Final Report 

Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico 

and Utah 

William J. Miller and Jonathan A. Ptacek 

Miller Ecological Consultants, Inc. 

Fort Collins, Colorado 

January 31, 2000 

MILLER ECOLOGICAL 

CONSULTANTS, INC. 
Final Report 

Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico 

and Utah 

William J. Miller and Jonathan A. Ptacek 

Miller Ecological Consultants, Inc. 

Fort Collins, Colorado 

January 31, 2000 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page i 

Miller Ecological Consultants, Inc. January 31, 2000 

EXECUTIVE SUMMARY 

Historically, the Colorado pikeminnow, Ptychocheilus lucius, occurred in the mainstem 

Colorado River and its tributaries from Wyoming to the Gulf of California. The San Juan 

River in New Mexico and Utah contains a small population of Colorado pikeminnow. 

The Colorado pikeminnow was listed as a federally endangered species in 1967 (32 

Federal Register 4001) and is protected under the provisions of the Endangered Species 

Act of 1973 (39 Federal Register 1175). 

In 1991, The U.S. Fish and Wildlife Service released a Biological Opinion which 

required seven years of research to be conducted on the San Juan River and it's 

tributaries. One element of the San Juan River Seven-Year Research Program was to 

determine habitat requirements of the endangered species found in the San Juan River. 

The habitat utilization data will be used to fulfill the long range plan objective 5.2, 

specifically 5.2.5 and 5.2.6 (San Juan River Recovery Implementation Program Biology 

Committee 1995). The objective of this study was to describe habitat use by adult 

Colorado pikeminnow during summer months in the San Juan River. 

This study determined Colorado pikeminnow habitat use during the summer in the San 

Juan River, New Mexico and Utah. Although the study area included the entire San Juan 

River, radio implanted Colorado pikeminnow were only contacted in Reaches 3,4 and 5 

for study years 1993 and 1994 and Reaches 5 and 6 for study year 1998. The most 

downstream contact occurred in 1994 near Bluff, Utah (RM 73.8). The farthest upstream 

contact was near Farmington, New Mexico (RM 178.8). 

Radio implanted fish were intensively tracked to determine both the location within a 

reach of river and the habitat use by those fish. Radio telemetry was conducted on seven 

wild adult Colorado pikeminnow that were opportunistically implanted in the spring of 

1993 (4 fish) and 1994 (3 fish) with radio transmitters by U.S. Fish and Wildlife Service 

(Grand Junction, CO) personnel. Seven hatchery-reared Colorado pikeminnow were 

intensively followed during the summer of 1998. 

Any locations where the fish remained for more than 30 minutes were recorded, and if 

possible, habitat parameters were measured. Data on habitat characteristics near the fish 

location were acquired by habitat mapping on aerial videography plates and digitizing the 

habitat maps. Habitat maps were created for each separate fish location during the 

observation day. 

Habitat usage data included a sketch of the habitat surrounding the fish locations and 

included fish positions marked on the map. Data collected at the fish location included 

date, time of day, weather conditions, time monitored, and any notes on movement 

during the observation period. When possible, other physical habitat data was collected 

at each fish location. These measurements included water depth, water velocity (mean 

column and bottom), substrate type, proximity to cover, description of cover at the 

location, general description of the site; measurements of the habitat type including 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page ii 

Miller Ecological Consultants, Inc. January 31, 2000 

length, width, bank features, shoreline vegetation, dominant substrate and cover for the 

habitat type. Other parameters measured included water and ambient air temperature, 

conductivity, and pH. Discharge was obtained from the nearest USGS gaging station. 

Radio telemetry studies on Colorado pikeminnow provided seasonal habitat use, river 

reach use, and spawning behavior for San Juan River fish. These studies also identified 

possible spawning areas. The majority of wild Colorado pikeminnow contacts were 

between RM 120.0 and RM 142.0. Only one fish was located outside of this range. 

Ryden and Ahlm (1996) also found Colorado pikeminnow to be concentrated within this 

section of the San Juan River. Three of the stocked Colorado pikeminnow were also 

found in this area, although all three of the transmitters were eventually recovered. It is 

unknown whether the fish expelled the transmitters or died. Generally, stocked Colorado 

pikeminnow did not behave like the wild fish monitored in 1993 and 1994. Only the 

stocked Colorado pikeminnow 40.051 exhibited behaviors and habitat use similar to a 

wild fish. 

Habitat use during the suspected spawning period is concentrated in areas of very diverse 

habitats with numerous habitat types present. These areas are located in conjunction with 

complex bar and island systems that have many different habitat types in a small local 

area. Main features present at the suspected spawning areas include eddies or pools as 

resting habitat located in close proximity to chutes or steep riffles with very loose cobble 

substrate. 

Two (RM 131.1 and RM 132.0) potential spawning locations were identified for wild fish 

and one (RM 168.4) for stocked Colorado pikeminnow. One of those locations had a 

documented visual sighting of two paired Colorado pikeminnow, male and female, that 

were implanted with radio transmitters. The potential sites at RM 131.1 and RM 132.0 

were used during both 1993 and 1994 and were used in the same sequence each year. 

The uppermost site at RM 132.0 was used first followed by the RM 131.1 site. 

The use of various habitat types is related to the flow regime as well as life history traits 

of the Colorado pikeminnow. The pre-spawn time period is during the ascending limb of 

runoff, which floods local embayments, tributary mouths and secondary channels that 

provide Colorado pikeminnow staging habitat. During the descending limb of runoff, the 

habitat complexes for spawning become available, provided sufficient cleaning is done 

during the peak runoff. These habitats appear to be used for varying lengths of time 

depending on the suitability of velocities in chute/riffle habitats and the embeddedness of 

cobble substrate. 

Maintaining habitat richness is an important component of maintaining the potential 

spawning habitats for the fish. Highest habitat use during the spawning periods was in 

the area of highest habitat richness. Flows that develop and maintain complex habitats 

over the long term should provide the physical characteristics necessary to provide the 

spawning habitat. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page iii 

Miller Ecological Consultants, Inc. January 31, 2000 

Table of Contents 

EXECUTIVE SUMMARY ................................................................................................. i 

INTRODUCTION .............................................................................................................. 1 

METHODS ......................................................................................................................... 3 

Study Area ....................................................................................................................... 3 

Seven-Year Research Program..................................................................................... 3 

Colorado Pikeminnow Habitat Use Study ................................................................... 6 

Radio Telemetry .............................................................................................................. 6 

RESULTS ......................................................................................................................... 11 

1993 ............................................................................................................................... 11 

Pre-spawn................................................................................................................... 17 

Spawning.................................................................................................................... 19 

River Mile 132.0 ..................................................................................................... 21 

River Mile 131.1—Red Wash Side Channel .......................................................... 22 

Visual Sighting of Spawning Colorado Pikeminnow. ............................................ 24 

Post-spawn ................................................................................................................. 24 

1994 ............................................................................................................................... 26 

Winter......................................................................................................................... 28 

Pre-spawn................................................................................................................... 31 

Spawning.................................................................................................................... 36 

River Mile 132.0 ..................................................................................................... 37 

River Mile 131.1—Red Wash Side Channel .......................................................... 37 

Fall.............................................................................................................................. 39 

1993 and 1994 Combined.............................................................................................. 41 

Pre-spawn................................................................................................................... 41 

Spawning.................................................................................................................... 45 

1998 – Stocked Adult Colorado Pikeminnow ............................................................... 47 

Pre-spawn................................................................................................................... 51 

Spawning.................................................................................................................... 51 

River Mile 168.4—Hatch Trading Post.................................................................. 53 

DISCUSSION................................................................................................................... 57

CONCLUSIONS............................................................................................................... 60 

ACKNOWLEDGEMENTS.............................................................................................. 61 

LITERATURE CITED ..................................................................................................... 62 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page iv 

Miller Ecological Consultants, Inc. January 31, 2000 

List of Tables 

Table 1. San Juan River Colorado pikeminnow radio frequencies and capture or stock 

locations. ...................................................................................................................... 7 

Table 2. Habitat categories used during monitoring........................................................ 10 

Table 3. River mile locations for monitored Colorado pikeminnow, June – August 1993. 

Multiple contact times (24 hr) are in parentheses. ..................................................... 12 

Table 4. Distance (m) moved upstream or downstream by Colorado pikeminnow during 

daily monitoring in the San Juan River, June – August 1993.................................... 13 

Table 5. Distance (mi) moved between the first and last daily contact of monitored 

Colorado pikeminnow, June – August 1993. ............................................................. 14 

Table 6. Habitat richness values for Colorado pikeminnow locations during 1993, 1994, 

1993 and 1994 combined and 1998 on the San Juan River. ...................................... 16 

Table 7. Water temperatures (Co) for pikeminnow locations during the pre-spawn 1993 

and 1994 where main channel and side channel or tributary temperatures were 

concurrently taken...................................................................................................... 17 

Table 8. Microhabitat measurements for possible spawning activities. .......................... 22 

Table 9. River mile locations for monitored Colorado pikeminnow, Winter and Fall 

1994............................................................................................................................ 29 

Table 10. River mile locations for Colorado pikeminnow, May – July 1994. ................ 32 

Table 11. Distance (m) moved upstream or downstream by Colorado pikeminnow during 

daily monitoring in the San Juan River, July 1994. ................................................... 33 

Table 12. Distance (mi) moved between the first and last daily contact of monitored 

Colorado pikeminnow, July 1994. ............................................................................. 34 

Table 13. River mile locations for stocked Colorado pikeminnow, June – July 1998. 

Multiple contact times (24 hr) are in parentheses. ..................................................... 48 

List of Figures 

Figure 1. Study Area Map.................................................................................................. 8 

Figure 2. Habitat use as a percent of time monitored during the summer 1993.............. 15 

Figure 3. Habitat usage and habitat availability as a percent of total during the summer 

1993............................................................................................................................ 16 

Figure 4. Habitat use as a percent of time monitored during the pre-spawn period 1993.

.................................................................................................................................... 18 

Figure 5. Habitat usage and habitat availability as a percent of total during the pre-spawn 

period, 1993................................................................................................................ 19 

Figure 6. Habitat use as a percent of time monitored during the spawning period, 1993.

.................................................................................................................................... 20 

Figure 7. Habitat usage and habitat availability as a percent of total during the spawning 

period, 1993................................................................................................................ 21 

Figure 8. Suspected spawning location 1993................................................................... 23 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page v 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 9. Habitat use as a percent of time monitored during the post-spawn period 1993.

.................................................................................................................................... 25 

Figure 10. Habitat usage and habitat availability as a percent of total during the postspawn period, 1993. ................................................................................................... 26 

Figure 11. Habitat use as percent of time monitored during the summer 1994............... 27 

Figure 12. Habitat usage and habitat availability as a percent of total during the summer 

1994............................................................................................................................ 28 

Figure 13. Habitat use as percent of time monitored during the winter 1994. ................ 30 

Figure 14. Habitat use as a percent of time monitored during the pre-spawn period 1994.

.................................................................................................................................... 35 

Figure 15. Habitat usage and habitat availability as a percent of total during the prespawn period, 1994. ................................................................................................... 36 

Figure 16. Habitat use as percent of time monitored during the spawning period 1994. 38 

Figure 17. Habitat usage and habitat availability as a percent of total during the spawning 

period, 1994................................................................................................................ 39 

Figure 18. Suspected spawning location 1994................................................................. 40 

Figure 19. Habitat use as a percent of time monitored during the summers 1993 and 1994 

combined. ................................................................................................................... 42 

Figure 20. Habitat usage and habitat availability as a percent of total during the summers 

of 1993 and 1994........................................................................................................ 43 

Figure 21. Habitat use as a percent of time monitored during the pre-spawn periods 1993 

and 1994. .................................................................................................................... 44

Figure 22. Habitat usage and habitat availability as a percent of total during the prespawn period, 1993 and 1994..................................................................................... 45 

Figure 23. Habitat use as a percent of time monitored during the spawning period 1993 

and 1994. .................................................................................................................... 46

Figure 24. Habitat usage and habitat availability as a percent of total during the spawning 

period, 1993 and 1994................................................................................................ 47 

Figure 25. Habitat use as a percent of time monitored during the summer 1998............ 50 

Figure 26. Habitat usage and habitat availability as a percent of total during the summer 

1998............................................................................................................................ 51 

Figure 27. Habitat use as a percent of time monitored during the pre-spawn period 1998.

.................................................................................................................................... 52 

Figure 28. Habitat usage and habitat availability as a percent of total during the prespawn period, 1998. ................................................................................................... 53 

Figure 29. Habitat use as a percent of time monitored during the spawning period 1998.

.................................................................................................................................... 54 

Figure 30. Habitat usage and habitat availability as a percent of total during the spawning 

period, 1998................................................................................................................ 55 

Figure 31. Suspected spawning location 1998................................................................. 56 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 1 

Miller Ecological Consultants, Inc. January 31, 2000 

INTRODUCTION 

Historically, the Colorado pikeminnow, Ptychocheilus lucius, occurred in the mainstem 

Colorado River and its tributaries from Wyoming to the Gulf of California. The San Juan 

River in New Mexico and Utah contains a small population of Colorado pikeminnow. 

The Colorado pikeminnow was listed as a federally endangered species in 1967 (32 

Federal Register 4001) and is protected under the provisions of the Endangered Species 

Act of 1973 (39 Federal Register 1175). 

In 1991, The U.S. Fish and Wildlife Service released a Biological Opinion which 

required seven years of research to be conducted on the San Juan River and it's 

tributaries. One element of the San Juan River Seven-Year Research Program was to 

determine habitat requirements of the endangered species found in the San Juan River. 

The habitat utilization data will be used to fulfill the long range plan objective 5.2, 

specifically 5.2.5 and 5.2.6 (San Juan River Recovery Implementation Program Biology 

Committee 1995). The objective of this study was to describe habitat use by adult 

Colorado pikeminnow during summer months in the San Juan River. 

Researchers have been studying movement and habitat use of Colorado pikeminnow 

since the mid 1970s (Twedt and Holden 1980; Holden and Wick 1982; Wick et al. 1983, 

1986; Tyus and McAda 1984; Osmundson and Kaeding 1989). The focus of these 

previous research efforts has been either long range spawning migrations or intensive 

study of localized habitat use. Researchers have found that Colorado pikeminnow habitat 

use varies seasonally and by habitat availability (Holden and Wick 1982; Wick et al. 

1983; Tyus and McAda 1984; Osmundson et al. 1995). However, none of these previous 

studies were conducted on the San Juan River. 

During spring runoff, many native fish species (including Colorado pikeminnow) utilize 

backwater habitats as refuge from high flows (Wick et al. 1983, 1986; Tyus and McAda 

1984; Osmundson and Kaeding 1989; Tyus 1990). Water temperatures are higher in 

backwaters, providing better conditions for growth and gonad maturation (Wick et al. 1983, 

1986; Osmundson and Kaeding 1989; Tyus 1990). Osmundson and Kaeding (1989) 

observed a high use of backwaters by adult Colorado pikeminnow during spring and early 

summer in the upper Colorado River. They recorded temperatures in backwater areas up to 

10.5°C warmer than in the main channel. In the Green River subbasin, (Tyus 1990) 

reported high usage of backwater and flooded bottomlands in the Green and Yampa rivers. 

Colorado pikeminnow were most often found in to backwaters in low-water years and 

flooded bottomlands in high water years. Holden and Stalnaker (1975) found adult 

pikeminnow in all habitat types but mainly in slow velocity habitats (eddies, backwaters, 

and flooded canyon mouths). Tyus and McAda (1984) reported that adult Colorado 

pikeminnow predominately used shoreline habitats associated with sandy substrate. They 

also noted use of eddy, run, backwater, and pool habitats and silt, boulder, rubble, and 

gravel substrates. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 2 

Miller Ecological Consultants, Inc. January 31, 2000 

There were significant differences between rivers for water depths and velocities selected 

by the fish. In the '15 mile reach' of the Colorado River near Grand Junction, Colorado, run 

habitats were most often used by Colorado pikeminnow during the summer (Osmundson 

and Kaeding 1989; Osmundson et al. 1995). These researchers also noted that Colorado 

pikeminnow sought deep water when water clarity was high. Tyus and Karp (1989) 

reported that adult Colorado pikeminnow occupied a variety of habitats in mid-to-late 

summer, but were most common in eddies, pools, runs, and shoreline backwaters. Wick et 

al. (1983) noted a high use of runs during the summer and pool habitat during October and 

November on the Yampa River. However, Miller and Rees (1997) found that adult 

pikeminnow in the Yampa River used predominately pool habitat from late July through 

October. 

During the winter, Wick and Hawkins (1989) and Valdez and Masslich (1991) observed 

Colorado pikeminnow utilizing embayment, backwater, and run habitats in the Yampa and 

Green rivers. Valdez and Masslich (1991) noted that wintering pikeminnow were often 

associated with an instream cover element (e.g. sand shoals, sand ridges, cobble jetties, or 

ice jams). They reported that Colorado pikeminnow preferred areas of low velocity (0.0-

0.15 m/sec) and moderate depths (0.6-1.1 m) during wintertime monitoring. 

Wick et al. (1986) censused habitat types (pools, eddies, and backwaters) on the Yampa 

River during spring runoff and base flows. They reported a strong relationship between the 

quantity and quality of habitat and the number of pikeminnow captured during the daytime. 

Several studies have found pikeminnow to be more abundant in higher diversity habitats 

than in lower diversity habitats (Wick et al. 1986; Osmundson and Kaeding 1991). Wick et 

al. (1986) found at base flows, the strata with the highest amount of class 1 ( > 2 m 

maximum depth) pools and eddies (n=1.7, area = 5900 m2

 per mile) contained 51% (total n 

= 74) of the pikeminnow captured. The existing information on pikeminnow habitat use in 

the San Juan River includes habitat suitability criteria developed for the San Juan River 

from habitat use information from other rivers in the upper Colorado River basin (Twedt 

and Holden 1980). 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 3 

Miller Ecological Consultants, Inc. January 31, 2000 

METHODS 

Study Area 

Seven-Year Research Program 

The San Juan River is a major tributary of the Colorado River and drains 99,200 km2

 in 

Colorado, Utah, Arizona, and New Mexico (Figure 1). From its origins in the San Juan 

Mountains of southwestern Colorado at elevations exceeding 4,250 m, the river flows 

westward for about 570 km to the Colorado River. The major perennial tributaries to the 

San Juan River are the Navajo, Piedra, Los Pinos, Animas, La Plata, and Mancos rivers, 

and McElmo Creek. In addition there are numerous ephemeral arroyos and washes 

contributing little total flow but large sediment loads. 

Navajo Reservoir, completed in 1963, impounds the San Juan River, isolating the upper 

124 km of river and partially regulating downstream flows. The completion of Glenn 

Canyon Dam and subsequent filling of Lake Powell in the early 1980's inundated the 

lower 87 km of the river, leaving about 359 km of river between the two bounding 

features. 

From Navajo Dam to Lake Powell, the mean gradient of the San Juan River is 1.67 

m/km. Locally, the gradient can be as high as 3.5 m/km, but taken in 30 km increments, 

the range is from 1.24 to 2.41 m/km. Between the San Juan River mouth into Lake 

Powell and the confluence with Chinle Creek about 20 km downstream of Bluff, UT, the 

river is canyon bound and restricted to a singled channel. Upstream of Chinle Creek the 

river is multi-channeled to varying degrees with the highest density of secondary 

channels between the Hogback Diversion about 13 km east of Shiprock and Bluff, Utah. 

The reach of river between Navajo Dam and Farmington, NM is relatively stable with 

predominantly embedded cobble substrate and few secondary channels. Below the 

confluence with the Animas River, the channel is less stable and more subject to floods 

from the unregulated Animas River. Between Farmington and Shiprock cobble substrate 

still dominates, although it is less embedded. Between Shiprock and Bluff the cobble 

substrate becomes mixed with sand to an increasing degree with distance downstream, 

resulting in decreasing channel stability. 

Except in canyon-bound reaches, the river is bordered by nonnative salt cedar (Tamarix 

chinensis) and Russian olive (Eleagnus angustifolia) and native cottonwood (Populas 

fremonti) and willow (Salix sp.). Nonnative woody plants are most abundant with 

cottonwood and willow accounting for less than 15% of the riparian vegetation. 

Discharge of the San Juan River is typical of rivers in the American Southwest. The 

characteristic annual pattern is one of large flows during spring snowmelt, followed by 

low summer, autumn, and winter base flows. Base flows are frequently punctuated by 

convective storm-induced flow spikes during summer and early autumn. Prior to closure 

of Navajo Dam about 73% of the total annual discharge (based on USGS Bluff, Utah 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 4 

Miller Ecological Consultants, Inc. January 31, 2000 

gage) of the drainage occurred during spring runoff (1 March through 31 July). The 

median daily peak discharge during spring runoff was 10,400 cfs (range = 3,810 to 

33,800 cfs). Although flows resulting from summer and autumn storms contributed a 

comparatively small volume to total annual discharge in the basin, the magnitude of 

storm-induced flows exceeded the peak snowmelt discharge about 30% of the years, 

occasionally exceeding 40,000 cfs (mean daily discharge). Both magnitude and 

frequency of these storm induced flow spikes are greater than those seen in the Green or 

Colorado rivers. 

Closure of Navajo Dam altered the annual discharge pattern of the San Juan River. The 

natural flows of the Animas River ameliorated some aspects of regulated discharge by 

augmenting spring discharge. Regulation resulted in reduced magnitude and increased 

duration spring runoff in wet years and seriously reduced magnitude and duration spring 

flows during dry years. Overall, flow regulation by operation of Navajo Dam has 

resulted in post-dam peak spring discharge averaging about 54% of pre-dam values. 

After dam closure, base flows were increased substantially over pre-dam base flows. 

Since 1992, Navajo Dam has been operated to mimic a “natural” hydrograph with the 

volume of release during spring linked to the amount of precipitation during the 

preceding winter. Thus in years with high spring snowmelt, reservoir releases were 

“large” and “small” in low runoff years. Base flows since 1992 were typically greater 

than during pre-dam years but less than post-dam years. 

The primary study area for most studies conducted under the auspices of the San Juan 

River Seven-Year Research Program, including that reported herein, were accomplished 

in the mainstem San Juan River and its immediate vicinity between Navajo Dam and 

Lake Powell. Between Navajo Dam and Shiprock there is considerable human activity 

within the floodplain of the San Juan River. Irrigated agriculture is practiced throughout 

this portion of the valley and much of the immediate uplands. Much of the river valley 

not devoted to agriculture (crop production and grazing) consists of small communities 

(e.g. Blanco and Kirtland) and several larger towns (e.g. Bloomfield and Farmington). 

The valley of the Animas River, the San Juan's largest tributary in the study area, is 

similarly developed. Downstream of Shiprock to Bluff small portions of the river valley 

(and uplands) are farmed; dispersed livestock grazing is the primary land use. In the 

vicinity of Montezuma Creek and Aneth, petroleum extraction occurs within the 

floodplain and the adjacent uplands. Between Bluff and the confluence with Lake 

Powell, there are few human-caused modifications of the system. 

To enhance comparisons among studies and to provide a common reference for all 

research, a multivariate analysis of a variety of geomorphic features of the drainage was 

performed to segregate the river into distinct geomorphic reaches. This effort (Bliesner 

and Lamarra, 1999) identified eight reaches between Navajo Dam and Lake Powell. The 

following provides a brief characterization of each reach. 

Reach 1 (RM 0 to 16, Lake Powell confluence to near Slickhorn Canyon) has been 

heavily influenced by the fluctuating reservoir levels of Lake Powell and its backwater 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 5 

Miller Ecological Consultants, Inc. January 31, 2000 

effect. Fine sediment (sand and silt) has been deposited to a depth of about 12 m in the 

lowest end of the reach since the reservoir first filled in 1980. This deposition of 

suspended sediment into the delta-like environment of the river/reservoir transition has 

created the lowest-gradient reach in the river. This reach is canyon bound with an active 

sand bottom. Although there is an abundance of low velocity habitat at certain flows, it is 

highly ephemeral, being influenced by both river flow and the elevation of Lake Powell. 

Reach 2 (RM 17 to 67, near Slickhorn Canyon to confluence with Chinle Creek) is also 

canyon bound but is located above the influence of Lake Powell. The gradient in this 

reach is higher than in either adjacent reach and the fourth highest in the system. The 

channel is primarily bedrock confined and is influenced by debris fans at ephemeral 

tributary mouths. Riffle-type habitat dominates, and the major rapids in the San Juan 

River occur in this reach. Backwater abundance is low in this reach, occurring most in 

association with the debris fans 

Reach 3 (RM 68 to 105, Chinle Creek to Aneth, Utah) is characterized by higher 

sinuosity and lower gradient (second lowest) than the other reaches, a broad floodplain, 

multiple channels, high island count, and high percentage of sand substrate. This reach 

has the second highest density of backwater habitats after spring peak flows, but is 

extremely vulnerable to change during summer and autum storm events, after which this 

reach may have the second lowest density of backwaters. The active channel leaves 

debris piles deposited throughout following spring runoff, leading to the nickname 

“Debris Field”. 

Reach 4 (RM 107 to 130, Aneth, Utah, to below “the Mixer”) is a transitional reach 

between the upper cobble-dominated reaches and the lower sand-dominated reaches. 

Sinuosity is moderate compared with other reaches, as is gradient. Island area is higher 

than in Reach 3 but lower than in Reach 5, and the valley is narrower than in either 

adjacent reach. Backwater habitat abundance is low overall in this reach (third lowest 

among reaches) and there is little clean cobble. 

Reach 5 (RM 131 to 154, the "Mixer" to just below Hogback Diversion) is 

predominantly multi-channeled with the largest total wetted area (TWA) and largest 

secondary channel area of any of the reaches. Secondary channels tend to be longer and 

more stable than in Reach 3 but fewer in number overall. Riparian vegetation is more 

dense in this reach than in lower reaches but less dense than in upper reaches. Cobble 

and gravel are more common in channel banks than sand, and clean cobble areas are 

more abundant than in lower reaches. This is the lowermost reach containing a diversion 

dam (Cudei). Backwaters and spawning bars in this reach are much less subject to 

perturbation during summer and fall storm events than the lower reaches. 

Reach 6 (RM 155 to 180, below Hogback Diversion to confluence with the Animas 

River) is predominately a single channel, with 50% fewer secondary channels than 

Reaches 3, 4, or 5. Cobble and gravel substrates dominate, and cobble bars with clean 

interstitial space are more abundant in this reach than in any other. There are four 

diversion dams that may impede fish passage in this reach. Backwater habitat abundance 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 6 

Miller Ecological Consultants, Inc. January 31, 2000 

is low in this reach, with only Reach 2 having less. The channel has been altered by 

dike construction in several area to control lateral channel movement and over-bank flow. 

Reach 7 (RM 181 to 213, Animas River confluence to between Blanco and Archuleta, 

New Mexico) is similar to Reach 6 in terms of channel morphology. The river channel is 

very stable, consisting primarily of embedded cobble substrate as a result of controlled 

releases from Navajo Dam. In addition, much of the river bank has been stabilized 

and/or diked to control lateral movement of the channel and over-bank flow. Water 

temperature is influenced by the hypolimnetic release from Navajo Dam and is colder 

during the summer and warmer in the winter than the river below the Animas confluence. 

Reach 8 (RM 213 to 224, between Blanco and Archuleta and Navajo Dam) is the most 

directly influenced by Navajo Dam, which is situated at its uppermost end (RM 224). 

This reach is predominantly a single channel, with only four to eight secondary channels, 

depending on the flow. Cobble is the dominant substrate type, and because lateral 

channel movement is less confined in this reach, some loose, clean cobble sources are 

available from channel banks. In the upper end of the reach, just below Navajo Dam, the 

channel has been heavily modified by excavation of material used in dam construction In 

addition, the upper 10 km of this reach above Gubernador Canyon are essentially 

sediment free, resulting in the clearest water of any reach. Because of Navajo Dam, this 

area experiences much colder summer and warmer winter temperatures. These cool, 

clear water conditions have allowed development of an intensively managed blue-ribbon 

trout fishery to the exclusion of the native species in the uppermost portion of the reach. 

Colorado Pikeminnow Habitat Use Study 

This study determined Colorado pikeminnow habitat use during the summer in the San 

Juan River, New Mexico and Utah. Although the study area included the entire San Juan 

River, radio implanted Colorado pikeminnow were only contacted in Reaches 3,4 and 5 

for study years 1993 and 1994 and Reaches 5 and 6 for study year 1998. The most 

downstream contact occurred in 1994 near Bluff, Utah (RM 73.8). The farthest upstream 

contact was near Farmington, New Mexico (RM 178.8). This is the location where the 

stocked pikeminnow were released in September 1997. 

Radio Telemetry 

Radio implanted fish were intensively tracked to determine both the location within a 

reach of river and the habitat use by those fish. Seven wild adult Colorado pikeminnow 

were opportunistically implanted in the spring of 1993 (4 fish) and 1994 (3 fish) with 

radio transmitters by U.S. Fish and Wildlife Service (Grand Junction, CO) personnel 

(Table 1). On 23 September 1997, 15 hatchery-reared Colorado pikeminnow were 

implanted with radio tags and released (Table 1). Seven of the fifteen stocked fish were 

located during the summer of 1998. The remaining eight radio tags were either recovered 

or presumed lost. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 7 

Miller Ecological Consultants, Inc. January 31, 2000 

Table 1. San Juan River Colorado pikeminnow radio frequencies and capture or 

stock locations. 

Capture (1993-1994) or 

Stock (1997) Information Years 

Frequency Date River Mile Monitored Sex TL (mm) SL (mm) Weight (g) 

40.030 5/15/93 122.05 1993,1994 F 764 643 4760 

40.100 4/14/93 126.25 1993 F 948 820 8050 

40.200 4/13/93 130.6 1993 M 521 445 1200 

40.848/980 4/14/93 128.8 1993,1994 F 797 685 5550 

40.280 4/15/94 133.00 1994 M 617 510 2000 

40.848/980 4/12/94 128.60 1993,1994 F 820 695 5810 

40.910 5/16/94 74.70 1994 F 759 630 4000 

40.940 4/14/94 122.60 1994 F 754 628 4450 

40.020* 9/23/97 178.8 1998 M 580 1326 

40.030 9/23/97 178.8 1998 F 698 2238 

40.040* 9/23/97 178.8 1998 F 734 2410 

40.051* 9/23/97 178.8 1998 F 753 3100 

40.060 9/23/97 178.8 1998 F 660 1825 

40.070* 9/23/97 178.8 1998 F 707 2502 

40.080 9/23/97 178.8 1998 F 703 2110 

40.090 9/23/97 178.8 1998 F 629 1583 

40.100 9/23/97 178.8 1998 F 650 1848 

40.110* 9/23/97 178.8 1998 

40.120 9/23/97 178.8 1998 F 745 2933 

40.130* 9/23/97 178.8 1998 F 641 1582 

40.140 9/23/97 178.8 1998 F 734 2700 

40.600 9/23/97 178.8 1998 F 698 2067 

40.611 9/23/97 178.8 1998 F 742 2910 

40.780* 9/23/97 178.8 1998 F 671 2435 

Note: An asterisk (*) denotes stocked pikeminnow monitored during the summer of 1998. All 

1997 fish are hatchery origin. 

Radio tracking was conducted for five consecutive days each observation week. One fish 

was selected to be monitored for a continuous twenty-four hour period each week. 

During the 1993 and 1994 study years, each day scheduled for observation was divided 

into four observation periods. Each observation period was six hours long and 

determined by sunrise and sunset. Time periods were numbered as follows: Period 1 - 

three hours before to three hours after sunrise; Period 2 - three hours after sunrise to three 

hours before sunset; Period 3 - three hours before sunset to three hours after sunset; and 

Period 4 - three hours after sunset to three hours before sunrise. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 8 

Miller Ecological Consultants, Inc. January 31, 2000 Figure 1. Study Area Map. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 9 

Miller Ecological Consultants, Inc. January 31, 2000 

Observations were made during Periods 1 and 3 every day of a scheduled observation 

week. A random selection process was used to determine which fish was observed 

during Period 1 and 2. Limited observations were made during Period 4. In 1998, 

observed fish were not randomly selected or related to time period due to widespread fish 

distribution and access constraints. In all years selected fish were successfully located 

and generally monitored for two hours. 

Radio telemetry was conducted using an Advanced Telemetry Systems (ATS) 

programmable receiver and a directional antenna. To determine approximate fish 

locations, aerial surveys using a wing-mounted directional antenna were conducted at the 

beginning of the summer observations 1993, 1994 and 1998. Ground contact surveys 

began immediately after the air surveys to confirm fish locations. Fish locations in the 

river were obtained during ground surveys by walking the shoreline or floating the river. 

After signal contact was made, the crew would determine the fish position using a 

triangulation method from positions along the shore. Whenever possible, the crew would 

obtain a strong signal and a null at a location upstream of the fish location, then the crew 

would move to a position directly across from the fish and obtain a second null signal. 

The fish position was the intersection point on the lines from the two null signals. 

Usually this location was verified by obtaining third null signal at a downstream location. 

At times, fish position or topography inhibited this procedure. In those instances, fish 

position was estimated from at least one shore or boat position. 

Any locations where the fish remained for more than 30 minutes were recorded, and if 

possible, habitat parameters were measured. Data on habitat characteristics near the fish 

location were acquired by habitat mapping on aerial videography plates and digitizing the 

habitat maps. Bureau of Indian Affairs (1993 and 1994) or Ecosystems Research 

Institute (1998) personnel were responsible for the onstream habitat mapping. Habitat 

maps were created for each separate fish location during the observation day. 

Habitat usage data included a sketch of the habitat surrounding the fish locations and 

included fish positions marked on the map. Habitat was classified with the same system 

used for the quantification of habitat availability (Table 2, see Bliesner and Lamarra 

(1995)). Data collected at the fish location included date, time of day, weather 

conditions, time monitored, and any notes on movement during the observation period. 

When possible, other physical habitat data was collected at each fish location. These 

measurements included water depth, water velocity (mean column and bottom), substrate 

type, proximity to cover, description of cover at the location, general description of the 

site; measurements of the habitat type including length, width, bank features, shoreline 

vegetation, dominant substrate and cover for the habitat type. Other parameters measured 

included water and ambient air temperature, conductivity, and pH. Discharge was 

obtained from the nearest USGS gaging station. 

Telemetry data was divided into pre-spawn (May-June), spawn (July) and post-spawn 

(August) periods. Period break-lines were based upon observed behaviors of Colorado 

pikeminnow in the San Juan River during the study years. Observations were analyzed 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 10 

Miller Ecological Consultants, Inc. January 31, 2000 

Table 2. Habitat categories used during monitoring. 

Habitat Habitat Habitat 

Number Type Number Type Number Type 

1 Backwater 11 Scour Run 26 Rootwad Pool 

2 Backwater 

Pool 

12 Shore Run 27 Abandoned Channel 

3 Pool 13 Undercut Run 28 Sand Bar 

4 Debris Pool 14 Run/Riffle 29 Tributary 

5 Rootwad Pool 15 Riffle 30 Shoal/Riffle 

6 Eddy 16 Riffle Eddy 31 Island 

7 Edge Pool 17 Shore Riffle 32 Rapid 

8 Shoal 18 Riffle/Chute 33 Irrigation Return 

8a Sand Shoal 19 Chute 34 Inundated Veg. 

8b Cobble Shoal 20 Slackwater 35 Pocket Water 

9 Shoal/Run 21 Isolated Pool 36 Boulders 

9a Sand 

Shoal/Run 

22 Embayment 37 Waterfall 

9b Cobble 

Shoal/Run 

24 Overhanging 

Veg. 

 

10 Run 25 Cobble Bar 

for 1993, 1994, 1993 and 1994 combined, and 1998. Observations from 1998 were not 

combined with 1993 and 1994 data because the 1998 monitored fish were hatcheryreared. Gross movement (difference between most upstream location and farthest 

downstream location), and daily movement were calculated. These parameters will be 

reported in miles because contact locations were recorded by river mile. Habitat maps 

were digitized into Arcview version 3.1 and the areas of individual habitats were 

calculated. Areas of each habitat type, including the habitat with the fish location were 

used to develop total available habitat within a specific reach of stream. Habitat richness 

was measured by averaging the number of unique habitat types per habitat mapping plate. 

Richness was calculated for pre-spawn, spawn, and post-spawn telemetry periods. 

Habitat selectivity was determined by the comparison of habitat usage to habitat 

availability (Swanson et al. 1974; Johnson 1980). Selectivity for a habitat type occurs if 

the percent of time that radio implanted fish were monitored in that habitat type is greater 

than the percent of the total habitat area that the particular habitat type accounted for. If 

no selectivity occurred then all habitats should be used in the same proportion as they 

occur within the system. Low numbers of monitored pikeminnow and small numbers of 

contacts for individual fish precluded the use of the methodology used by Osmundson et 

al. (1995) and Ryden (1999) for the quantification of habitat selectivity. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 11 

Miller Ecological Consultants, Inc. January 31, 2000 

RESULTS 

1993 

Intensive radio tracking of Colorado pikeminnow was conducted for 30 days during the 

period from 21 June 1993 through 13 August 1993. Radio frequencies for the four 

Colorado pikeminnow monitored during 1993 were 40.030, 40.100, 40.200, and 40.848. 

Length, weight, sex and river mile capture information are located in Table 1. One 

Colorado pikeminnow captured in 1993 was implanted with tag 40.980, upon its 

recapture in 1994, it was implanted with radio tag 40.848. Results from 1993 and 1994 

for this fish are presented using the 1994 transmitter frequency 40.848. 

All radio implanted fish remained upstream of RM 122.6 during the 1993 study period. 

The four radio implanted fish had an average gross movement of 8.0 mi during the 1993 

monitoring. Colorado pikeminnow 40.848 had the largest gross movement (11.00 mi), 

while fish 40.200 had the least with 2.28 mi (Table 3). Fish 40.030 and 40.100 moved 

9.25 and 9.45 mi, respectively. 

The localized movement within and between habitat types resulted in relatively short 

distances moved during each day (Table 4). Implanted fish had the least localized 

movement from 26 July – 30 July 1993, averaging only 3.6 m of movement during 

monitoring (Table 4). Radio implanted fish moved more than one river mile in a day on 

four occasions (Table 5). During the 1993 monitoring period radio implanted fish spent 

the majority of time in run (43.0%), eddy (25.5%), and run/riffle (11.9%) habitats (Figure 

2). Radio implanted fish were found in 11 different habitat types and individual fish used 

an average of 5.5 habitats. Overall, eddy habitat had the highest selectivity, although 

radio implanted fish also showed some selectivity for backwater, edge pool, slackwater, 

undercut run, run/riffle and chute habitats (Figure 3). Habitat richness was highest during 

the spawning period followed by the post-spawn period (Table 6). 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 12 

Miller Ecological Consultants, Inc. January 31, 2000 

Table 3. River mile locations for monitored Colorado pikeminnow, June – August 

1993. Multiple contact times (24 hr) are in parentheses. 

Fish Frequency 

Date 40.030 40.100 40.200 40.848 

6/21/93 131.90 

6/22/93 122.60 130.80 

6/23/93 122.8 (0845) 130.80 

6/23/93 123.10 (1045) 

6/24/93 122.60 122.60 137.70 

6/25/93 122.60 122.60 

6/28/93 137.30 

6/29/93 122.60 

6/30/93 122.60 137.30 

7/1/93 122.60 (0800) 123.40 137.30 

7/12/93 132.05 (1430) 132.00 132.00 

7/12/93 132.00 (1500) 

7/13/93 132.00 132.00 (0740) 

7/13/93 131.15 (1645) 

7/14/93 132.00 (0740) 131.15 (1010) 

7/14/93 132.01 (1730) 131.00 (1850) 

7/15/93 131.50 (0815) 

7/15/93 131.40 (1200) 

7/15/93 131.60 (1800) 

7/15/93 132.00 (2010) 

7/15/93 132.02 (2300) 

7/16/93 132.02 (0000) 

7/16/93 132.15 (0150) 

7/16/93 132.08 (0600) 

7/19/93 131.01 (1545) 131.15 

7/19/93 131.06 (1730) 

7/20/93 131.15 131.15 

7/21/93 130.30 (1845) 131.15 141.30 

7/21/93 130.48 (2200) 

7/22/93 130.30 (0815) 131.15 (1035) 

7/22/93 130.65 (1140) 

7/26/93 128.83 

7/27/93 131.40 

7/28/93 131.40 141.95 

7/29/93 128.10 131.15 

7/30/93 141.30 

8/9/93 131.85 131.15 

8/10/93 131.85 (0910) 131.15 (1200) 

8/10/93 131.60 (1055) 129.80 (1830) 

8/11/93 131.40 131.15 142.00 

8/12/93 142.00 (1015) 

8/12/93 141.85 (2220) 

8/13/93 141.65 (0645) 

8/13/93 141.85 (0815) 

Movement 40.030 40.100 40.200 40.848 

MIN (RM) 122.60 122.60 129.80 131.00 

MAX (RM) 131.85 132.05 132.08 142.00 

GROSS (mi) 9.25 9.45 2.28 11.00 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 13 

Miller Ecological Consultants, Inc. January 31, 2000 

Table 4. Distance (m) moved upstream or downstream by Colorado pikeminnow 

during daily monitoring in the San Juan River, June – August 1993. 

Fish Frequency 

Date 40.030 40.100 40.200 40.848 

6/21/93 9 

6/22/93 6 966 

6/23/93 510 12 

6/24/93 9 9 5 

6/25/93 11 11 

6/28/93 30 

6/29/93 6 

6/30/93 6 40 

7/1/93 521 0 87 

7/2/93 35 

7/12/93 134 0 0 

7/13/93 3 49 

7/14/93 9 15 

7/15/93 685 

7/16/93 0 

7/19/93 76 0 

7/20/93 12 8 

7/21/93 835 35 73 

7/22/93 76 

7/26/93 6 6 

7/27/93 5 

7/28/93 6 0 

7/29/93 0 6 

7/30/93 0 

8/9/93 18 8 

8/10/93 468 457 

8/11/93 6 0 46 

8/12/93 326 

8/13/93 805 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 14 

Miller Ecological Consultants, Inc. January 31, 2000 

Table 5. Distance (mi) moved between the first and last daily contact of monitored 

Colorado pikeminnow, June – August 1993. 

Fish Frequency 

Date 40.030 40.100 40.200 40.848 

6/21/93 0 

6/22/93 0 0 

6/23/93 0.3 0 

6/24/93 0 0 0 

6/25/93 0 0 

6/28/93 0 

6/29/93 0 

6/30/93 0 0 

7/1/93 0 0 0 

7/2/93 0 

7/12/93 0.05 0 0 

7/13/93 0 0.85 

7/14/93 0.10 0.14 

7/15/93 0.87 

7/16/93 0.07 

7/19/93 0.05 0 

7/20/93 0 0 

7/21/93 1.38 0 0 

7/22/93 0 

7/26/93 0 0 

7/27/93 0 

7/28/93 0 0 

7/29/93 0 0 

7/30/93 0 

8/9/93 0 0 

8/10/93 0.3 1.35 

8/11/93 0 0 0 

8/12/93 0.16 

8/13/93 0.55 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 15 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 2. Habitat use as a percent of time monitored during the summer 1993. 

Habitat use as percent of time monitored for all radio implanted Colorado pikeminnow in the San Juan 

River during the 1993 summer monitoring

0

10

20

30

40

50

60

70

80

90

100

Backwater Edge Pool Slackwater Eddy Cobble

Shoal/Run

Run Shore Run Undercut

Run

Run/Riffle Riffle Chute

Habitat Type

Percent of Time

Habitat use as percent of time monitored for individual radio implanted Colorado pikeminnow in the San 

Juan River during the 1993 summer monitoring

0

10

20

30

40

50

60

70

80

90

100

Backwater

Edge Pool

Slackwater

Eddy

Cobble Shoal/Run

Run

Shore Run

Undercut Run

Run/Riffle

Riffle

Chute

Habitat Type

Percent of Time

40.030

40.200

40.100

40.848
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 16 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 3. Habitat usage and habitat availability as a percent of total during the 

summer 1993. 

Habitat usage (time monitored) and availability (total habitat area) for Colorado pikeminnow in the San Juan 

River, Summer 1993

0

10

20

30

40

50

60

70

80

90

100

Backwater Edge Pool Slackwater Eddy Cobble

Shoal/Run

Run Shore Run Undercut

Run

Run/Riffle Riffle Chute

Habitat Type

Percent of Total

Total Habitat Area

Time Monitored

Table 6. Habitat richness values for Colorado pikeminnow locations during 1993, 

1994, 1993 and 1994 combined and 1998 on the San Juan River. 

Study Year 

Period 1993 1994 1993/1994 1998 

Pre-spawn 5.15 4.64 4.92 4.67 

Spawn 5.92 4.78 5.13 9.00 

Post-spawn 5.44 n/a 5.44* n/a 

Summer 5.63 4.76 5.11 7.70 

Fall 6.67 

Winter 6.30 

Note: Telemetry was not conducted during the post-spawn period in 1994. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 17 

Miller Ecological Consultants, Inc. January 31, 2000 

Pre-spawn 

Radio implanted fish were widely separated during most of the pre-spawn period. Fish 

40.030 and 40.100 used the area around the Mancos River confluence (RM 122.6), while 

fish 40.200 was found near RM 131. Fish 40.848 was found at RM 137.3 - the farthest 

upstream location of any fish monitored in 1993 (Table 3). Habitat types used included 

main channel eddies, side-channels and the Mancos River confluence. Water 

temperatures in these side-channels and Mancos River confluence were approximately 

two to four degrees warmer than main channel habitats for the same dates (Table 7). 

Radio implanted pikeminnow used eddy habitat most often, spending over 45% of the total 

time in that habitat (Figure 4). Run, undercut run, edge pool and shore run accounted for 

27.8%, 13.7%, 5.1%, and 5.1% of the time monitored, respectively. Individually, fish 

40.030 and 40.100 spent the majority of the pre-spawn period in eddy habitat (Figure 4). 

Fish 40.848 spent the most time in run habitat, although this fish also utilized undercut run 

habitat (Figure 4). Colorado pikeminnow 40.848 and 40.200 did not use eddy habitat. 

Radio implanted fish in the pre-spawn period had a high selectivity for eddy habitat and to 

a lesser extent for edge pool (Figure 5). 

Table 7. Water temperatures (Co

) for pikeminnow locations during the pre-spawn 

1993 and 1994 where main channel and side channel or tributary temperatures were 

concurrently taken. 

Water Temperature (Co) 

Date Fish Frequency River Mile Side channel, tributary Main channel 

6/22/93 40.200 130.8 17.2 15.0 

6/24/93 40.100, 40.030 122.6 17.2 13.9 

6/25/93 40.030 122.6 16.7 13.3 

6/29/93 40.100 122.6 20.0 15.6 

6/30/93 40.100 122.6 18.3 15.6 

6/03/94 40.940 122.6 17.8 13.3 

6/17/94 40.940 122.6 15.6 13.3 

6/20/94 40.030 122.6 20.6 17.2 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 18 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 4. Habitat use as a percent of time monitored during the pre-spawn period 

1993. 

Habitat use as percent of time monitored for all radio implanted Colorado pikeminnow in the San Juan 

River during the 1993 pre-spawn period

0

10

20

30

40

50

60

70

80

90

100

Edge Pool Eddy Cobble Shoal/Run Run Shore Run Undercut Run

Habitat Type

Percent of Time

Habitat use as percent of time monitored for individual radio implanted Colorado pikeminnow in the San 

Juan River during the 1993 pre-spawn period

0

10

20

30

40

50

60

70

80

90

100

Edge Pool Eddy Cobble Shoal/Run Run Shore Run Undercut Run

Habitat Type

Percent of Time

40.030

40.200

40.100

40.848
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 19 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 5. Habitat usage and habitat availability as a percent of total during the prespawn period, 1993. 

Habitat usage (time monitored) and availability (total habitat area) for Colorado pikeminnow in the San Juan 

River, Pre-spawn 1993

0

10

20

30

40

50

60

70

80

90

100

Edge Pool Eddy Cobble Shoal/Run Run Shore Run Undercut Run

Habitat Type

Percent of Total

Total Habitat Area

Time Monitored

Spawning 

During the 1993 spawning period, radio implanted fish spent over 40% of the time in run 

habitat and approximately 20% of the time in eddy and run/riffle habitats (Figure 6). 

Backwater, slackwater, riffle and chute habitats were also utilized, but none accounted 

for more than 8% of the time monitored (Figure 6). All radio implanted pikeminnow 

except 40.100, which could not be located after 12 July 1993, used higher velocity 

habitats (run/riffle, riffle and chute) during the spawning period (Figure 6). Fish 40.100 

spent the majority (58%) of its time in backwater habitat. Slackwater, eddy and run/riffle 

habitats had the highest selectivity (Figure 7). Selectivity was also shown for backwater 

and chute habitats, but to a lesser extent than slackwater, eddy and run/riffle habitats 

(Figure 7). 

Based upon fish aggregations and visual observations, two locations were identified as 

potential spawning areas. Both of the locations are within the "Mixer" reach of the river. 

The upper spawning location was at RM 132.0 and the lower spawning location was at 

RM 131.1. Both locations are characterized by cobble bar and island complexes. Radio 

implanted fish displayed directional movement to these potential spawning sites. 

Between 1 July 1993 and 12 July 1993, fish 40.100 moved 8.6 miles upstream and fish 

40.848 moved 5.3 miles downstream to reach the RM 132.0 site. Fish 40.030 moved 8.6 

miles upstream to reach the RM 131.1 site. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 20 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 6. Habitat use as a percent of time monitored during the spawning period, 

1993. 

Habitat use as percent of time monitored for all radio implanted Colorado pikeminnow in the San Juan 

River during the 1993 spawning period

0

10

20

30

40

50

60

70

80

90

100

Backwater Slackwater Eddy Run Run/Riffle Riffle Chute

Habitat Type

Percent of Time

Habitat use as percent of time monitored for individual radio implanted Colorado pikeminnow in the San 

Juan River during the 1993 spawning period

0

10

20

30

40

50

60

70

80

90

100

Backwater Slackwater Eddy Run Run/Riffle Riffle Chute

Habitat Type

Percent of Time

40.030

40.200

40.100

40.848
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 21 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 7. Habitat usage and habitat availability as a percent of total during the 

spawning period, 1993. 

 Habitat usage (time monitored) and availability (total habitat area) for Colorado pikeminnow in the San Juan 

River, Spawn 1993

0

10

20

30

40

50

60

70

80

90

100

Backwater Slackwater Eddy Run Run/Riffle Riffle Chute

Habitat Type

Percent of Total

Total Habitat Area

Time Monitored

River Mile 132.0 

Three implanted fish moved to the potential spawning location at RM 132.0 prior to 12 

July 1993. On 12 July, fish 40.100 and 40.848 were located and monitored near the side 

channel on river left, while fish 40.200 was located in a main channel riffle. RM 132.0 

had 12 different habitat types present during the 12 – 16 July 1993 period. This area is 

similar to spawning habitats found in the Yampa River, Colorado; a side channel 

branches to form several fast, deep chute, run/riffle or riffle habitats. Resting habitats 

were adjacent to the chutes where a large slackwater (main channel edge) and a smaller 

backwater were located. The chutes and riffles emptied into a uniformly deep, slow run 

habitat approximately 60-75 m downstream from the entrance of the side channel. This 

long, slow run may provide a feeding/resting area for spawning fish. Cobble in the riffle 

areas was unsettled and clean in the higher velocity areas, while on the slower riffle edges 

the cobble was covered with a thin growth of algae. Water temperatures on 12 July 1993 

were 25o

C in all local habitat types. 

The RM 132.0 site was occupied until 16 July 1993 and then abandoned by all radio 

implanted fish. Contact with fish 40.100 was lost after 12 July 1993 and not regained for 

the remainder of monitoring. Fish 40.030, 40.200, and 40.848 moved to the suspected 

downstream spawning area at RM 131.1.
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 22 

Miller Ecological Consultants, Inc. January 31, 2000 

River Mile 131.1—Red Wash Side Channel

The suspected spawning area at RM 131.1 is located at the mouth of the side channel 

containing the Red Wash confluence. This location was a side channel in 1992, but has 

carried main channel flow since high runoff in the spring of 1993 eroded a narrow bank 

separating the primary and secondary channels. This area was similar in physical 

features to RM 132.0; there was an island complex with a side channel and chute, and the 

dominant substrate was cobble. Seven different aquatic habitat types were present on 20 

July 1993 (Figure 8). The discharge on this date at the Four-Corners gage was 1110 cfs. 

The first use of this location by radio implanted fish (40.848) was documented on 13 July 

1993. 

Habitat in the suspected spawning location included a fast, narrow chute with an adjacent 

small eddy, which may act as resting habitat. Depth and velocity measurements in the 

eddy were 0.85 m and 0.29 m/s, respectively (Table 8). Cobble diameter was 8-10 cm in 

the chute. Russian olive trees overhang the chute providing shade and cover. 

Table 8. Microhabitat measurements for possible spawning activities. 

Habitat Habitat Function Depth (m) Mean Velocity (ms) Year 

Eddy Resting 0.85 0.29 1993 

Eddy Resting 0.91 0.02 1994 

Run/Riffle Spawning 0.46 1.25 1994 

Eddy (pt 1) Resting 0.70 1998 

Eddy (pt 2) Resting 0.98 1998 

Riffle (pt 3) Spawning 0.55 1998 

Riffle (pt 4) Spawning 0.46 1998 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 23 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 8. Suspected spawning location 1993. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 24 

Miller Ecological Consultants, Inc. January 31, 2000 

Visual Sighting of Spawning Colorado Pikeminnow. 

On 20 July 1993, at 0825 hrs fish 40.200 and 40.030 (male and female, respectively) 

were located together at RM 131.15. Both fish were approximately 12-18 m downstream 

of the side channel entrance. A large debris pile at the front of an island formed a large 

(5 m x 6 m), deep (>1.0 m) eddy and a deep run/riffle. Although the cobble (8-10 cm 

diameter) had a thin growth of algae on the surface, the interstitial spaces were clean and 

extended 16-20 cm deep. 

At 0940 hrs both fish were located near the top of a shaded run/riffle in the deepest, 

fastest area. When not together, the male would maintain a 2 - 4 m downstream 

separation with the female. Occasionally, the male (40.200) would move up to the 

female and then move downstream 7 - 10 m. In contrast to the male's active movement, 

the female's movement appeared to be slow and deliberate. When the shade left the 

lower run/riffle, the fish moved up into deeper water at the top end of the run/riffle. 

At 1025 hrs the fish were visually observed and confirmed by radio telemetry in a side by 

side pairing. The fish moved upstream of the fast current (run/riffle) and into the bottom 

end of the eddy. The larger female fish was positioned in front of the male who was on 

her right side, snout even with her vent. The fish were within 14 cm of each other. The 

observation lasted approximately 3-5 seconds before both fish moved into the deeper part 

of the eddy. The fish spent approximately 10 to 15 minutes in the deep swift water 

before they moved into the eddy. At 1035 hrs two smaller, paired fish were observed 

moving slowly through the eddy. One fish had a fungal growth on its dorsal side. The 

two fish were dark gray in appearance and smaller than the radio implanted fish. Neither 

of the radio implanted fish had any observed fungal growth. On two different occasions, 

a very large, reddish brown caudal fin was observed coming out of the water at the upper 

edge of the eddy. On the river right bank, a caudal fin approximately 7.5 cm in height, 

lobed, and orange tinted was observed breaking the surface, but the body was not visible. 

Post-spawn 

During the post-spawn period radio implanted fish locations ranged from RM 129.8 

upstream to RM 142.0. Fish 40.848 moved upstream to RM 142.0 and remained in that 

area until the end of monitoring , while fish 40.030 and 40.200 remained within the RM 

131.0 to RM 132.0 area. These fish showed little directional movement during this 

period, moving only an average of 0.72 miles. 

Radio implanted fish spent over 80% of the time in runs and 15% of the time in chute 

habitat (Figure 9). Fish 40.848 and 40.030 spent the majority of time in runs while fish 

40.200 used chute habitat exclusively (Figure 9). Chute habitat was the only habitat 

selected for during the post-spawn period (Figure 10). 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 25 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 9. Habitat use as a percent of time monitored during the post-spawn period 

1993. 

Habitat use as percent of time monitored for all radio implanted Colorado pikeminnow in the San Juan 

River during the 1993 post-spawn period

0

10

20

30

40

50

60

70

80

90

100

Run Run/Riffle Chute

Habitat Type

Percent of Time

Habitat use as percent of time monitored for individual radio implanted Colorado pikeminnow in the San 

Juan River during the 1993 post-spawn period

0

10

20

30

40

50

60

70

80

90

100

Run Run/Riffle Chute

Habitat Type

Percent of Time

40.030

40.200

40.848
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 26 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 10. Habitat usage and habitat availability as a percent of total during the 

post-spawn period, 1993. 

Habitat usage (time monitored) and availability (total habitat area) for Colorado pikeminnow in the San Juan 

River, Post-spawn 1993

0

10

20

30

40

50

60

70

80

90

100

Run Run/Riffle Chute

Habitat Type

Percent of Total

Total Habitat Area

Time Monitored

1994 

Radio implanted Colorado pikeminnow were opportunistically tracked in conjunction 

with other San Juan River studies during February, May, June, October and November, 

1994. Intensive radio tracking of Colorado pikeminnow was conducted during the period 

from 27 May – 29 July 1994. Three new pikeminnow were captured in 1994 and 

implanted with radio transmitters. Additionally, two pikeminnow monitored during 1993 

were monitored again in 1994 bringing the total number of fish monitored to five (Table 

1). 

Radio implanted fish used predominately run habitat followed by slackwater, run/riffle 

and eddy habitat (Figure 11). Cobble shoal/run, riffle, riffle/chute and chute habitat were 

also used but none accounted for more than 3% of the total time monitored (Figure 11). 

Individually, all five fish monitored spent more than 50% of their time in run habitat 

(Figure 11). Monitored fish used a total of eight different habitat types, but only run and 

slackwater habitat was used by all fish. Cumulative data indicates a high degree of 

selectivity for slackwater and eddy habitats (Figure 12). 

Habitat richness was highest during the fall and winter monitoring periods (Table 6). 

During the summer, the spawning period had more habitat richness than the pre-spawn 

and post-spawn periods (Table 6). 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 27 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 11. Habitat use as percent of time monitored during the summer 1994. 

Habitat use as percent of time monitored for all radio implanted Colorado pikeminnow in the San Juan 

River during the 1994 summer monitoring

0

10

20

30

40

50

60

70

80

90

100

Slackwater Eddy Cobble

Shoal/Run

Run Run/Riffle Riffle Riffle/Chute Chute

Habitat Type

Percent of Time

Habitat use as percent of time monitored for individual radio implanted Colorado pikeminnow in the San 

Juan River during the 1994 summer monitoring

0

10

20

30

40

50

60

70

80

90

100

Slackwater Eddy Cobble

Shoal/Run

Run Run/Riffle Riffle Riffle/Chute Chute

Habitat Type

Percent of Time

40.030

40.848

40.280

40.910

40.940
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 28 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 12. Habitat usage and habitat availability as a percent of total during the 

summer 1994. 

Habitat usage (time monitored) and availability (total habitat area) for Colorado pikeminnow in the San Juan 

River, Summer 1994

0

10

20

30

40

50

60

70

80

90

100

Slackwater Eddy Cobble

Shoal/Run

Run Run/Riffle Riffle Riffle/Chute Chute

Habitat Type

Percent of Total

Total Habitat Area

Time Monitored

Winter 

One week of monitoring was conducted in February, 1994. Three fish, radio tag numbers 

40.030, 40.910 and 40.848, were tracked from 17 February – 21 February 1994. Fish 

40.030 and 40.910 moved 0.50 mi during this period and fish 40.848 moved 0.10 mi 

(Table 9). Radio implanted fish used run habitat almost exclusively, although, eddy, sand 

shoal/run, undercut run and riffle habitats were also utilized (Figure 13). All individual 

fish used run habitat over 60% of the time (Figure 13). Fish 40.848 showed the most 

diversity in habitat use, using run, eddy, sand shoal/run and riffle habitats (Figure 13). 

All fish monitored were active during observation periods and the highest level of 

activity occurred during mid-day. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 29 

Miller Ecological Consultants, Inc. January 31, 2000 

Table 9. River mile locations for monitored Colorado pikeminnow, Winter and Fall 

1994. 

Fish Frequency 

Date 40.030 40.848 40.910 

2/17/94 128.20 131.90 

2/18/94 75.10 

2/19/94 127.90 131.80 

2/20/94 127.70 74.60 

2/21/94 127.70 131.80 

Movement 

MIN (RM) 127.70 131.80 74.60 

MAX (RM) 128.20 131.90 75.10 

GROSS (mi) 0.50 0.10 0.50 

 

Fish Frequency 

Date 40.030 40.280 40.848 40.910 40.940 

10/3/94 133.50 135.70 

10/4/94 128.70 133.50 120.90 

10/5/94 74.30 

11/14/94 136.30 

11/15/94 74.85 119.80 

11/16/94 136.30 74.85 119.80 

Movement 

MIN (RM) 133.50 135.70 74.30 119.80 

MAX (RM) 133.50 136.30 74.85 120.90 

GROSS (mi) 0.00 0.60 0.55 1.10 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 30 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 13. Habitat use as percent of time monitored during the winter 1994. 

Habitat use as percent of time monitored for all radio implanted Colorado pikeminnow in the San Juan 

River during the 1994 winter monitoring

0

10

20

30

40

50

60

70

80

90

100

Eddy Sand Shoal/Run Run Undercut Run Riffle

Habitat Type

Percent of Time

Habitat use as percent of time monitored for individual radio implanted Colorado pikeminnow in the San 

Juan River during the 1994 winter monitoring

0

10

20

30

40

50

60

70

80

90

100

Eddy Sand Shoal/Run Run Undercut Run Riffle

Habitat Type

Percent of Time

40.030

40.848

40.910
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 31 

Miller Ecological Consultants, Inc. January 31, 2000 

Pre-spawn 

Radio implanted Colorado pikeminnow were widely distributed during this period, with 

locations ranging from RM 73.8 to RM 137.5 (Table 10). However, three fish (40.030, 

40.280, and 40.940) were located at the same river mile (122.6), although each was found 

in distinctly different sections of the river. These three fish moved only short distances 

during this period, exhibiting gross movements of only 2.50, 0.10, and 0.0 mi, 

respectively. Two fish (40.940 and 40.030) were found using the Mancos River, which 

had water temperatures two to four degrees warmer than the San Juan River main channel 

(Table 7). 

Two fish showed directional movement during this period. Fish 40.848 left RM 137.5, 

where she had been located since 27 May 1994, on 20 June 1994 and moved 9.17 

kilometers downstream by 30 June 1994. Fish 40.910 moved the longest distance of any 

monitored fish in 1994. On 1 June 1994, fish 40.910 was located at RM 73.8 and by 30 

June 1994 this fish had moved upstream to RM 131.2—a distance of 57.40 mi and a rate 

of almost than 2.0 mi per day (Table 10). 

Radio implanted fish used only three habitat types during this period (Figure 14). The 

fish predominately used run habitat, but they were also found in slackwater and eddy 

habitats (Figure 14). Fish 40.910 spent 80% of its time in runs, while fish 40.280 used 

runs exclusively (Figure 14). Fish 40.848 and 40.030 spent over half of their time in the 

low velocity slackwater and eddy habitats (Figure 14). Cumulative data indicates a 

selectivity toward slackwater and eddy habitats during the pre-spawn period (Figure 15). 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 32 

Miller Ecological Consultants, Inc. January 31, 2000 

Table 10. River mile locations for Colorado pikeminnow, May – July 1994. 

Fish Frequency 

Date 40.030 40.280 40.848 40.910 40.940 

5/27/94 137.50 

6/1/94 73.80 

6/3/94 122.60 

6/6/94 137.50 122.60 

6/7/94 122.60 122.60 137.50 122.60 

6/10/94 122.60 137.50 122.60 

6/14/94 87.20 

6/17/94 122.70 122.60 

6/20/94 122.75 122.70 137.50 

6/21/94 120.00 122.70 96.10 

6/27/94 133.00 

6/28/94 120.7 126.50 

6/29/94 128.20 

6/30/94 124.40 (1330) 122.60 131.80 131.20 

6/30/94 122.20 (1700) 

7/1/94 135.40 

7/2/94 132.00 134.50 

7/3/94 132.00 133.20 

7/4/94 132.00 133.20 

7/5/94 132.00 132.00 131.80 

7/6/94 132.00 132.00 (0845) 

7/6/94 131.90 (1345) 

7/6/94 132.00 (2145) 

7/7/94 132.10 (1700) 122.60 132.00 131.40 (0915) 

7/7/94 132.00 (1830) 131.50 (1915) 

7/8/94 132.00 122.60 132.00 131.60 

7/11/94 122.60 131.20 131.60 (1245) 

7/11/94 131.20 (1540) 

7/12/94 131.20 131.20 (1155) 131.20 134.40 

7/12/94 132.00 (1925) 

7/13/94 131.20 134.50 

7/14/94 129.20 122.00 

7/15/94 135.40 133.50 135.40 

7/18/94 122.30 133.40 

7/19/94 135.40 133.20 

7/20/94 124.20 122.05 135.80 133.30 

7/21/94 122.05 135.80 133.40 

7/22/94 133.30 

7/25/94 131.40 133.50 

7/26/94 129.70 (0750) 122.05 131.20 134.20 

7/26/94 129.90 (1945) 

7/27/94 129.80 131.10 134.10 142.05 

7/28/94 129.80 122.05 142.05 

7/29/94 130.50 131.05 133.50 

Movement 40.030 40.280 40.848 40.910 40.940 

MIN (RM) 120.70 122.05 131.05 73.80 122.50 

MAX (RM) 132.10 122.70 137.50 135.40 142.05 

GROSS (mi) 11.40 1.65 6.45 61.60 19.55 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 33 

Miller Ecological Consultants, Inc. January 31, 2000 

Table 11. Distance (m) moved upstream or downstream by Colorado pikeminnow 

during daily monitoring in the San Juan River, July 1994. 

Fish Frequency 

Date 40.030 40.280 40.848 40.910 40.940 

7/5/94 36 9 5 

7/6/94 175 294 

7/7/94 91 12 

7/8/94 125 

7/11/94 18 3 155 

7/12/94 169 107 

7/13/94 6 

7/14/94 70 

7/15/94 21 6 9 

7/18/94 

7/19/94 6 

7/20/94 122 6 

7/21/94 

7/22/94 24 

7/25/94 134 

7/26/94 113 3 500 

7/27/94 12 21 256 

7/28/94 6 207 24 

7/29/94 6 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 34 

Miller Ecological Consultants, Inc. January 31, 2000 

Table 12. Distance (mi) moved between the first and last daily contact of monitored 

Colorado pikeminnow, July 1994. 

Fish Frequency 

Date 40.030 40.280 40.848 40.910 40.940 

7/5/94 0 0 0 

7/6/94 0 0.10 

7/7/94 0.10 0 0 0.10 

7/8/94 0 0 0 0 

7/11/94 0 0 0.40 0.10 

7/12/94 0 0.80 

7/13/94 0 0 

7/14/94 0 0 

7/15/94 0 0 0 

7/18/94 0 0 

7/19/94 0 0 

7/20/94 0 0 0 0 

7/21/94 0 0 0 

7/22/94 0 

7/25/94 0.20 0 

7/26/94 0.20 0 0 0.10 

7/27/94 0 0 0 0 

7/28/94 0 0 0 

7/29/94 0 0 0 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 35 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 14. Habitat use as a percent of time monitored during the pre-spawn period 

1994. 

Habitat use as percent of time monitored for all radio implanted Colorado pikeminnow in the San Juan 

River during the 1994 pre-spawn period

0

10

20

30

40

50

60

70

80

90

100

Slackwater Eddy Run

Habitat Type

Percent of Time

Habitat use as percent of time monitored for individual radio implanted Colorado pikeminnow in the San 

Juan River during the 1994 pre-spawn period

0

10

20

30

40

50

60

70

80

90

100

Slackwater Eddy Run

Habitat Type

Percent of Time

40.030

40.848

40.280

40.910
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 36 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 15. Habitat usage and habitat availability as a percent of total during the 

pre-spawn period, 1994. 

Habitat usage (time monitored) and availability (total habitat area) for Colorado pikeminnow in the San Juan 

River, Pre-spawn 1994

0

10

20

30

40

50

60

70

80

90

100

Slackwater Eddy Run

Habitat Type

Percent of Total

Total Habitat Area

Time Monitored

Spawning 

The potential spawning locations used during the 1993 monitoring were once again used 

in 1994 by radio implanted Colorado pikeminnow, however, different sections of the 

river channel at RM 131.1 were used in 1994 than in 1993. Fish 40.030, 40.848, and 

40.910 were all located during the spawning period at the potential spawning sites at 

either RM 131.1, RM 132.0 or both. Fish 40.280 stayed near RM 122.0 for the entire 

period. Fish 40.940, who had not been contacted since 17 June 1994, was located on 12 

July 1994 at RM 134.4 and subsequently moved upstream to RM 142.05 by 27 July 1994 

(Table 10). 

Colorado pikeminnow exhibited daily movements of several to several hundred meters 

during the spawning period (Table 11). Pikeminnow did not show long distance 

movement during this July period but were rather sedentary at particular river miles for 

each date (Table 12). The largest daily movement was 0.80 mi by Colorado pikeminnow 

40.910. Most fish remained at the same river mile between the first and last daily 

contact. 

Run habitat was the most used habitat during the 1994 spawning period, accounting for 

over 60% of the total time monitored (Figure 16). The second most used habitat was 

slackwater, which was used 17.2% of the time. Overall, radio implanted fish were found 

in eight different habitats during this period (Figure 16). Fish 40.848 had the highest 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 37 

Miller Ecological Consultants, Inc. January 31, 2000 

diversity in habitat use, using six of the eight habitat types. All fish, except for 

40.280, spent more than 50% of their total time using run habitat. Fish showed definite 

selectivity for slackwater habitat and to a lesser extent for eddy, run/riffle, riffle and chute 

habitat (Figure 17). 

River Mile 132.0 

Fish moved to this location the first week in July, 1994. On 5 July 1994, fish 40.030 and 

40.848 were located and monitored near the entrance to the river left side channel. The 

potential spawning site at RM 132.0 was used by radio implanted fish from 2 July – 8 

July 1994. Individual fish were never monitored in the same location and at the same 

time as another implanted fish, although each fish did use the same location at different 

times. The area used during 1994 is similar to the suspected spawning habitats used at 

this location in 1993; a side channel branches off then splits at the top to form several 

fast, deep chute, run/riffle or riffle habitats. Resting habitats are adjacent to these chutes 

where a large slackwater (main channel edge) and a smaller backwater are available. 

Water temperatures on 11 July were 20o

C in all local habitat types. The RM 132.0 area 

was occupied through 12 July 1994 and then abandoned. 

River Mile 131.1—Red Wash Side Channel

This suspected spawning area is located in the main channel upstream of the mouth of 

Red Wash. This location was used in 1993 and in 1994 it was occupied by radio 

implanted fish from 11 July - 13 July 1994 (Figure 18). Use of this potential spawning 

site changed from 1993 to 1994. In 1993, the radio implanted fish had used the river left 

channel , but in 1994 the fish used an area in the river right channel (Figure 18). 

Microhabitat depth and velocity measurements were 0.91 m and 0.02 m/s for the resting 

habitat (eddy) and 0.46 m and 1.25 m/s for the spawning habitat, respectively. On 12 

July 1994, three fish, 40.030, 40.848 and 40.910 were present at the same time at this 

suspected location. At the Four Corners gage the discharge was 2190 cfs on this date. 

The last fish (40.910) left the site on 13 July 1994. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 38 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 16. Habitat use as percent of time monitored during the spawning period 

1994. 

Habitat use as percent of time monitored for all radio implanted Colorado pikeminnow in the San Juan 

River during the 1994 spawning period

0

10

20

30

40

50

60

70

80

90

100

Slackwater Eddy Cobble

Shoal/Run

Run Run/Riffle Riffle Riffle/Chute Chute

Habitat Type

Percent of Time

Habitat use as percent of time monitored for individual radio implanted Colorado pikeminnow in the San 

Juan River during the 1994 spawning period

0

10

20

30

40

50

60

70

80

90

100

Slackwater Eddy Cobble

Shoal/Run

Run Run/Riffle Riffle Riffle/Chute Chute

Habitat Type

Percent of Time

40.030

40.848

40.280

40.910

40.940
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 39 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 17. Habitat usage and habitat availability as a percent of total during the 

spawning period, 1994. 

Habitat usage (time monitored) and availability (total habitat area) for Colorado pikeminnow in the San Juan 

River, Spawn 1994

0

10

20

30

40

50

60

70

80

90

100

Slackwater Eddy Cobble

Shoal/Run

Run Run/Riffle Riffle Riffle/Chute Chute

Habitat Type

Percent of Total

Total Habitat Area

Time Monitored

Fall 

All fish remained separated during fall observations in October and November. Three 

fish, 40.030, 40.910 and 40.940, moved downstream from their last spawning period 

locations, while two fish, 40.280 and 40.848, moved upstream from their last contact. 

From 29 July to 5 October 1994, fish 40.910 moved almost 60 miles downstream to 

within 0.5 miles of his 1 June 1994 contact (Table 9). 

Cumulatively, the most used habitat type during the fall monitoring was run habitat. All 

fish used just one type of habitat during the monitoring. Fish 40.848, 40.910, and 40.940 

used run habitat, while fish 40.280 used a pool and fish 40.030 used eddy habitat. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 40 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 18. Suspected spawning location 1994. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 41 

Miller Ecological Consultants, Inc. January 31, 2000 

1993 and 1994 Combined 

A total of seven Colorado pikeminnow were monitored during 1993 and 1994 (Table 1). 

Five were monitored for only one year (two in 1993, three in 1994), while two fish 

(40.030 and 40.848) were monitored both years. The majority of fish contacts occurred 

in the area from RM 120 to RM 142. Fish 40.910 had the farthest downstream contact at 

RM 73.8, while fish 40.940 had the highest upstream contact at RM 142.05. Fish 40.910 

exhibited the longest migratory movement of all monitored fish. This fish moved from 

RM 73.8 in early June 1993 up to RM 135.4 by July 1993 and back down to RM 74.3 in 

October 1993. The six remaining fish had an average gross movement of 8.70 miles. 

Radio implanted fish spent the majority of the time monitored in run habitat followed by 

eddy, slackwater, and run/riffle (Figure 19). Together, those four habitats accounted for 

over 88% of the total time monitored, although, a total of 12 different habitat types were 

used. Only fish 40.100 and 40.200 spent less than 50% of their time in run habitat, the 

remaining five fish spent the majority of their time in runs (Figure 19). Slackwater was 

the only other habitat used by all fish (Figure 19). Eddy, slackwater and run/riffle were 

the most selected for habitats (Figure 20). 

Pre-spawn 

During the 1993 and 1994 pre-spawn period most fish did not display directional 

movement. Four fish moved less than 0.5 mi during the period. Fish 40.030 and 40.848, 

the only fish monitored both years, showed the same movement trend. In 1993, fish 

40.030 and 40.848 moved 0.0 and 0.4 mi, respectively, however, in 1994 fish 40.030 

moved 4.40 mi and fish 40.848 moved 5.70 mi. 

Radio implanted fish used eddy and run habitat the majority of the time, accounting for 

37.3% and 38.5% of the total time, respectively (Figure 21). No other habitat type 

accounted for more than 10% of the time monitored. Individually, fish 40.030 and 

40.100 spent the majority of their time in eddy habitat; fish 40.200 in cobble shoal/run, 

and fish 40.280, 40.848 and 40.910 in run habitat (Figure 21). Fish showed a high 

amount of selectivity for eddy habitat during this period (Figure 22). 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 42 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 19. Habitat use as a percent of time monitored during the summers 1993 and 

1994 combined. 

Habitat use as percent of time monitored for all radio implanted Colorado pikeminnow in the San Juan 

River during the 1993 and 1994 summer monitoring

0

10

20

30

40

50

60

70

80

90

100

Backwater

Edge Pool

Slackwater

Eddy

Cobble Shoal/Run

Run

Shore Run

Undercut Run

Run/Riffle

Riffle

Riffle/Chute

Chute

Habitat Type

Percent of Time

Habitat use as percent of time monitored for individual radio implanted Colorado pikeminnow in the San 

Juan River during the 1993 and 1994 summer monitoring

0

10

20

30

40

50

60

70

80

90

100

Backwater

Edge Pool

Slackwater

Eddy

Cobble Shoal/Run

Run

Shore Run

Undercut Run

Run/Riffle

Riffle

Riffle/Chute

Chute

Habitat Type

Percent of Time

40.030

40.848

40.280

40.910

40.940

40.100

40.200
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 43 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 20. Habitat usage and habitat availability as a percent of total during the 

summers of 1993 and 1994. 

Habitat usage (time monitored) and availability (total habitat area) for Colorado pikeminnow in the San 

Juan River, Summer 1993 and 1994

0

10

20

30

40

50

60

70

80

90

100

Backwater

Edge Pool

Slackwater

Eddy

Cobble Shoal/Run

Run

Shore Run

Undercut Run

Run/Riffle

Riffle

Riffle/Chute

Chute

Habitat Type

Percent of Total

Total Habitat Area

Time Monitored
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 44 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 21. Habitat use as a percent of time monitored during the pre-spawn periods 

1993 and 1994. 

Habitat use as percent of time monitored for all radio implanted Colorado pikeminnow in the San Juan 

River during the 1993 and 1994 pre-spawn periods

0

10

20

30

40

50

60

70

80

90

100

Slackwater Edge Pool Eddy Cobble

Shoal/Run

Run Shore Run Undercut Run

Habitat Type

Percent of Time

Habitat use as percent of time monitored for individual radio implanted Colorado pikeminnow in the San 

Juan River during the 1993 and 1994 pre-spawn periods

0

10

20

30

40

50

60

70

80

90

100

Slackwater Edge Pool Eddy Cobble

Shoal/Run

Run Shore Run Undercut Run

Habitat Type

Percent of Time

40.030

40.848

40.280

40.910

40.100

40.200
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 45 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 22. Habitat usage and habitat availability as a percent of total during the 

pre-spawn period, 1993 and 1994. 

Habitat usage (time monitored) and availability (total habitat area) for Colorado pikeminnow in the San 

Juan River, Pre-spawn 1993 and 1994

0

10

20

30

40

50

60

70

80

90

100

Edge Pool Slackwater Eddy Cobble Shoal/Run Run Shore Run Undercut Run

Habitat Type

Percent of Total

Total Habitat Area

Time Monitored

Spawning 

During both 1993 and 1994 radio implanted pikeminnow used the potential spawning 

sites at RM 132.0 and RM 131.1. Fish 40.848 used both sites during 1993 and 1994, 

while fish 40.030 used both in 1994, but only the RM 131.1 site in 1993. All fish that 

used both spawning sites in one year used the RM 132.0 site first and then moved 

downstream to the RM 131.1 site. Two fish did not use either spawning site. Fish 

40.280 remained near the Mancos River confluence at RM 122.6 during 1994. Fish 

40.940 was also located near the Mancos River confluence, but contact with it was lost 

on 20 June 1994 and when it was finally recontacted it had moved up to RM 134.4. 

Although fish 40.940 must have traveled by both spawning sites, it was never located by 

field crews at either spawning site. Run habitat was the predominate habitat used by 

radio implanted fish (Figure 23). All individual fish used slackwater and run habitat 

during this period. Slackwater and eddy habitats had the highest selectivity, followed by 

run/riffle and chute (Figure 24). 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 46 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 23. Habitat use as a percent of time monitored during the spawning period 

1993 and 1994. 

Habitat use as percent of time monitored for all radio implanted Colorado pikeminnow in the San Juan 

River during the 1993 and 1994 spawning periods

0

10

20

30

40

50

60

70

80

90

100

Backwater Slackwater Eddy Cobble

Shoal/Run

Run Run/Riffle Riffle Riffle/Chute Chute

Habitat Type

Percent of Time

Habitat use as percent of time monitored for individual radio implanted Colorado pikeminnow in the San 

Juan River during the 1993 and 1994 spawning periods

0

10

20

30

40

50

60

70

80

90

100

Backwater Slackwater Eddy Cobble

Shoal/Run

Run Run/Riffle Riffle Riffle/Chute Chute

Habitat Type

Percent of Time

40.030

40.848

40.280

40.910

40.940

40.100

40.200
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 47 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 24. Habitat usage and habitat availability as a percent of total during the 

spawning period, 1993 and 1994. 

Habitat usage (time monitored) and availability (total habitat area) for Colorado pikeminnow in the San 

Juan River, Spawn 1993 and 1994

0

10

20

30

40

50

60

70

80

90

100

Backwater Slackwater Eddy Cobble

Shoal/Run

Run Run/Riffle Riffle Riffle/Chute Chute

Habitat Type

Percent of Time

Total Habitat Area

Time Monitored

1998 – Stocked Adult Colorado Pikeminnow 

Hatchery-reared Colorado pikeminnow were intensively radio tracked for 15 days from 

23 June – 22 July 1998. Of the 15 stocked Colorado pikeminnow only 7 were located 

and monitored during the 1998 summer study period (Table 1). Four radio transmitters 

(40.020, 40.070, 40.110, and 40.130) were recovered during the study period. Fish 

40.020, 40.070, 40.110, and 40.130 were alive and monitored before expelling the 

transmitter or dying. None of the transmitters were recovered in or around any fish 

remains. Attempts to disturb the fish or recover the transmitter were only performed after 

the fish had remained in the same exact location for several days of observations. The 

U.S. Fish and Wildlife Service (Grand Junction, CO) provided the bulk of river mile 

contact locations for implanted pikeminnow. They provided all contacts from November 

1997 through May 1998, as well as contacts from September 1998. 

The farthest downstream contact was for fish 40.040 at RM 133.2, while no fish was 

observed to move upstream of the stocking location (Table 13). Fish 40.110 was located 

in a small side channel at RM 140.4. All fish demonstrated downstream movement, only 

fish 40.040 and 40.051 exhibited any upstream movement. Generally, monitored fish 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 48 

Miller Ecological Consultants, Inc. January 31, 2000 

showed little movement during June and July 1998. Fish 40.040 and 40.780 moved the 

farthest, but only 1.20 and 1.40 mi, respectively. 

Table 13. River mile locations for stocked Colorado pikeminnow, June – July 1998. 

Multiple contact times (24 hr) are in parentheses. 

Fish Frequency 

Date 40.020 40.040 40.051 40.070 40.110 40.130 40.780 

09/23/97 178.80 178.80 178.80 178.80 178.80 178.80 

09/29/97 171.50 177.30 171.50 177.45 177.70 177.70 

11/18/97 177.40 168.00 177.10 

11/20/97 158.50 

12/11/97 140.50 

02/03/98 177.30 

02/04/98 168.00 176.80 

02/05/98 158.10 

03/31/98 177.30 173.60 

04/27/98 141.30 140.40 137.90 

04/28/98 153.70 

04/29/98 177.30 168.60 173.60 

05/05/98 141.20 140.10 137.85 

06/15/98 177.30 168.50 140.50 137.85 172.90 

06/16/98 140.20 152.80 

6/23/98 140.40 140.40 137.80 

6/24/98 152.80 

6/25/98 168.40 171.80 

6/26/98 140.50 140.40 137.80 

7/7/98 140.40 140.40 137.80 

7/8/98 175.60 168.40 

(1300) 

 

7/8/98 168.30 

(1415) 

 

7/9/98 168.40 

7/10/98 168.40 

7/15/98 168.50 170.40 

7/16/98 176.50 168.50 

7/17/98 168.50 

7/21/98 176.70 168.50 

7/22/98 176.70 

(0930) 

 

7/22/98 176.60 

(1830) 

7/22/98 176.80 

(2230) 

09/30/98 133.20 

Movement 

MIN (RM) 140.20 133.20 168.00 152.80 140.10 137.80 170.40 

MAX (RM) 178.80 178.80 178.50 178.80 178.80 178.80 173.60 

GROSS (mi) 38.60 45.60 10.50 26.00 48.70 41.00 3.20 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 49 

Miller Ecological Consultants, Inc. January 31, 2000 

Table 13 (continued). River mile locations for stocked Colorado pikeminnow, June 

– July 1998. Multiple contact times (24 hr) are in parentheses. 

Fish Frequency 

Date 40.030 40.060 40.080 40.090 40.100 40.120 40.140 40.490 40.600 40.611 

09/23/97 178.80 178.80 178.80 178.80 178.80 178.80 178.80 178.80 178.80 

09/29/97 177.40 175.10 176.90 173.90 177.45 177.60 178.50 

11/18/97 176.60 173.10 170.00 

11/20/97 155.60 

02/04/98 

02/05/98 

03/31/98 177.20 

04/29/98 178.20 

06/15/98 

Movement 

MIN (RM) 176.60 175.10 176.90 173.10 170.00 178.80 177.60 177.20 155.60 178.50 

MAX (RM) 178.80 178.80 178.80 178.80 178.80 178.80 178.80 178.20 178.80 178.80 

GROSS(mi) 2.20 3.70 1.90 5.70 8.80 0.00 1.20 1.00 23.20 0.30 

Radio implanted fish spent over 60% of the total time monitored in run habitat, with eddy 

and pool habitat being the second and third most used (Figure 25). Four fish (40.020, 

40.070, 40.130, 40.780) used run habitat exclusively. Fish 40.110, which was located in 

a side channel, only used pool habitat. Eddy habitat had the highest selectivity followed 

by pool habitat (Figure 26). Habitat richness was significantly higher for the spawning 

period compared to the pre-spawn period (Table 6). 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 50 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 25. Habitat use as a percent of time monitored during the summer 1998. 

Habitat use as percent of time monitored for all radio implanted Colorado pikeminnow in the San Juan 

River during the 1998 summer monitoring

0

10

20

30

40

50

60

70

80

90

100

Pool Eddy Edge Pool Run Run/Riffle Riffle Sand Shoal/Run

Habitat Type

Percent of Time

Habitat use as percent of time monitored for individual radio implanted Colorado pikeminnow in the San 

Juan River during the 1998 summer monitoring

0

10

20

30

40

50

60

70

80

90

100

Pool Eddy Edge Pool Run Run/Riffle Riffle Sand Shoal/Run

Habitat Type

Percent of Time

40.020

40.130

40.110

40.780

40.051

40.070

40.040
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 51 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 26. Habitat usage and habitat availability as a percent of total during the 

summer 1998. 

Habitat usage (time monitored) and availability (total habitat area) for Colorado pikeminnow in the San Juan 

River, Summer 1998

0

10

20

30

40

50

60

70

80

90

100

Edge Pool Pool Eddy Sand

Shoal/Run

Run Run/Riffle Riffle

Habitat Type

Percent of Total

Total Habitat Area

Time Monitored

Pre-spawn 

One week of monitoring was completed during the last week of June, 1998. All seven 

fish were contacted, although 40.040 was stranded in a gravel pit near RM 178.5. Run 

habitat was used almost exclusively during this period (Figures 27 and 28). Only one fish 

(40.110) used a habitat type besides run. 

Spawning 

During the spawning period only three fish (40.040, 40.051, and 40.780) were actively 

monitored due to the recovery of the other four transmitters. Fish 40.040 was slowly 

moving upstream during this period. On 8 July 1998 it was located at RM 175.6 and on 

22 July 1998 it was contacted at RM 176.8 (Table 13). Fish 40.051 was located around 

RM 168.4, near the Hatch Trading Post. Run habitat was the predominate habitat used, 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 52 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 27. Habitat use as a percent of time monitored during the pre-spawn period 

1998. 

Habitat use as percent of time monitored for all radio implanted Colorado pikeminnow in the San Juan River 

during the 1998 pre-spawn period.

0

10

20

30

40

50

60

70

80

90

100

Pool Run

Habitat Type

Percent of Time

Habitat use as percent of time monitored for individual radio implanted Colorado pikeminnow in the San Juan 

River during the 1998 pre-spawn period.

0

10

20

30

40

50

60

70

80

90

100

Pool Run

Habitat Type

Percent of Time

40.020

40.130

40.110

40.780

40.051

40.070
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 53 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 28. Habitat usage and habitat availability as a percent of total during the 

pre-spawn period, 1998. 

Habitat usage (time monitored) and availability (total habitat area) for Colorado pikeminnow in the San Juan 

River, Pre-Spawn 1993

0

10

20

30

40

50

60

70

80

90

100

Pool Run

Habitat Type

Percent of Total

Total Habitat Area

Time Monitored

although fish were found in seven different habitat types (Figure 29). Fish 40.020, 

40.130, and 40.780 used run habitat exclusively, while fish 40.110 remained in the side 

channel pool habitat (Figure 29). Fish 40.051 displayed the greatest diversity in habitat 

use, using six of the seven habitats. During this spawning period, radio implanted 

Colorado pikeminnow demonstrated a selectivity toward pool and eddy habitats 

(Figure 30). 

River Mile 168.4—Hatch Trading Post

A potential Colorado pikeminnow spawning site was identified at RM 168.4, which is 

near the Hatch Trading Post (Figure 31). Fish 40.051 was located in this area during the 

entire 1998 monitoring. This site is physically similar to the RM 132.0 and RM 131.1 

spawning areas. All three locations include island, cobble bar, run/riffle or riffle, and 

resting habitat complexes. On two occasions fish 40.051 exhibited possible spawning 

type behavior. During a 24 hour observation on 8 July and 9 July 1998 it used a near 

shore eddy and occasionally moved up into a side channel riffle, remain there for 20 

minutes or more, and finally return to the eddy. On 15 July 1998, fish 40.051 moved 0.10 

miles upstream into a side channel on river left. It repeated the previous behavior of 

using an eddy, moving up into a riffle and subsequently returning to the eddy. Eddy 

depths (two points) were 0.70 and 0.98 m, while riffle depths (two points) were 0.55 and 

0.46 m. Due to poor water clarity no visual observation of the fish was possible. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 54 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 29. Habitat use as a percent of time monitored during the spawning period 

1998. 

Habitat use as percent of time monitored for all radio implanted Colorado pikeminnow in the San Juan River 

during the 1998 spawning period

0

10

20

30

40

50

60

70

80

90

100

Pool Edge Pool Eddy Sand Shoal/Run Run Run/Riffle Riffle

Habitat Type

Percent of Time

Habitat use as percent of time monitored for individual radio implanted Colorado pikeminnow in the San Juan 

River during the 1998 spawning period

0

10

20

30

40

50

60

70

80

90

100

Pool Edge Pool Eddy Sand Shoal/Run Run Run/Riffle Riffle

Habitat Type

Percent of Time

40.020

40.130

40.110

40.780

40.040

40.051
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 55 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 30. Habitat usage and habitat availability as a percent of total during the 

spawning period, 1998. 

Habitat usage (time monitored) and availability (total habitat area) for Colorado pikeminnow in the San Juan 

River, Spawn 1998

0

10

20

30

40

50

60

70

80

90

100

Pool Edge Pool Eddy Sand

Shoal/Run

Run Run/Riffle Riffle

Habitat Type

Percent of Total

Total Habitat Area

Time Monitored
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 56 

Miller Ecological Consultants, Inc. January 31, 2000 

Figure 31. Suspected spawning location 1998. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 57 

Miller Ecological Consultants, Inc. January 31, 2000 

DISCUSSION 

Radio telemetry studies on Colorado pikeminnow provided seasonal habitat use, river 

reach use, and spawning behavior for San Juan River fish. These studies also identified 

possible spawning areas. The majority of wild Colorado pikeminnow contacts were 

between RM 120.0 and RM 142.0. Only one fish was located outside of this range. 

Ryden and Ahlm (1996) also found Colorado pikeminnow to be concentrated within this 

section of the San Juan River. Three of the stocked Colorado pikeminnow were also 

found in this area, although all three of the transmitters were eventually recovered. It is 

unknown whether the fish expelled the transmitters or died. 

There was a high loss of transmitters from stocked fish due to mortality or transmitter 

expulsion. High rates of mortality and transmitter expulsion have also been documented 

for other fish species (Summerfelt and Mosier 1984; Chisholm and Hubert 1985; Ryden 

1999). All three of these studies used hatchery raised fish. During the 1993 and 1994 

monitoring of wild fish neither transmitter expulsion or mortality occurred. Miller and 

Rees (1997) had similar success in transmitter retention and low mortality with wild 

Colorado pikeminnow in the Yampa River, Colorado. Wild Colorado pikeminnow may 

be able to endure the required surgery and placement of a transmitter in the abdominal 

cavity better than hatchery raised individuals. 

Generally, stocked Colorado pikeminnow did not behave like the wild fish monitored in 

1993 and 1994. Only the stocked Colorado pikeminnow 40.051 exhibited behaviors and 

habitat use similar to a wild fish. After release, only two (40.040 and 40.051) stocked 

Colorado pikeminnow exhibited any upstream downstream movement. These fish only 

moved upstream a short distance (0.3 and 0.5 mi, respectively). All other monitored fish 

only displayed downstream movement, which was probably the result of poor health of 

the fish. Tyus and McAda (1984) noted a steady downstream movement associated with 

Colorado pikeminnow known to be in poor condition. At the conclusion of the intensive 

monitoring period in July 1998 only three of the fifteen stocked pikeminnow were alive 

and carrying transmitters. During a September 1998 survey, only one pikeminnow could 

be located by U.S. Fish and Wildlife Service (Grand Junction, CO) personnel. 

Studies on other upper basin rivers have found that Colorado pikeminnow habitat use 

varies seasonally (Holden and Wick 1982; Wick et al. 1983; Tyus and McAda 1984; 

Osmundson and Kaeding 1991; Osmundson et al. 1995). The results of this study further 

substantiate those previous findings. Habitat use also varies between river systems (Tyus 

and McAda 1984). Not only are the river systems unique but habitat type designations 

are often subjective decisions made by researchers. This creates some difficulty in 

comparing specific habitat type usage between other river systems and other studies. 

During the pre-spawn period, Colorado pikeminnow use predominately slower velocity 

habitats such as runs, eddies, undercut runs, slackwaters, and edge pools. Four of seven 

radio implanted wild Colorado pikeminnow, including fish 40.030 in both 1993 and 

1994, used the area around RM 122.6 (Mancos River mouth). Ryden and Ahlm (1996) 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 58 

Miller Ecological Consultants, Inc. January 31, 2000 

also documented Colorado pikeminnow congregating near the mouth of the Mancos 

River before the spawning period. Many authors have reported high use of backwater 

habitats during run-off flows in other upper basin tributaries (Osmundson and Kaeding 

1989; Tyus 1990; Wick et al. 1983). In the San Juan River, the pre-spawn period usually 

corresponds to the ascending limb of spring runoff. The lack of backwater use by 

Colorado pikeminnow in the San Juan River may simply be a function of lack of habitat. 

The channel morphology of the San Juan River does not allow extensive formation of 

backwaters. Bliesner and Lamarra (1995) reported that during June high flows the 

amount of backwater, embayment, pool, and eddy habitat was the lowest compared to 

other periods. The area around the Mancos River mouth functions much as a backwater 

habitat, offering Colorado pikeminnow refuge from high velocities and low temperatures 

in the main channel. 

Three potential spawning sites were identified, two in the "Mixer" (RM 131.1, RM 

132.0) and one at Hatch Trading Post (RM 168.4). Telemetry and visual observation data 

from 1993 and 1994 indicate possible spawning aggregations of fish at RM 132.0 and 

RM 131.1. Repeated use of these sites suggests that Colorado pikeminnow in the San 

Juan River, like pikeminnow in the Green, Yampa and Colorado Rivers, show fidelity 

toward specific spawning sites. Three wild Colorado pikeminnow were documented 

using both potential spawning sites in the "Mixer" during a single spawning period. The 

three fish (one in 1993, one in 1994, and one in both years) were present at the RM 132.0 

site for 2 or 3 days and subsequently moved down to the RM 131.1. This repeated, 

ordered use of spawning the potential spawning sites at RM 131.1 and RM 132.0 is 

possibly an unique feature of this population. A repeated, ordered use of spawning sites 

has not been reported for any other Colorado pikeminnow populations. This behavior 

could be in response to the effects of decreasing flows on the sites. The upstream site 

may have better habitat at higher flows, and conversely, the downstream site may 

function better at lower flows. The third potential spawning location at RM 168.4 was 

located during the 1998 monitoring of stocked pikeminnow. The island complex at RM 

168.4 was physically similar to physical characteristics. This site was previously 

identified in habitats surveys as having the potential to be a spawning location. While no 

other radio implanted pikeminnow used the area during the study, there may have been 

stocked or wild fish without radio transmitters present, which may have caused the one 

implanted fish to remain in the area. The stocked pikeminnow's behavior was very 

similar to the spawning behaviors exhibited by wild fish in 1993 and 1994. Larval fish 

sampling was conducted on 22 July 1998 by the University of New Mexico 

(Albuquerque, NM) downstream of the RM 168.4 area. Marsh (1985) the incubation 

period for pikeminnow eggs held at 20o

C was 3-5 days. The larval fish sampling may 

have been to late to capture larval pikeminnow because the possible spawning occurred 

on 9 July and 16 July 1998. 

This site is well upstream of the "Mixer" area. Stocked, hatchery-reared Colorado 

pikeminnow did not migrate downstream to either of the potential spawning sites in the 

"Mixer". The upstream (RM 178.8) stocking location, non-imprinting of stocked fish, as 

well as poor health may have contributed to the lack of movement to the downstream 

spawning sites. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 59 

Miller Ecological Consultants, Inc. January 31, 2000 

During the spawning period, higher velocity habitats such as riffles, riffle/chutes and 

chutes are utilized. The use of these habitats is likely due to the velocities and substrates 

required for successful spawning. General spawning behaviors of Colorado pikeminnow 

in the San Juan River appear to include activities such as: the fish moving from low 

velocity habitats, like eddies, into the higher velocity habitats run/riffle, riffle, and chute 

and finally move back into the resting habitat. This observed behavior is similar to 

Colorado pikeminnow spawning behaviors reported by other researchers (Miller et al. 

1982). Colorado pikeminnow used run habitats as possible resting/foraging areas during 

the spawning time. 

After the post-spawn dispersal, Colorado pikeminnow move into simpler habitat 

complexes. The use of run habitat is much more widespread than in the previous prespawn and spawning periods. This behavior has been noted in other upper basin 

populations (Osmundson et al. 1995). Fall and winter behavior seemed to be similar for 

Colorado pikeminnow as shown in other rivers, with fish mainly using main channel 

pools or runs during these periods (Osmundson et al. 1995). Activity tended to peak 

during the middle of the day. This behavior is similar to that exhibited by razorback 

suckers in the San Juan River (Ryden, 1999) 

The fragmentation of populations due to the creation of impassable dams and diversions 

is one reason the Colorado pikeminnow has declined from historic levels. The San Juan 

River has many diversions used to divert river water for irrigation and municipal 

purposes. This study documented the first confirmed movement of a Colorado 

pikeminnow upstream through Cudei diversion. This event showed that Cudei diversion 

is passable by Colorado pikeminnow. The movement of a Colorado pikeminnow through 

Cudei diversion occurred during the 1994 study year, when fish 40.940 was located just 

upstream of the earth and rock diversion structure on 27 July 1994. Discharge at the 

USGS Shiprock gage ranged from 1920 cfs on 17 July 1994 (last contact below Cudei 

diversion) to 820 cfs on 27 July 1994 (first contact above Cudei diversion). 

The methodology of Osmundson et al. (1995) and Ryden (1999) was not used for 

determined habitat selectivity because there can be some bias associated with those 

calculations. The "aggregate percent method" (Swanson et al. 1974) may offset a lot of 

the bias associated with using small data sets, but when data sets are extremely low, bias 

may still become evident. The influence of one pikeminnow's habitat use can skew the 

selectivity to that particular habitat. For example, one pikeminnow (40.100) spent nearly 

60% of its time monitored in backwater habitats during the spawning period. But that 

fish was only monitored for three hours of one day during that period. Calculating 

selectivity using the method of Osmundson et al. (1995) and Ryden (1999) indicated that 

backwater habitat was the most preferred habitat, which does not appear to be the case by 

visual examination of usage versus availability. Their methodology would have been 

credible had more monitored fish and contact data been available. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 60 

Miller Ecological Consultants, Inc. January 31, 2000 

CONCLUSIONS 

• Habitat use during the suspected spawning period is concentrated in areas of very 

diverse habitats with numerous habitat types present. These areas are located in 

conjunction with complex bar and island systems that have many different habitat 

types in a small local area. Main features present at the suspected spawning areas 

include eddies or pools as resting habitat located in close proximity to chutes or steep 

riffles with very loose cobble substrate. 

• Two (RM 131.1 and RM 132.0) potential spawning locations were identified for wild 

fish and one (RM 168.4) for stocked Colorado pikeminnow. One of those locations 

had a documented visual sighting of two paired Colorado pikeminnow, male and 

female, that were implanted with radio transmitters. The potential sites at RM 131.1 

and RM 132.0 were used during both 1993 and 1994 and were used in the same 

sequence each year. The uppermost site at RM 132.0 was used first followed by the 

RM 131.1 site. 

• The use of various habitat types is related to the flow regime as well as life history 

traits of the Colorado pikeminnow. The pre-spawn time period is during the 

ascending limb of runoff, which floods local embayments, tributary mouths and 

secondary channels that provide Colorado pikeminnow staging habitat. During the 

descending limb of runoff, the habitat complexes for spawning become available, 

provided sufficient cleaning is done during the peak runoff. These habitats appear to 

be used for varying lengths of time depending on the suitability of velocities in 

chute/riffle habitats and the embeddedness of cobble substrate. 

• Maintaining habitat richness is an important component of maintaining the potential 

spawning habitats for the fish. Highest habitat use during the spawning periods was 

in the area of highest habitat richness. Flows that develop and maintain complex 

habitats over the long term should provide the physical characteristics necessary to 

provide the spawning habitat. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 61 

Miller Ecological Consultants, Inc. January 31, 2000 

ACKNOWLEDGEMENTS 

The authors would like to thank the following individuals and organizations, without 

whom this project would not have been possible. Funding for this study was provided by 

the Southern Ute Indian Tribe. The Bureau of Indian Affairs (Farmington, NM) was 

extremely helpful in providing shuttles as well as river access information.. The U.S. 

Fish and Wildlife Service (Grand Junction, CO) was lead on capturing all wild 

pikeminnow and implantation of radio transmitters. They also provided all stocked 

Colorado pikeminnow. Dale Ryden (USFWS) and others provided additional radio 

contact information for both stocked and wild pikeminnow. Ray Smith (BIA) created the 

habitat maps of pikeminnow contact locations in 1993 and 1994, while Ralph Mitchell 

(Ecosystems Research Institute, Logan, UT) did the maps in 1998. University of New 

Mexico (Albuquerque, NM) conducted larval fish sampling during the 1998 study year. 

We would also like to thank the following individuals from Miller Ecological Consultants 

(Fort Collins, CO) who participated in the field data collection trips, Charlie Morris 

(Field Supervisor,1993 and 1994), Jim White (1993 and 1994), Matt Krakow (1998) and 

Dave Rees (Field Supervisor, 1998). We would also like to thank the San Juan River 

Biology Committee, researchers, and peer-review panel for comments on earlier versions 

of this paper. 
Colorado Pikeminnow Habitat Use in the San Juan River, New Mexico and Utah Page 62 

Miller Ecological Consultants, Inc. January 31, 2000 

LITERATURE CITED 

Bliesner, R. and V. Lamarra. 1995. San Juan River Seven Year Research Program. San 

Juan River Habitat Studies. 

Bliesner, R. and V. Lamarra. 1999. San Juan River Seven Year Research Program. San 

Juan River Habitat Studies. 

Chisholm, I.M. and W.A. Hubert. 1985. Expulsion of dummy transmitters by rainbow 

trout. Transactions of the American Fisheries Society 114(5):766-767 

Holden, P.B. and C.B. Stalnaker. 1975. Distribution and abundance of mainstream 

fishes of the middle and upper Colorado River basins, 1967-1973. Transactions of 

the American Fisheries Society 104(2):217-231. 

Holden, P.B. and E.J. Wick. 1982. Life history and prospects for recovery of Colorado 

squawfish. Pages 98-108 in Miller, W.H., H.M. Tyus, and C.A. Carlson, editors. 

Fishes of the upper Colorado River system: present and future. American Fisheries 

Society, Western Division, Bethesda, Maryland. 

Johnson, D.H. 1980. The comparison of usage and availability measurements for 

evaluating resource preference. Ecology 61(1):65-71. 

Marsh, P.C. 1985. Effect of incubation temperature on survival of embryos of native 

Colorado River fishes. Southwestern Naturalist 30(1):129-140. 

Miller, W.H., D. Archer, H.M. Tyus, and R.M. McNatt. 1982. Yampa River fishes 

study. Final Report. U.S. Fish and Wildlife Service, Salt Lake City, Utah. 

Miller, W.J. and D.E. Rees. 1997. Colorado squawfish habitat use and movement during 

summer low flow in the Yampa River upstream of Cross Mountain Canyon. Final 

Report prepared for Colorado River Water Conservation District by Miller Ecological 

Consultants, Fort Collins, Colorado. 

Minckley, W.L. 1991. Native fishes of the Grand Canyon region: An obituary? Pages 

124-177 in Colorado River ecology and dam management. Washington, DC: 

National Academy Press. 

Osmundson, D.B. and L.R. Kaeding. 1989. Studies of Colorado squawfish and 

razorback sucker use of the "15-Mile Reach" of the upper Colorado River as part of 

conservation measures for the Green Mountain and Ruedi Reservoir water sales. 

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