah and Wyoming (UDWR 2004). 

This study and its associated recommendations may support the efforts of the 

RWCA’s Coordination Team to achieve its conservation objectives on the 

Animas River. 

6 
Fish Passage and Canal Entrainment Evaluation 

Methods

Fish Barriers 

Reclamation hypothesized that the APS and FDD diversion dams were partial or 

full barriers to juvenile and adult FMS and BHS attempting to migrate upstream. 

Figure 6 depicts SUDW and Reclamation staff surveying at the APS using a barge 

to carry the electrofishing apparatus.

Figure 6: Electrofishing at the Animas Pump Station #2. 

In order to evaluate whether or not these diversions were significantly inhibiting 

upstream movement (migration) of native suckers, a multi-year study was

initiated in 2001. The main tasks of the study were to capture and uniquely mark 

adult FMS and BHS below the two diversion dams (APS and FDD) suspected to 

be barriers to native fish migration via electrofishing and FLOY-tagging 

techniques (Figure 7, below) and to conduct subsequent surveys upstream of the

dams to examine any movement of marked fish past the structures. 

Further, electrofishing surveys were conducted immediately below each diversion

dam to determine the presence or absence of juvenile native suckers, as well as to

collect additional data on species composition, relative abundance and metrics. 

7 
Fish Passage and Canal Entrainment Evaluation 

Figure 7: FLOY-tagging a native sucker. 

Sampling 

Sampling was conducted with a Smith-Root 5.0 Gas Powered Pulsator 

electrofisher mounted on either a barge or raft. Sampling was conducted from 

near the Colorado/New Mexico state line downstream to the confluence of the 

Animas and San Juan Rivers. The electrofisher and the anodes generated a pulsed 

220-volt DC electrical field of approximately 5 amps in order to temporarily stun 

the fish. All stunned fish were netted and then placed in a live well. 

Recording

Upon completion of each sampling effort, fish collected were processed and total 

electrofishing time (effort) was recorded. Global Positioning System (GPS) 

readings were taken at each sampling site to record locations. All captured fish

were identified to species, measured for total length, checked for visible 

abnormalities and sometimes weighed. All large native suckers (>150 mm Total 

Length) were checked for the presence of FLOY anchor tags. All native suckers

greater than 150 mm with no FLOY-tag present were tagged with a uniquely 

coded FLOY-tag. All tag numbers for recaptured or newly marked fish were 

recorded. 

8 
Fish Passage and Canal Entrainment Evaluation 

Analysis 

After the data collection and an initial analysis in conjunction with the SUWD, 

Reclamation contracted with SWCA Environmental Consultants (SWCA) in 2006 

to perform a more refined analysis of the mark-recapture data to better define 

implications for adult native sucker movement past the diversions. SWCA 

identified reference reaches on the Animas River and examined data collected in

three study reaches (below APS, between APS and FDD and above FDD) against 

the reference reaches. SWCA performed the statistical analysis of the recapture 

data and net movement per year. 

SUWD also provided detailed analysis of fishery composition, length-frequency 

data and the relative occurrence of juvenile native fish above and below the 

diversion structures. 

Fish Entrainment in Canals 

To document small/YOY fish occurrence in the Animas River, sampling using a

small-mesh beach seine was conducted at multiple locations in Colorado and New

Mexico (Figure 8) in 2001. 

Figure 8: Seine-netting YOY fish. 

9 
Fish Passage and Canal Entrainment Evaluation 

Sampling 

Habitats selected for YOY sampling were generally low-flow side channel or 

backwater habitats along the Animas River. Sampling involved a single “sweep” 

of a beach seine through all or most of a given patch of habitat in order to

maximize capture rates of YOY fish. The beach seine was 1/8-inch nylon mesh, 

25 feet long, 7 feet high and included a bag, weight line and float line. Samples

of YOY fish from each seine haul (Figure 9) were preserved in 10% formalin 

solution and excess fish were returned to the river. Sampling occurred in August

of 2001. 

Recording

For each collection sample, a sample number was assigned, locations were 

recorded with a GPS unit, and notes were taken on various site characteristics. 

Samples were returned to a laboratory and fish were identified to species, 

counted, and measured for total length. 

Figure 9: A sample of YOY fish collected. 

Analysis 

Reclamation consulted with local fisheries biologists and known experts in the 

field to determine the general efficacy of directly studying the issue of small/YOY 

fish entrainment in canals from the Animas River and the possible implications of

such entrainment on the long-term conservation of native suckers. SUWD worked 

with Reclamation to describe YOY fish samples taken from Colorado and from 

10 
Fish Passage and Canal Entrainment Evaluation 

New Mexico in terms of species composition and the relative abundance per 

species. 

Reclamation also hired SWCA to perform a literature review and analysis of

options available for YOY sucker canal entrainment management in the Animas 

River. 

11 
Fish Passage and Canal Entrainment Evaluation 

Results 

General Results 

Species Encountered 

Table 1 lists the fish species collected from the Animas River from 2001 through 

2005 during this study. Of note, most of the green sunfish (Lepomis cyanellus) 

and smallmouth (Micropterus dolomieu) and largemouth bass (M. salmoides) 

collected were found immediately below the two diversion dams being evaluated. 

Table 1: Fish species captured during sampling of the Animas River. 

Common Name Species Name Native? 

Bluehead Sucker Catostomus discobolus discobolus Yes 

Flannelmouth Sucker Catostomus latipinnis Yes 

Bluhead / Flannelmouth hybrid Catostomus d. discobolus X latipinnis Yes 

White Sucker Catostomus commersoni No 

Flannelmouth / White Sucker hybrid Catostomus d. discobolus X commersoni No 

Bluhead / White Sucker hybrid Catostomus latipinnis X commersoni No 

Speckled Dace Rhynichtys osculus Yes 

Mottled Sculpin Cottus bairdi Yes 

Common Carp Cyprinus carpio No 

Brown Trout Salmo trutta No 

Rainbow Trout Onchorhynchus mykiss No 

Cutthroat Trout Onchorhynchus clarki No 

Smallmouth bass Micropterus dolomieu No 

Largemouth Bass Micropterus salmoides No 

Green sunfish Lepomis cyanellus No 

Fathead Minnow Pimephales promelas No 

Channel catfish Ictalurus punctatus No 

Black Bullhead Ictalurus melas No 

Fish Barriers 

Recapture Rate 

Recapture rates were relatively low for both native sucker species (12.3% for 

FMS and 2.1% for BHS) but comparable to other mark recapture studies of FMS 

(Chart and Bergersen 1992 and McKinney et al. 1999 in SWCA 2007). 

12 
Fish Passage and Canal Entrainment Evaluation 

In total, 3,369 FMS and 836 BHS were FLOY-tagged in the lower Animas River. 

Of the 4,205 total suckers tagged, 398 were subsequently recaptured during the 

five year study period (most in 2004 and 2005). Of the recaptured suckers, two 

were recaptured three times, thirty were recaptured two times and 366 were 

recaptured only once. In the lower section below the APS (RM 0.0-11.9), 322 

BHS and 1,144 FMS were tagged and/or subsequently recaptured. In the middle 

section between the two diversions (RM 12.0-21.9), 322 BHS and 2,290 FMS 

were tagged and/or later recaptured. In the upper section upstream of FDD 

(RM21.9-36.0) 655 BHS and 1,550 FMS were tagged and/or later recaptured 

(Table 2). 

Table 2: Total FLOY tagged native sucker marks and recaptures. 

Year FMS Tagged BHS Tagged FMS over 

APS 

BHS over

APS 

FMS over

FDD 

BHS over 

FDD 

2001 239 319 0 0 0 0

2002 122 59 0 1 0 0

2003 1,264 131 0 0 0 0

2004 2,105 705 31 0 5 1

2005 754 193 26 2 5 0

Total 3,369 836 57 3 10 1

The APS had the highest number of tagged suckers moving upstream of it. A 

total of sixty FLOY-tagged native suckers that were originally tagged downstream 

of the APS were subsequently recaptured above it, all but one in either 2004 or 

2005. Fifty-seven FMS and three BHS managed to move upstream of this 

diversion. The FDD had only ten FMS and one BHS tagged below it 

subsequently recaptured above it. 

Length/Frequency

Figures 10 and 11 (below) illustrate the length/frequency distributions for FMS 

and BHS sampled and recaptured. Observations in the field by various agency

biologists led to general agreement that one or both of these diversions might be

limiting recruitment of native suckers to the section of the Animas River above 

these two diversions (personal communication, M. Wethington, S. Whiteman and 

R. Valdez, 1999). 

The populations of both of these species shows a much higher percentage of 

juvenile native suckers in the lower Animas River downstream of the APS and 

FDD indicating that smaller-bodied fishes might not be able to gain access to the 

upper reaches of the Animas River (Figures 12 and 13, below) (Zimmerman 

2004). 

13 
Fish Passage and Canal Entrainment Evaluation 

Figure 10: Length frequencies of BHS tagged and recaptured by river section 

(SWCA 2007). 

Bottom Section

0

10

20

30

40

50

60

70

100140180220260300340380420460500540580620660700740780

More

Total Length (mm)

Number of Fish

Tagged

Recaptured

Middle Section

0

20

40

60

80

100

120

100140180220260300340380420460500540580620660700740780

More

Total Length (mm)

Number of Fish

Tagged

Recaptured

Top Section

0

20

40

60

80

100

120

140

160

180

200

100140180220260300340380420460500540580620660700740780

More

Total Length (mm)

Number of Fish

Tagged

Recaptured

14 
Fish Passage and Canal Entrainment Evaluation 

Figure 11: Length frequencies of FMS tagged and recaptured by river section 

(SWCA 2007). 

Bottom Section

0

50

100

150

200

250

100140180220260300340380420460500540580620660700740780

More

Total Length (mm)

Number of Fish

Tagged

Recaptured

Middle Section

0

50

100

150

200

250

300

350

400

450

100140180220260300340380420460500540580620660700740780

More

Total Length (mm)

Number of Fish

Tagged

Recaptured

Top Section

0

50

100

150

200

250

300

100140180220260300340380420460500540580620660700740780

More

Total Length (mm)

Number of Fish

Tagged

Recaptured

15 
Fish Passage and Canal Entrainment Evaluation 

Figure 12: Length frequencies of FMS captured between River Miles 6.0 through 

0.0, 2004 (n=427), below both diversions (Zimmerman 2004). 

FMS 2004 < rm 6.0) n=427 

0%

5%

10%

Size Class (mm TL)

Frequency (

% of Sample)

Figure 13: Length frequencies of FMS captured between River Miles 37.0 

through 21.9, (n=881), above both diversions (Zimmerman 2004).

FMS (2004 >rm 21.9) n=881

0%

5%

10%

Size Class (mm TL)

Fr

equenc

y (% of S

a

m

ple) 

Comparing Figure 12 to Figure 13 clearly depicts the general lack of juveniles in

the FMS population above the two diversions. It is reasonable to assume that the 

diversion structures are the reason for this disparity in juvenile fish distribution. 

16 
Fish Passage and Canal Entrainment Evaluation 

Figure 14 describes the length-frequency relationship for BHS collected from the 

lower six miles of the Animas River below the diversions. This reach of river had

the highest percentage of juvenile BHS of any reach sampled in 2004. 

Figure 14: Length frequencies of BHS captured between River Miles 6.0 through 

0.0, (n=1,116), below both diversions. (Zimmerman 2004).

BHS (2004, < rm 6.0) n=1,116 

0%

5%

10%

15%

Size Clas s (m m TL)

Frequency (

% of Sample)

Comparing the data in Figure 14 to Figure 15 (below) suggests the same situation 

exists for BHS as for FMS relative to the effects of the diversions in preventing 

upstream migration of juvenile fish. 

17 
Fish Passage and Canal Entrainment Evaluation 

Figure 15: Length frequencies of BHS captured between River Miles 37.0 

through 21.9, (n=881), above both diversions. (Zimmerman 2004).

BHS (2004, > rm 21.9) n=567

0%

5%

10%

15%

Size Class (mm TL)

Fr

e

quenc

y (

% of Sam

ple)

Net Annual Movement 

The recapture sample size for BHS was too small for effective statistical analysis,

but recaptured FMS generally moved little distance and on average in a slight

downstream direction. No significant difference was found in the mean net 

distance moved per year by FMS in the middle and top sections (two-sample ttest, t183 = 0.491, p = 0.624) (Figure10 below, SWCA 2007). 

FMS moved significantly farther upstream on average in the bottom section when 

compared to the top section (two-sample t-test, t269 = 5.782, p<0.0001), but 

sampling bias that precludes sampling fish moving upstream out of the sampled 

area may affect this finding (SWCA 2007). The SUDW reports that other river 

sampling above the target reaches did not exclude native sucker data collection 

and that all such fish collected were reported and included in the dataset provided 

to SWCA for analysis, therefore the potential bias for upstream movement is 

negated (personal communication, S. Whiteman 2007). However, such a sampling 

exclusion bias may still exist for the bottom section where fish could move 

downstream out of the sampling area (SWCA 2007). 

18 
Fish Passage and Canal Entrainment Evaluation 

Figure 10: Histogram of net river miles moved per year by FMS tagged in the 

top, middle, and bottom sections by percentage. Percentages based on initial 

capture location (SWCA 2007).

0.00%

5.00%

10.00%

15.00%

20.00%

25.00%

30.00%

-20-18-16-14-12-10

-8-6-4-2

02468

101214161820

Miles traveled per year (negative numbers indicate downstream movement)

Percentage of fish recaptured

top

middle

bottom

FMS tagged in the bottom section moved a mean net distance of 2.8 miles per 

year farther upstream than those tagged in the middle section (two-sample t-test,

t221 = 5.117, p<0.0001). When only the upstream-moving fish were examined, 

FMS tagged in the bottom section (N = 79) moved a median net distance of 2.4 

miles per year farther upstream than those tagged in the middle section (N = 63) 

(Mann-Whitney U test, U = 3516.00, p<0.0001) (SWCA 2007). 

Upstream Movement 

Farmer’s Ditch Diversion 

Recaptured sucker numbers ascending FDD from the middle section were 

compared to the number of suckers that moved upstream of Reference Reaches 1 

and 2 in the top section (both 10 RM in length). A higher proportion of the 

recaptured fish moved upstream of Reference Reach 1 than Reference Reach 2 

(Table 3, below). The cause for this may be linked to habitat quality. 

Testing against Reference Reach 1 indicated that the FDD does pose a significant 

barrier to the upstream movement of FMS (chi-square test, df =1, χ2 = 13.285, 

p<0.001), blocking approximately 24% of the fish moving upstream from the

middle to the top section. Testing against Reference Reach 2 indicated that the 

FDD does not pose a significant barrier to the upstream movement of FMS (chisquare test, df =1, χ2 = 0.012, p>0.05) (SWCA 2007). 

19 
Fish Passage and Canal Entrainment Evaluation 

Table 3: Data used in chi-square analysis of FMS in the middle section and 

Reference Reach 2 (RM 24.9-34.9) in the top section (SWCA 2007).

Sections Compared Number that 

Stayed in Section 

Number that 

Moved Upstream 

of Section 

Totals 

Middle section, RM 11.9-21.9 

(observed) 71 6 77

Top section, RM 24.9-34.9 only

(expected) 44 4 48

Totals 115 10 125

Additional reference reaches would have been necessary to strengthen (or refute) 

a statistical determination that the FDD poses a significant barrier to upstream 

migration of adult FMS. However, one reach comparison indicating a significant 

barrier to fish passage is enough for Reclamation to formulate a recommendation. 

Animas Pump Station #2 

FMS numbers ascending APS from the bottom section were compared to the

number of suckers moving upstream of Reference Reach 3 and Reference Reach 4 

in the top section. Approximately 45% more recaptured FMS ascended APS from

the bottom section than had moved upstream of Reference Reach 3 (chi-square 

test, df =1, χ2 = 33.309, p<0.001) (Table 4) and approximately 48% more than 

Reference Reach 4 (chi-square test, df =1, χ2 = 26.706, p<0.001) (Table 5). 

Table 4: Data used in chi-square analysis of flannelmouth sucker in the middle 

section and Reference Reach 3 (RM 21.9-33.8) in the top section (SWCA 2007).

Sections Compared Number that 

Stayed in Section 

Number that 

Moved Upstream 

of Section 

Totals 

Bottom section, RM 0-11.9 

(observed) 55 65 120

Top section, RM 21.9-33.8 only

(expected) 52 5 57

Totals 107 70 177

Table 5: Data used in chi-square analysis of FMS in the middle section and 

Reference Reach 4 (RM 24.9-36.8) in the top section (SWCA 2007).

Sections Compared Number that 

Stayed in Section 

Number that 

Moved Upstream 

of Section 

Totals 

Bottom section, RM 0-11.9 

(observed) 55 65 120

Top section, RM 24.9-36.8 only

(expected) 34 2 36

Totals 89 67 156

20 
Fish Passage and Canal Entrainment Evaluation 

Both chi-square tests indicate that movement above APS was significantly greater 

than movement above the unconstrained reach in the top section, but movement

may be under-represented due to variability in the reference reaches. 

Farmer’s Ditch Diversion Compared to Animas Pump Station #2 

FMS numbers ascending the APS were compared to those ascending the FDD 

(chi-square test, df =1, χ2 = 43.760, p<0.001). Of the fish tagged in the bottom 

section and later recaptured, 54.2% had ascended the APS while 7.79% of FMS 

tagged in the middle section and later recaptured had ascended the FDD (Table 6). 

Table 6: Data used in chi-square analysis of FMS in the middle section and 

bottom section (SWCA 2007).

Sections Compared Number that 

Stayed in Section 

Number that 

Moved Upstream 

of Section 

Totals 

Bottom section, RM 0-11.9 

(observed) 55 65 120

Middle section, RM 11.9-21.9 

(expected) 71 6 77

Totals 126 71 197

Of the few BHS recaptured upstream of their original tagging location, 4 out of 5

ascended the APS from the lower section and only 1 out of 4 ascended the FDD 

from the middle section. While insufficient samples of BHS were available for

statistical analysis, the observations are in general agreement with the statistical 

findings for FMS. 

Downstream Movement 

Similar to the upstream movement analysis above, a greater proportion of FMS 

descended the APS than descended the FDD (chi-square test, df =1, χ2 = 4.268, 

p<0.05) (Table 7). This test indicates that the FDD may also inhibit downstream

movement of native suckers. BHS were insufficiently represented to conduct an 

analysis. 

Table 7: Data used in chi-square analysis of flannelmouth sucker in the middle 

section and Reference Reach 1 (RM 21.9-31.9) in the top section (SWCA 2007).

Sections Compared Number that 

Stayed in Section 

Number that 

Moved

Downstream of

Section 

Totals 

Middle section, RM 11.9-21.9 

(observed) 125 75 200

Top section, RM 21.9-31.9 only

(expected) 26 6 32

Totals 151 81 232

21 
Fish Passage and Canal Entrainment Evaluation 

Fish Entrainment in Canals 

Observations of sucker YOY in the Little Colorado River have shown that FMS 

and BHS YOY drifted an average of 5.3 miles while actively seeking nearshore 

areas (Robinson et al. 1998). The native sucker YOY congregate in shallow pools 

and backwater areas, as well as the shoreline areas of slow runs or pools (Haines 

and Tyus 1990 and Robinson et al. 1998 in SWCA 2007). The percentage of 

YOY suckers lost to entrainment would likely be greater when concentrated along 

the shoreline than if evenly distributed through the water column where YOY 

suckers lost would be proportional to the percentage of the flow diverted (SWCA 

2007). 

The Animas River was sampled for the presence of YOY native suckers from 

2000-2002 (personal communication, B. Zimmerman 2007). Data indicates that 

successful FMS and BHS reproduction in the upper Animas River was at very 

high levels (Zimmerman 2002, Tables 8 and 9). Sampling below the FDD and 

APS diversions indicates that much of the YOY that drift downstream of the

diversions survive to attempt a return to the upper reaches of the Animas River

(Figures 12 and 14 above). 

Table 8: Fish species composition and relative abundance results of overall 

Animas River YOY fish sampling (Zimmerman 2002).

Common Name Scientific Name Total Sample 

Size

Overall 

Relative 

Abundance 

Flannelmouth Sucker Catostomus latipinnis 8,681 89.7% 

Bluehead Sucker Catostomus discobolus discobolus 853 8.8% 

Mottled Sculpin Cottus bairdi 75 0.8% 

Speckled Dace Rhinichthys osculus 56 0.6% 

Fathead Minnow Pimephales promelas 4 0.0% 

Common Carp Cyprinus carpio 4 0.0% 

White Sucker Catostomus commersoni 1 0.0% 

Table 9: Fish species relative abundance comparison between Colorado and New 

Mexico YOY sampling (Zimmerman 2002).

Colorado

Relative 

Abundance 

New Mexico 

Relative 

Abundance 

Common Name Scientific Name 

N=6,918 N=2,755

Flannelmouth Sucker Catostomus latipinnis 87.9% 94.3%

Bluehead Sucker Catostomus discobolus discobolus 10.6% 4.4%

Mottled Sculpin Cottus bairdi 0.8% 0.7%

Speckled Dace Rhinichthys osculus 0.6% 0.5%

Fathead Minnow Pimephales promelas 0.0% 0.1%

Common Carp Cyprinus carpio 0.1% 0.0%

White Sucker Catostomus commersoni 0.0% 0.0%

22 
Fish Passage and Canal Entrainment Evaluation 

The Colorado Division of Wildlife (CDOW) has researched various types of 

screens to keep native fish out of irrigation canals and non-native fish out of 

reclaimed ponds. CDOW’s experience indicates that screens would not exclude 

fish larvae from canals. CDOW employed a 0.5 mm wedgewire screen and found 

it permeable to larval fish. The 0.5 mm screens effectively excluded larger fish 

and were self cleaning when installed at the proper angle, but were expensive 

(personal communication, A. Martinez, CDOW 2007 in SWCA 2007). Screens 

down to 0.1 mm are available on the market but would be more expensive and 

likely to become frequently obstructed (SWCA 2007). 

Similar projects to protect fisheries resources by planning, design, construction, 

and maintenance of a fish screen on the Santiam Water Control District canal (N.

Santiam River) in Stayton, Oregon have costs estimated at close to $400,000.00 

for just the fish screen portions of the project (CBFWA 2007). A similar project 

in the Yakima Basin, the Fogarty Fish Screen, had an ultimate cost of 

$560,000.00 (Hudson 2000). 

23 
Fish Passage and Canal Entrainment Evaluation 

Discussion 

Fish Barriers 

In order to assess native fish migration barriers in the Animas River, SUDW and 

Reclamation implanted 4,205 adult native suckers with uniquely numbered and 

colored FLOY tags in the lower Animas River below Bondad, Colorado (RM 

41.9) from 2001 through 2005. Recurring sampling of the Animas River in the 

lower portions revealed that neither the APS nor the FDD is a complete barrier to

upstream migration of adult native fish but the FDD is likely a significant barrier 

and is certainly a more significant barrier to fish migration up the Animas River 

than the APS. A conservative assumption would be that the FDD is a significant 

barrier to upstream fish migration as evidenced in the comparison to Reference 

Reach 1. The effect of the two diversions combined may form an even more 

significant barrier to fish movement in the Animas River. 

As the study could not feasibly identify when or at what flow native suckers

moved past the diversions, absolute conclusions cannot be made about whether or 

not upstream movement is seasonal or flow related, but it is reasonable to assume

that most, if not all, movement past the APS would be associated with the opening 

of a gate on the west side of the structure (Figure 3) due to the nature of its

construction, where the lower portion is a vertical wall rather than a ramped 

structure (personal communication, S. Whiteman and S. Williams 2007). The

FDD has no gates and, based on field observations, native suckers could only pass 

upstream of the FDD during periods of relatively high flow along the western 

edge of the structure where the top of the concrete structure is lower than the 

remainder (Figure 2). 

Since this study shows that sexually mature native suckers are capable of moving 

upstream of the APS, manually moving suckers from the bottom section to the 

middle section alone would be impractical, but moving suckers from the bottom 

and/or middle section to the top section could possibly improve the long-term 

conservation of the species as the FDD is apparently a significant barrier to

upstream fish movement (SWCA 2007). 

Before employing manual translocation as a mitigative species conservation tool 

on the Animas River, agencies should determine whether or not the sucker 

population above the FDD is currently sustainable. This may depend upon where

the native suckers spawn now and perhaps where they spawned prior to 

construction of the diversions. Spawning migration has not been conclusively 

documented for these species (Ptacek et al. 2005 and Rees et al. 2005 in SWCA

2007) and most studies have found the species to be relatively sedentary (Vanicek 

24 
Fish Passage and Canal Entrainment Evaluation 

1967, Holden and Crist 1981, Beyers et al. 2001, and Rees and Miller 2001 in

Ptacek 2005) but migrations and distance movements have been observed 

(Weitzel 2002, Vanicek 1967 and Holden and Crist 1981 in Ptacek 2005). 

Reclamation cannot assume that individuals in the bottom and middle sections 

would preferentially spawn in the top section. 

Further, it is unknown if the habitat in the top section is of adequate quality (or 

quantity) to support a larger native sucker population. If quality habitat is not 

readily available, translocated suckers may quickly return to previously

established home ranges downstream, and young suckers may emigrate from the 

reach (SWCA 2007). It is likely that as older classes of native suckers die out, 

habitats will be available for new occupancy for younger breeding fish. 

It is evident by the disparity of extant size classes between that found above 

versus below these Animas River diversions, that the possibility exists that

younger size classes may not be replacing the sexually mature sizes of native 

suckers in the upper Animas River (Figures 12 and 14, above) (personal 

communication, R. Valdez in Whiteman 1999). This could eventually lead to a 

sharp decline in the numbers of native suckers in the upper reaches of the Animas

River as the older fish decline in number due to age-related die-off. This sizeclass disparity strengthens the validity of physically translocating native fish to 

the upper reaches of the Animas River as a mitigative conservation measure. 

Fish Entrainment in Canals 

Due to the apparent impracticality and expense of fish screens to prevent native 

sucker YOY entrainment as well as the apparently strong reproduction occurring 

in the upper Animas River, Reclamation did not conduct a specific study to 

estimate entrainment losses, as a reasonable mitigative measure could not be 

recommended to exclude entrainment. 

The proportion of native sucker larvae produced in the top section that are 

retained in suitable nursery habitats before reaching FDD is unknown. FMS

YOY drift with the current for a period after hatching (Rees et al. 2005). Carter et 

al. (1986) and Robinson et al. (1998) indicate that YOY can and do actively 

choose to enter or escape the downstream drift from nursery habitats. Drift may 

serve as a mechanism to facilitate population dispersal and to locate suitable 

larval nursery habitat (Rees et al. 2005). 

YOY suckers not retained in nursery habitats in the upper Animas River may drift 

downstream of the diversions or may be entrained in canals or at pump stations.

Some may find suitable nursery habitat in lower sections or in canals and survive, 

but their repopulation of the upper section would be inhibited. If the YOY 

retention rates in the upper section are very low, the translocation of additional 

breeding-age fish to the top section may not significantly improve recruitment in 

the top section (SWCA 2007). 

25 
Fish Passage and Canal Entrainment Evaluation 

Chart and Bergersen (1992 in Rees et al. 2005) indicate that long-distance 

seasonal migration might be essential to the life history of FMS. Bezzerides and 

Bestgen (2002 in Rees et al. 2005) also indicate that periodic long-distance 

migration would be necessary to maintain relatively isolated populations that 

occur in smaller tributaries at higher elevations (perhaps such as the population in 

the upper Animas River). Rees et al. (2005) follow this discussion with the 

conclusion that upstream movement of juveniles and adults would be required to 

offset downstream drift of YOY fish. 

The results of YOY sampling indicate that there is enough native YOY sucker 

recruitment in the reaches above the APS and FDD in Colorado to reasonably 

assume that reproduction rate is not currently a limiting factor for these species in

the Animas River. If canal entrainment proves to be a minor issue in the overall 

conservation of the species due to high retention of larval suckers in the upper 

reaches of the Animas River, losses to entrainment or drift may not have 

significant bearing on the long-term viability of the Animas River populations of 

FMS and BHS. However, the length-frequency data presented above indicate that 

native YOY suckers may not be retained in sufficient numbers to maintain the

populations over the long-term.

If a significant portion of YOY native suckers drift downstream of the diversions 

(as evidenced by the general lack of smaller size classes above the diversions and

the high density of small size classes encountered below the diversion structures) 

juvenile translocation should be considered along with sexually mature adults as

described above. These fish may be able to re-colonize the upper reaches of the

Animas River once they reach larger sizes, but such inhibited upstream movement 

might not be sufficient for the maintenance of a viable long-term population 

without manual translocation. 

Mitigative conservation efforts for native YOY suckers might benefit from 

improving retention of YOY suckers in existing or new nursery habitats upstream

of the diversions once YOY retention rates are known and if such rates indicate a 

limiting factor for the species. River management to increase the availability of 

nursery habitats may improve the survival and recruitment of young native 

suckers (SWCA 2007). However, habitat management and manipulation is costly 

and difficult and often cannot guarantee results, only estimate or provide 

reasonable guesses as to the ultimate population effects. 

Additional approaches for native sucker YOY management could include 

installation of partial canal screening or other instream structures capable of 

deflecting a portion of the drifting YOY that would normally become entrained in 

canals, acknowledging that not all could be screened, but perhaps enough to make

a significant change in overall YOY sucker survivorship should YOY 

survivorship become identified as a limiting factor for native suckers in the

Animas River system by future studies. 

26 
Fish Passage and Canal Entrainment Evaluation 

Lastly, population dynamics data should continue to be collected on the Animas 

River sucker populations as overall population, fecundity, survival, and growth 

are not well understood for these species in this system. A population viability

analysis might substantially support more comprehensive native fish conservation 

planning in the Animas River. 

27 
Fish Passage and Canal Entrainment Evaluation 

Recommendations 

Reclamation’s fish passage evaluation demonstrates that neither Animas River

diversion structure studied is a complete barrier to upstream movement of adult 

native suckers but FDD appears to be a significant barrier for the movement of 

native suckers. 

Further, the YOY evaluation indicates that reproduction may not be limiting the 

native sucker populations in the upper Animas River, but the disparity of size 

classes recorded indicates that the diversions may prohibit the re-entry of younger 

classes of native suckers back into the reaches above the APS and FDD. 

Based on an analysis of the results of the native sucker mark-recapture data, the 

YOY entrainment discussion provided above and the length-frequency data 

comparing above- to below-barrier sites, Reclamation recommends the following 

actions as mitigative conservation measures for native suckers in the Animas 

River for impacts resulting from the existence and operation of the FDD and APS 

which could potentially be compounded or alleviated by the operation of the ALP

Project. 

Fish Barriers 

Animas Pump Station #2 

The APS does not appear to be a year-round significant barrier to upstream 

movement of native suckers. However, the APS may only be passable when one

of its gates is open. This happens in the winter or during high runoff flows

(personal communication, P. Montoya, 2007). Reclamation therefore 

recommends that the City of Farmington (APS’s owner and operator) be 

contacted to attempt coordination of gate operations to allow greater native fish

access to upstream sections of the river without negatively impacting pump 

station operations, particularly targeting native fish migratory seasons where 

feasible. 

Farmer’s Ditch Diversion 

As the FDD is an apparently significant barrier to native sucker movement, 

Reclamation recommends that native suckers be manually collected in both adult 

and juvenile size classes immediately downstream of the FDD (and perhaps the 

APS) and transported at least two miles upstream of the FDD. Such a collection

should be conducted at least twice per calendar year when river conditions are 

suitable for safe collection of fish, such as in the fall and late winter. 

28 
Fish Passage and Canal Entrainment Evaluation 

If this recommendation is implemented, the most effective techniques known for

collection are barge or bank electrofishing similar to what is depicted in Figure 6 

above. Reclamation does not know if the number of suckers that could be

collected would be sufficient to support a stable population of native suckers in 

the upper reaches of the Animas River. Reclamation cannot claim with absolute 

certainty that the current population would actually benefit from such 

translocation at this time, but indications are that the populations would, at some

time, benefit from this action. 

If implemented, extreme care should be taken to avoid the translocation of nonnative predatory fish (bass or sunfish in particular) into the upper reaches of the 

Animas River as the FDD and APS structures also appear to be barriers to the 

upstream movement of non-native fish. 

Fish Entrainment in Canals 

As our evidence suggests that native sucker reproduction is not currently a 

limiting factor for the conservation of either the BHS or the FMS in the upper

Animas River and that the prevention of YOY entrainment in canals would be at 

best moderately effective and very costly, Reclamation does not recommend the 

management of YOY sucker entrainment in canals as a mitigative conservation 

measure for the species. 

As a significant portion of YOY apparently drift downstream through the 

diversions and later cannot return upstream through the diversions, juvenile native 

suckers should be included in translocations upstream of the diversions as 

described above. 

Other Considerations 

It is recognized that this report’s investigations and resulting recommendations 

are based on the best data available as acquired in the four-year study period. 

Reclamation offers the following as other points to be considered in determining

if the above recommendations should be implemented. 

Population Viability Analysis 

Additional collection of population, fecundity, survival, and growth data for these 

species in the Animas River system should be conducted so that a population 

viability analysis (PVA) could be completed to better identify threats and to 

evaluate the likelihood that the species would persist into the future. The results of

a PVA would better determine if any actual benefit would be derived from native 

fish translocation in the Animas River. 

29 
Fish Passage and Canal Entrainment Evaluation 

Conservation Planning and Implementation 

The Range-Wide Conservation Agreement for Roundtail Chub Gila robusta, 

Bluehead Sucker Catostomus discobolus, and Flannelmouth Sucker Catostomus 

latipinnis (RWCA) is the current large-scale inter-agency conservation effort

supporting FMS and BHS. The RWCA Coordination Team could develop 

partnerships for the implementation of the recommendations in this report and in

the formulation of future long-term conservation planning or other 

recommendations based in part upon this evaluation. 

Other Reclamation Commitments 

While this report and its recommendations constitute completion of certain

environmental commitments for unspecified potential impacts of the ALP Project 

to the Animas River fishery, Reclamation has further related commitments: 

“Monitoring studies of project-affected waters on the Animas River will be 

implemented both prior to and continuing for at least four years after project

operations begin (project pumping). These studies will be designed to better 

define the native fishery, to include better understanding apparent problems with 

native sucker recruitment, and to monitor trout populations. If it is concluded that 

the operation of the project is having significant adverse impacts to the 

downstream aquatic ecosystem, Reclamation will make every reasonable effort to 

modify project operations to either reduce or eliminate these impacts.”

(Reclamation 2000 and 2004).

Reclamation is currently monitoring ALP Project affected waters of the Animas 

River by fish mark-recapture / relative abundance surveys which will include at

least four consecutive years of post-operational monitoring. This monitoring will 

serve to better define the native fishery and to monitor trout populations. 

Reclamation is developing the study design to examine potential impacts of 

Project operations to the downstream ecosystem. The intended focus is to 

examine the Projects’ potential to affect YOY retention in upper Animas River 

native fish nursery habitats which will also serve to provide a better understanding 

of the apparent problems with native sucker recruitment. 

Reclamation will share the results of these studies with the RWCA members, the 

Fish and Wildlife Service and other affected or interested agencies in support of 

native sucker conservation efforts. 

30 
Fish Passage and Canal Entrainment Evaluation 

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Fish Passage and Canal Entrainment Evaluation 

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33