SEASONAL ABUNDANCE, DISTRIBUTION,

AND POPULATION SIZE-STRUCTURE

OF FISHES IN SAN JUAN RIVER

SECONDARY CHANNELS;

1991 – 1997

David L. Propst and Amber L. Hobbes

Conservation Services Division

New Mexico Department of Game and Fish

Santa Fe, New Mexico

21 February 2000

SAN JUAN RECOVERY IMPLEMENTATION PROGRAM
EXECUTIVE SUMMARY

Between Shiprock, New Mexico and Chinle Creek, Utah, secondary channels are

a common feature of the San Juan River. Prior to initiation of the San Juan River SevenYear Research Program no studies specific to secondary channels had been conducted.

As part of the Seven-Year Research Program, research was initiated in 1991 to

characterize the fish fauna of San Juan River secondary channels, to discern seasonal-use

patterns of secondary channels by common fishes, to evaluate the effects of different flow

regimes on common fish species, and to characterize use of secondary channels by rare

fishes (roundtail chub, Colorado pikeminnow, and razorback sucker). Summer

inventories of secondary channels were initiated in 1991 and spring and autumn

inventories began in 1993. Research on secondary channels occurred in Geomorphic

Reaches 5, 4, and 3. Flows of 1500 cfs wetted most secondary channels and flows of

2500 cfs inundated almost all.

During spring, when flows were at least 2500 cfs, native flannelmouth sucker and

bluehead sucker and nonnative common carp and channel catfish numerically dominated

secondary channel fish collections. Small-bodied fishes such as native speckled dace and

nonnative red shiner and fathead minnow, were uncommon in spring collections. The

sampling technique, raft-mounted electrofishing, was not an effective means of collecting

small-bodied fishes. Abundance of flannelmouth sucker was less in 1997 than 1993 in all

reaches, but the decline was most apparent in Reach 4. Although abundance evidently

declined, mean total length, mean biomass, size-structure, and age-structure were not

markedly different in 1997 from that found in 1993. Bluehead sucker abundance was

least in 1995 in all Reaches and second greatest in 1997. Neither mean total length nor

biomass was appreciably different in 1997 than that found in 1993. In Reach 5, where

bluehead was typically most common, there was little change in size- or age-structure,

but in Reach 3 (where least common), there was considerable variation in these

population attributes among years. In all years in all Reaches, most common carp

captured were > 400 mm total length and thus adults. Common carp were slightly more

common in all reaches in 1997 than 1993, but mean total length and biomass did not

change. Abundance of channel catfish in Reaches 5 and 4 was slightly greater in 1997

than 1993, but was considerably greater in Reach 3 in 1997 than 1993. Total biomass,

however, was greater in 1993 than 1997 in Reaches 5 and 4. In Reach 3, total biomass

was least in 1993, but from1995 through 1997 did not change. Mean total length and

biomass declined from 1993 through 1997 in all reaches, but most dramatically in

Reaches 5 and 4. Changes in size- and age-structure of channel catfish were also noted;

smaller and younger fish were more common in collections in 1997 than 1993. In most

years (1994 through 1997) and Reaches flannelmouth sucker was slightly more abundant

in secondary channels than the primary channel. Bluehead sucker, however, tended to be

more common in the primary than secondary channels. In Reach 5, common carp were

more common in secondary channels than primary channel in all years and usually so in
ii

Reach 3. In Reach 4, there was no pattern. In Reaches 5 and 4, channel catfish

abundance was usually slightly greater in secondary channels than primary; in Reach 3 in

1995 and 1996 secondary channel abundance was considerably greater. One adult

Colorado pikeminnow was collected in a secondary channel in 1994. Razorback suckers

(likely stocked individuals) were found in secondary channels in 1995, 1996, and 1997.

Fish species common during spring inventories were usually uncommon or rare in

summer collections; most individuals of these species found in summer were young-ofyear or juveniles. During summer, abundance of fishes in secondary channels varied

considerably from year to year (1991 through 1997). Greatest abundance (Reaches

combined) occurred in 1993 and 1995 and least in 1997. Shannon-Wiener Diversity was

slightly less in 1997 than 1993. In Reach 5, red shiner was the most abundant species in

four years, fathead minnow in two, and bluehead sucker in one. Bluehead sucker (almost

all Age 0) summer abundance was greatest in 1995, a high spring runoff year. Speckled

dace was usually second- or third-most abundant species. Total fish abundance peaked in

1993 and was least in 1997; Shannon-Wiener Diversity was least in 1991 and changed

little from 1993 through 1997. No attribute of spring runoff was significantly related to

summer abundance of red shiner, fathead minnow, speckled dace, flannelmouth sucker or

channel catfish in Reach 5. Summer abundance of bluehead sucker was, however,

significantly and positively related to four of five attributes of spring runoff. Red shiner

was the most abundant species in Reach 4 in all years except 1996 when fathead minnow

was most abundant. Speckled dace was the second-most common species in five of

seven years; it was third-most common in 1994 and sixth-most common in 1996 (a low

spring runoff and summer flow year). Total abundance of fishes in Reach 4 peaked in

1993 and 1995 and was least in 1997. Shannon-Wiener Diversity Index declined from

1991 through 1997. Summer abundance of red shiner was fairly strongly, but not

significantly, positively related to most attributes of spring discharge in Reach 4.

Speckled dace abundance was significantly and positively related to four of five spring

runoff attributes. Flannelmouth sucker abundance was strongly, but not significantly,

related to days discharge > 5000 cfs and bluehead sucker abundance was most strongly

related to days discharge > 8000 cfs. Abundance of fathead minnow and channel catfish

was not related to any attribute of spring runoff. Red shiner was the most abundant

species in Reach 3 in all years except 1995 and 1996, when fathead minnow was most

abundant. Speckled dace was the second-most abundant species in all years except 1994

and 1996; its abundance was least in 1996, a low spring runoff and summer flow year.

Similar to Reach 4, total abundance peaked in Reach 3 in 1993 and 1995 (high spring

runoff years) and was least in 1997. Shannon-Wiener Diversity declined from 1991

through 1997. Summer abundance of red shiner was significantly, and positively, related

to days spring discharge >5000 cfs. Speckled dace and bluehead sucker abundance was

significantly, and positively, related to four of five spring runoff attributes. Summer

abundance of flannelmouth sucker was most strongly related to days discharge > 5000

cfs. No attribute of spring runoff was related to summer abundance of fathead minnow or

channel catfish. Neither Colorado pikeminnow nor razorback sucker was collected in

secondary channels during summer.
iii

Fish species common in summer collections were also common in autumn

collections. Plains killifish and western mosquitofish were generally more common in

autumn than summer collections. Between 1993 and 1995 total autumn abundance of

fishes (Reaches combined) did not change appreciably. Total abundance in 1996 (a low

spring runoff and summer flow year) was substantially less than in preceding years. In

1997, total abundance was the lowest of the study. From 1993 through 1996, ShannonWiener Diversity declined but increased in 1997 to the second-highest value of the study.

Total abundance of fishes in Reach 5 peaked in 1993 and 1996 and was lowest in 1997.

Between 1993 and 1995, Shannon-Wiener Diversity changed little, declince in 1996, and

was highest in 1997. Red shiner was the most abundant species in autumn collections in

Reach 5 in all years, except 1997 (high spring runoff and summer flows) when speckled

dace was most abundant. Fathead minnow and specked dace were usually the second- or

third-most common species. Flannelmouth sucker and bluehead sucker were rare in

1996, a low spring runoff and summer flow year. Colorado pikeminnow, likely stocked

individuals, was the third-most common species in Reach 5 secondary channels in 1997.

Roundtail chub was found only in 1997. No attribute of summer discharge was

significantly related to any commonly-collected species, except the positive relationship

between autumn abundance of western mosquitofish and days discharge < 500 cfs.

Attributes indicative of low summer flow were negatively related to autumn abundance

of native species. Mean summer discharge was negatively related to red shiner

abundance. Between 1993 and 1996, total abundance of fishes in Reach 4 declined

slightly, but abundance in 1997 was considerably less than in preceding years. ShannonWiener Diversity changed little from 1993 through 1996 and increased slightly in 1997.

Red shiner was the most abundant species in all years and fathead minnow or speckled

dace were second-most abundant in all years. Neither flannelmouth sucker nor bluehead

sucker was common during autumn in Reach 4 secondary channels and bluehead sucker

was absent in 1996. Colorado pikeminnow and roundtail chub were found in Reach 4

secondary channels in 1997, but not in preceding years. Elevated summer flows were

negatively correlated with summer abundance of nonnative red shiner, fathead minnow,

channel catfish (significantly) and western mosquitofish; fathead minnow abundance was

significantly, and positively, related to days summer discharge < 500 cfs. Autumn

abundance of native flannelmouth sucker, bluehead sucker, and speckled dace were

negatively, but not significantly, related to days summer discharge < 500 cfs. Total

abundance of fishes in Reach 3 peaked in 1995 and was least in 1997. Shann0n-Wiener

Diversity declined from 1993 through 1996, but increased in 1997. Red shiner was

always the most abundant species in Reach 3 and fathead minnow or speckled dace were

always second- or third-most common, except in 1993 when channel catfish was thirdmost common. Flannelmouth sucker was uncommon in all years and bluehead sucker

was absent in 1993. Colorado pikeminnow and roundtail chub were found in 1997. No

attribute of summer discharge was significantly related to autumn abundance of any

commonly collected species. Speckled dace abundance was negatively related to days

discharge < 500 cfs.

In most years (1993 through 1997), summer abundance of fishes was usually

greater in summer than autumn; in Reaches 5 and 4 differences were substantial.

Between summer and autumn (years combined) abundance differences were typically
iv

significant. For red shiner, seasonal abundance differences were not significant, but

differences among years were. Seasonal, reach, and annual comparisons did not yield

significant differences for fathead minnow. Seasonal and annual (reaches combined)

differences in speckled dace abundance were significant as was that among years

(seasons combined). Flannelmouth sucker abundance relationships were similar to those

for speckled dace. Only annual comparisons (reaches combined) of bluehead sucker

abundance yielded significant differences. Abundance of western mosquitofish was

significantly different among years (reaches or seasons combined). Abundance of red

shiner, fathead minnow, flannelmouth sucker, and speckled dace generally declined (both

summer and autumn) from 1993 through 1997. Abundance of bluehead sucker and

western mosquitofish were variable with no evident pattern.

Total species abundance was not a good predictor of total autumn abundance.

However, summer abundance of fathead minnow, speckled dace, flannelmouth sucker,

bluehead sucker, and western mosquitofish was a good predictor of their autumn

abundance. Autumn abundance of red shiner and channel catfish was not related to their

summer abundance.

An array of biotic and abiotic factors influenced the seasonal abundance of fishes

in secondary channels of the San Juan River. Elevated flows during spring runoff made

most secondary channels accessible to all fish residents of the river, particularly largebodied individuals. Large-bodied fishes may enter secondary channels to forage, spawn,

and avoid higher velocity water of the primary channel. Habitat preferences and life

history strategies likely influenced the longitudinal abundance distribution of largebodied fishes in secondary channels. The rarity of Colorado pikeminnow and razorback

sucker in secondary channels during spring was likely more a consequence of their

overall rarity rather than avoidance of secondary channels. During summer and autumn,

fish assemblages of secondary channels are numerically dominated by small-bodied

fishes and young of large-bodied fishes. Among these species, nonnative fishes were

typically the most abundant. There was generally a positive relationship between

summer abundance of several common species, including red shiner, and elevated spring

discharge. Although a natural flow regime was mimicked, spring flows during the study

were never as high as occurred in some years prior to completion of Navajo Dam. Thus,

elevated spring flows evidently were not sufficient to displace some nonnative species, as

documented in several other southwestern systems having a natural hydrograph.

Elevated flows during summer, however, generally had negative effects on autumn

abundance of nonnative fishes and positive or no effect on native fishes. Abundance of

all commonly collected species was less in 1997 than in 1993. The low spring runoff and

low summer and autumn flows of 1996 depressed the abundance of all species, native

and nonnative. Abundance of most increased slightly in 1997 with higher spring runoff

and higher summer and autumn flows, but not to levels found prior to 1996. Although

the abundance of most species changed with mimicry of a natural hydrograph, it is likely

changes will continue as flows continue to mediate species relationships and interactions

and habitats change in response to a mimicked natural hydrograph.
v

TABLE OF CONTENTS

Executive Summary............................................................................i

Table of Contents...............................................................................v

List of Tables..................................................................................vii

List of Figures.................................................................................xiv

Seasonal Abundance, Distribution, and Size-Structure of

Fishes in San Juan River Secondary Channels, 1991-1997.....................1

Introduction...................................................................2

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

Fish Assemblages of San Juan River Secondary Channels

During Spring, 1993-1997.............................................................5

Introduction.....................................................................6

Study Area......................................................................6

Methods.........................................................................9

Results.........................................................................10

Water Quality........................................................11

Spring Secondary Channel Fish Assemblages...................11

Population Dynamics...............................................21

Flannelmouth Sucker......................................21

Bluehead Sucker...........................................27

Common Carp..............................................36

Channel Catfish.............................................42

Within Reach Species BiomassComparisons....................53

Secondary and Primary Channel Comparisons...................55

Rare Fish Occurrence in Secondary Channels..................58

Fish Assemblages of San Juan River Secondary Channels

During Summer, 1991 – 1997.......................................................66

Introduction..................................................................67

Study Area...................................................................67

Methods......................................................................69

Results........................................................................71

Water Quality.......................................................71

Summer Fish Assemblages.......................................73

Geomorphic Reach 5.....................................78

Geomorphic Reach 4......................................86

 Geomorphic Reach 3......................................92

Inter-Reach Comparisons................................97
vi

Fish Assemblages of San Juan River Secondary Channels

During Autumn, 1993 – 1997..................................................102

Introduction........................................................................103

Methods...........................................................................103

Results.............................................................................104

Water Quality............................................................106

Autumn Fish Assemblages.............................................106

Geomorphic Reach 5.......................................... 112

Geomorphic Reach 4.......................................... 122

Geomorphic Reach 3.......................................... 130

Inter-Reach Comparisons..................................... 138

Colorado Pikeminnow Capt................................. 138

Fish Assemblages of San Juan River Secondary Channels,

Seasonal Comparisons, 1993 – 1997.......................................... 141

Introduction....................................................................... 142

Methods........................................................................... 143

Results............................................................................. 143

Discussion................................................................................. 158

Conclusions and Management Implication.......................................... 172

Overall........................................................................... 173

Flannelmouth Sucker.......................................................... 173

Bluehead Sucker................................................................ 174

Common Carp.................................................................. 175

Channel Catfish................................................................. 175

Red Shiner....................................................................... 176

Fathead Minnow................................................................ 176

Speckled Dace................................................................... 177

Western Mosquitofish.......................................................... 177

Colorado Pikeminnow......................................................... 178

Razorback.Sucker.............................................................. 178

Roundtail Chub................................................................. 178

Other Nonnative Fishes....................................................... 178

Literature Cited.......................................................................... 179
vii

LIST OF TABLES

TABLE TITLE PAGE

1 Occurrence of fishes in San Juan River secondary 15

channels during spring, 1993 – 1997

2 Fish species collected in San Juan River secondary 16

Channels during spring inventories, 1993 – 1997

3 Number and abundance of fishes in San Juan River 18

secondary channels in Geomorphic Reach 5 during

spring, 1993 – 1997

4 Number and abundance of fishes in San Juan River 19

secondary channels in Geomorphic Reach 4 during

spring, 1993 – 1997

5 Number and abundance of fishes in San Juan River 20

secondary channels in Geomorphic Reach 3 during

spring, 1993 – 1997

6 Abundance of commonly collected fishes in San Juan 20

River secondary channels during spring, 1993 – 1997

7 Results of Kolomogorov-Smirov sequential comparisons 21

of size-structure of flannelmouth suckers in San Juan

River secondary channels, spring 1993 – 1997

8 Results of Kolomogorov-Smirov sequential comparisons 36

of size-structure of bluehead suckers in San Juan River

secondary channels, spring 1993 – 1997

9 Results of Kolomogorov-Smirov sequential comparisons 42

of size-structure of common carp in San Juan River

secondary channels, spring 1993 – 1997

10 Results of Kolomogorov-Smirov sequential comparisons 47

of size-structure of channel catfish in San Juan River

secondary channels, spring 1993 – 1997
viii

11 Post hoc comparisons from ANOVA of total biomass and 55

mean biomass of commonly collected fishes in San Juan

River secondary channels during spring inventories

12 Rare fishes captured in San Juan River secondary 59

channels during spring inventories, 1993-1997

13 Attributes of spring runoff, San Juan River, 71

1991-1997

14 Mean water quality parameters of San Juan River 73

primary and secondary channels during summer

inventories, 1991 - 1997

15 Occurrence of fishes in San Juan River secondary 76

channels during summer, 1991 – 1997

16 Fish species collected in San Juan River secondary 78

channels during summer inventories, 1991 – 1997

17 Number and abundance of fishes in San Juan River 80

secondary channels in Geomorphic Reach 5 during

summer, 1991 – 1997

18 Results of linear regression analysis of relationship 82

between spring runoff attributes and summer secondary

channel abundance of red shiner in Geomorphic Reach 5,

San Juan River, 1991 – 1997

19 Results of linear regression analysis of relationship 82

between spring runoff attributes and summer secondary

channel abundance of fathead minnow in Geomorphic

Reach 5, San Juan River, 1991 – 1997

20 Results of linear regression analysis of relationship 84

between spring runoff attributes and summer secondary

channel abundance of speckled dace in Geomorphic

Reach 5, San Juan River, 1991 – 1997

21 Results of linear regression analysis of relationship 84

between spring runoff attributes and summer secondary

channel abundance of flannelmouth sucker in Geomorphic

Reach 5, San Juan River, 1991 – 1997
ix

22 Results of linear regression analysis of relationship 84

between spring runoff attributes and summer secondary

channel abundance of bluehead sucker in Geomorphic

Reach 5, San Juan River, 1991 – 1997

23 Results of linear regression analysis of relationship 86

between spring runoff attributes and summer secondary

channel abundance of channel catfish in Geomorphic

Reach 5, San Juan River, 1991 – 1997

24 Number and abundance of fishes in San Juan River 88

secondary channels in Geomorphic Reach 4 during

summer, 1991 – 1997

25 Results of linear regression analysis of relationship 91

between spring runoff attributes and summer secondary

channel abundance of red shiner in Geomorphic

Reach 4, San Juan River, 1991 – 1997

26 Results of linear regression analysis of relationship 91

between spring runoff attributes and summer secondary

channel abundance of fathead minnow in Geomorphic

Reach 4, San Juan River, 1991 – 1997

27 Results of linear regression analysis of relationship 91

between spring runoff attributes and summer secondary

channel abundance of speckled dace in Geomorphic

Reach 4, San Juan River, 1991 – 1997

28 Results of linear regression analysis of relationship 91

between spring runoff attributes and summer secondary

channel abundance of flannelmouth sucker in Geomorphic

Reach 4, San Juan River, 1991 – 1997

29 Results of linear regression analysis of relationship 92

between spring runoff attributes and summer secondary

channel abundance of bluehead sucker in Geomorphic

Reach 4, San Juan River, 1991 – 1997

30 Results of linear regression analysis of relationship 92

between spring runoff attributes and summer secondary

channel abundance of channel catfish in Geomorphic

Reach 4, San Juan River, 1991 – 1997
x

31 Number and abundance of fishes in San Juan River 95

secondary channels in Geomorphic Reach 3 during

summer, 1991-1997

32 Results of linear regression analysis of relationship 96

between spring runoff attributes and summer secondary

channel abundance of red shiner in Geomorphic

Reach 3, San Juan River, 1991 – 1997

33 Results of linear regression analysis of relationship 96

between spring runoff attributes and summer secondary

channel abundance of fathead minnow in Geomorphic

Reach 3, San Juan River, 1991 – 1997

34 Results of linear regression analysis of relationship 96

between spring runoff attributes and summer secondary

channel abundance of speckled dace in Geomorphic

Reach 3, San Juan River, 1991 – 1997

35 Results of linear regression analysis of relationship 97

between spring runoff attributes and summer secondary

channel abundance of flannelmouth sucker in Geomorphic

Reach 3, San Juan River, 1991 – 1997

36 Results of linear regression analysis of relationship 97

between spring runoff attributes and summer secondary

channel abundance of bluehead sucker in Geomorphic

Reach 3, San Juan River, 1991 – 1997

37 Results of linear regression analysis of relationship 97

between spring runoff attributes and summer secondary

channel abundance of channel catfish in Geomorphic

Reach 3, San Juan River, 1991 – 1997

38 Attributes of summer discharge, San Juan River, 1993- 104

1997

39 Mean values of water quality parameters of San Juan 106

River secondary and primary channels during autumn

inventories, 1993 – 1997

40 Occurrence of fishes in San Juan River secondary 110

channels during autumn, 1993 – 1997
xi

41 Fishes collected in San Juan River secondary channels 112

during autumn inventories, 1993 – 1997

42 Number and abundance of fishes in San Juan River 114

secondary channels in Geomorphic Reach 5 during

autumn, 1993 – 1997

43 Results of linear regression analysis of relationship 118

between summer discharge and autumn secondary

channel abundance of red shiner in Geomorphic Reach

5, San Juan River, 1993 – 1997

44 Results of linear regression analysis of relationship 118

between summer discharge and autumn secondary

channel abundance of fathead minnow in Geomorphic

Reach 5, San Juan River, 1993 – 1997

45 Results of linear regression analysis of relationship 120

between summer discharge and autumn secondary

channel abundance of speckled dace in Geomorphic

Reach 5, San Juan River, 1993 – 1997

46 Results of linear regression analysis of relationship 120

between summer discharge and autumn secondary

channel abundance of flannelmouth sucker in

Geomorphic Reach 5, San Juan River, 1993 – 1997

47 Results of linear regression analysis of relationship 121

between summer discharge and autumn secondary

channel abundance of bluehead sucker in Geomorphic

Reach 5, San Juan River, 1993 – 1997

48 Results of linear regression analysis of relationship 121

between summer discharge and autumn secondary

channel abundance of channel catfish in Geomorphic

Reach 5, San Juan River, 1993 – 1997

49 Results of linear regression analysis of relationship 121

between summer discharge and autumn secondary

channel abundance of western mosquitofish in

Geomorphic Reach 5, San Juan River, 1993 – 1997

50 Number and abundance of fishes in San Juan River 122

secondary channels in Geomorphic Reach 4 during

autumn, 1993 – 1997
xii

51 Results of linear regression analysis of relationship 124

between summer discharge and autumn secondary

channel abundance of red shiner in Geomorphic

Reach 4, San Juan River, 1993 – 1997

52 Results of linear regression analysis of relationship 128

between summer discharge and autumn secondary

channel abundance of fathead minnow in Geomorphic

Reach 4, San Juan River, 1993 – 1997

53 Results of linear regression analysis of relationship 128

between summer discharge and autumn secondary

channel abundance of speckled dace in Geomorphic

Reach 4, San Juan River, 1993 – 1997

54 Results of linear regression analysis of relationship 128

between summer discharge and autumn secondary

channel abundance of flannelmouth sucker in

Geomorphic Reach 4, San Juan River, 1993 – 1997

55 Results of linear regression analysis of relationship 129

between summer discharge and autumn secondary

channel abundance of bluehead sucker in

Geomorphic Reach 4, San Juan River, 1993 – 1997

56 Results of linear regression analysis of relationship 129

between summer discharge and autumn secondary

channel abundance of channel catfish in

Geomorphic Reach 4, San Juan River, 1993 – 1997

57 Results of linear regression analysis of relationship 130

between summer discharge and autumn secondary

channel abundance of western mosquitofish in

Geomorphic Reach 4, San Juan River, 1993 – 1997

58 Number and abundance of fishes in San Juan River 130

secondary channels in Geomorphic Reach 3 during

autumn, 1993 – 1997

59 Results of linear regression analysis of relationship 131

between summer discharge and autumn secondary

channel abundance of red shiner in Geomorphic

Reach 3, 1993 – 1997
xiii

60 Results of linear regression analysis of relationship 135

between summer discharge and autumn secondary

channel abundance of fathead minnow in Geomorphic

Reach 3, 1993 – 1997

61 Results of linear regression analysis of relationship 135

between summer discharge and autumn secondary

channel abundance of speckled dace in Geomorphic

Reach 3, 1993 – 1997

62 Results of linear regression analysis of relationship 137

between summer discharge and autumn secondary

channel abundance of flannelmouth sucker in

Geomorphic Reach 3, 1993 – 1997

63 Results of linear regression analysis of relationship 137

between summer discharge and autumn secondary

channel abundance of bluehead sucker in

Geomorphic Reach 3, 1993 – 1997

64 Results of linear regression analysis of relationship 137

between summer discharge and autumn secondary

channel abundance of channel catfish in

Geomorphic Reach 3, 1993 – 1997

65 Results of linear regression analysis of relationship 138

between summer discharge and autumn secondary

channel abundance of western mosquitofish in

Geomorphic Reach 3, 1993 – 1997

66 San Juan River secondary channel captures of 140

Colorado squawfish during autumn inventories,

1993 – 1997

67 Mean abundance, standard deviation, and coefficients 145

of variation of fish in San Juan River secondary

channels during summer and autumn, 1993-1997

68 Number of days discharge > 2,500 cfs during spring 164

runoff and non-runoff seasons for seven years preceding

Seven-Year study and seven years of study
xiv

LIST OF FIGURES

FIGURE TITLE PAGE

1 Study area for San Juan River secondary channel 7

fish assemblage studies, 1991 – 1997

2 Mean weekly discharge of San Juan River during 8

spring runoff, 1993 – 1997

3 Water temperature (°C) of San Juan River secondary 12

channels during spring inventories, 1993 – 1997

4 Dissolved oxygen (mg/l) of San Juan River secondary 13

channels during spring inventories, 1993 – 1997

5 Conductivity (μmho/cm) of San Juan River secondary 14

channels during spring inventories, 1993 – 1997

6 Abundance of fishes in San Juan River secondary 17

channels during spring inventories, 1993 – 1997

7 Size-structure of the flannelmouth sucker population 22

in Geomorphic Reach 5, San Juan River, 1993 - 1997

8 Age-structure of the flannelmouth sucker population 23

in Geomorphic Reach 5, San Juan River, 1993 – 1997

9 Abundance and mean total length of flannelmouth sucker 24

in San Juan River secondary channels during spring,

1993 – 1997

10 Age-structure of the flannelmouth sucker population in 25

Geomorphic Reach 4, San Juan River, 1993 – 1997

11 Size-structure of the flannelmouth sucker population in 26

Geomorphic Reach 3, San Juan River, 1993 – 1997

12 Age-structure of the flannelmouth sucker population in 28

Geomorphic Reach 3, San Juan River, 1993 – 1997

13 Biomass of flannelmouth sucker population in 29

San Juan River secondary channels during spring inventories,

1993 – 1997
xv

14 Size-structure of the bluehead sucker population in 30

Geomorphic Reach 5, San Juan River, 1993 – 1997

15 Age-structure of the bluehead sucker population in 31

Geomorphic Reach 5, San Juan River, 1993 – 1997

16 Abundance and mean total length of bluehead sucker 32

in San Juan River secondary channels during spring,

1993 – 1997

17 Size-structure of the bluehead sucker population in 33

Geomorphic Reach 4, San Juan River, 1993 - 1997

18 Age-structure of the bluehead sucker population in 34

Geomorphic Reach 4, San Juan River, 1993 - 1997

19 Size-structure of the bluehead sucker population in 35

Geomorphic Reach 3, San Juan River, 1993 – 1997

20 Age-structure of the bluehead sucker population in 37

Geomorphic Reach 3, San Juan River, 1993 – 1997

21 Total and mean biomass of bluehead sucker in San 38

Juan River secondary channels during spring inventories,

1993 – 1997

22 Size-structure of the common carp population in 39

Geomorphic Reach 5, San Juan River, 1993 – 1997

23 Abundance and mean total length of common carp in 40

San Juan River secondary channels during spring,

1993 – 1997

24 Size-structure of the common carp population in 41

Geomorphic Reach 4, San Juan River, 1993 – 1997

25 Size-structure of the common carp population in 43

Geomorphic Reach 3, San Juan River, 1993 – 1997

26 Total and mean biomass of common carp in San Juan 44

River secondary channels during spring inventories,

1993 – 1997

27 Size-structure of the channel catfish population in 45

Geomorphic Reach 5, San Juan River, 1993 – 1997
xvi

28 Abundance and mean total length of channel catfish in 46

San Juan River secondary channels during spring,

1993 – 1997

29 Age-structure of the channel catfish population in 48

Geomorphic Reach 5, San Juan River, 1993 – 1997

30 Size-structure of the channel catfish population in 49

Geomorphic Reach 4, San Juan River, 1993 – 1997

31 Age-structure of the channel catfish population in 50

Geomorphic Reach 4, San Juan River, 1993 – 1997

32 Size-structure of the channel catfish population in 51

Geomorphic Reach 3, San Juan River, 1993 – 1997

33 Age-structure of the channel catfish population in 52

Geomorphic Reach 3, San Juan River, 1993 – 1997

34 Biomass of channel catfish in San Juan River 54

secondary channels during spring inventories,

1993 – 1997

35 Mean biomass of flannelmouth sucker in primary 56

and secondary channels of the San Juan River, 1994 –

1997

36 Abundance of flannelmouth sucker in San Juan River 57

primary and secondary channels during spring

inventories, 1994 – 1997

37 Mean biomass of bluehead sucker in primary and 60

secondary channels of the San Juan River, 1994 – 1997

38 Abundance of bluehead sucker in San Juan River 61

primary and secondary channels during spring

inventories, 1994 – 1997

39 Mean biomass of common carp in primary and 62

secondary channels of the San Juan River, 1994 –

1997

40 Abundance of common carp in San Juan River 63

primary and secondary channels during spring

inventories, 1994 - 1997
xvii

41 Mean biomass of channel catfish in primary and 64

secondary channels of the San Juan River, 1993 –

1997

42 Abundance of channel catfish in San Juan River 65

primary and secondary channels during spring

inventories, 1994 – 1997

43 Mean weekly discharge of San Juan River, 1 July 68

through 31 October, 1991 – 1997

44 Water temperature (°C) of San Juan River secondary 72

and primary channels during summer inventories,

1991 – 1997

45 Dissolved oxygen (mg/l) of San Juan River secondary 74

and primary channels during summer inventories,

1991 – 1997

46 Specific conductance (μmho/cm) of San Juan River 75

secondary and primary channels during summer

inventories, 1991 – 1997

47 Relative abundance of commonly collected fish 77

species in San Juan River secondary channels

during summer, 1991-1997

48 Abundance of fishes and Shannon-Wiener Diversity 79

Index values of fish assemblages in San Juan River

secondary channels during summer, 1991 – 1997

49 Abundance of fishes and Shannon-Wiener Diversity 81

Index values of fish assemblages in Geomorphic

Reach 5 secondary channels, San Juan River, 1991 –

1997

50 Relative abundance of commonly collected fish 83

species in Geomorphic Reach 5, San Juan River,

1991 – 1997

51 Secondary channel abundance of red shiner, fathead 85

minnow, speckled dace, flannelmouth sucker,

bluehead sucker, and channel catfish versus

spring discharge attributes, Geomorphic Reach 5,

San Juan River, 1991 – 1997
xviii

52 Relative abundance of commonly collected fish species 87

Geomorphic Reach 4, San Juan River, 1991 – 1997

53 Abundance of fishes and Shannon-Wiener Diversity 89

Index values of fish assemblages in Geomorphic Reach

4 secondary channels, San Juan River, 1991 – 1997

54 Secondary channel abundance of red shiner, fathead 90

minnow, speckled dace, flannelmouth sucker, bluehead

sucker, and channel catfish versus spring discharge

attributes, Geomorphic Reach 4 San Juan River,

1991 – 1997

55 Relative abundance of commonly collected fish species in 93

Geomorphic Reach 3, San Juan River, 1991 – 1997

56 Abundance of fishes and Shannon-Wiener Diversity 94

Index values of fish assemblages in Geomorphic Reach

3 secondary channels, San Juan River, 1991 – 1997

57 Secondary channel abundance of red shiner, fathead 98

minnow, speckled dace, flannelmouth sucker, bluehead

sucker, and channel catfish versus spring discharge

attributes, Geomorphic Reach 3, San Juan River,

1991 – 1997

58 Shannon-Wiener Diversity Index values of fish 100

assemblages and abundance of fishes in San Juan River

secondary channels during summer, 1991 – 1997

59 Abundance of fishes and Shannon-Wiener Diversity 101

Index values of secondary channel fish assemblages for

commonly sampled San Juan River secondary channels

during summer, 1991 – 1997

60 Mean weekly discharge (cfs) of San Juan River 1 July 105

through 31 October, 1993 – 1997

61 Water temperature (°C) of San Juan River secondary and 107

primary channels during autumn inventories, 1993 –

1997

62 Dissolved oxygen (mg/l) of San Juan River secondary 108

and primary channels during autumn inventories, 1993 –

1997
xix

63 Conductivity (μmho/cm) of San Juan River secondary and 109

primary channels during autumn inventories, 1993 – 1997

64 Abundance of fishes and Shannon-Wiener Diversity 111

Index values of fish assemblages in San Juan River

secondary channels during autumn, 1993 – 1997

65 Relative abundance of commonly collected fish species 113

in San Juan River secondary channels during autumn

inventories, 1993 – 1197

66 Abundance of fishes and Shannon-Wiener Diversity 115

Index values of fish assemblages during autumn in

Geomorphic Reach 5, San Juan River, 1993 – 1997

67 Relative abundance of commonly collected fish species 116

in Geomorphic Reach 5, 1993 – 1997

68 Mean abundance (1993 – 1997) and coefficient of 117

variation (CV) in abundance of fish species commonly

collected during autumn in Geomorphic Reach 5, San

Juan River, 1993 – 1997

69 Autumn abundance of commonly collected fish species 119

in Geomorphic Reach 5 versus summer flow attributes,

San Juan River, 1993-1997

70 Abundance of fishes and Shannon-Wiener Diversity Index 123

values of fish assemblages during autumn in Geomorphic

Reach 4, San Juan River, 1993 – 1997

71 Mean abundance (1993 – 1997) and coefficient of variation 125

(CV) of fish species commonly collected during autumn in

Geomorphic Reach 4, San Juan River, 1993 – 1997

72 Relative abundance of commonly collected fish species in 126

Geomorphic Reach 4 during autumn, San Juan River, 1993 –

1997

73 Autumn abundance of fishes in Geomorphic Reach 4 127

versus attributes of summer discharge, San Juan River,

1993-1997
xx

74 Abundance of fishes and Shannon-Wiener Diversity Index 132

values for fish assemblages during autumn in Geomorphic

Reach 3, San Juan River, 1993 – 1997

75 Mean abundance (1993 – 1997) and coefficient of variation 133

(CV) of abundance of fish species commonly collected

during autumn in Geomorphic Reach 3, San Juan River,

1993 – 1997

76 Relative abundance of commonly collected fish species in 134

Geomorphic Reach 3 during autumn, San Juan River,

1993 – 1997

77 Autumn abundance of fishes in Geomorphic Reach 3 136

versus attributes of summer discharge, San Juan River,

1993-1997

78 Shannon-Wiener Diversity Index values of fish 139

assemblages in San Juan River secondary channels,

1993 – 1997

79 Abundance of fishes in San Juan River secondary 139

Channels, 1993 – 1997

80 Summer and autumn abundance of fishes in San 144

Juan River secondary channels, Geomorphic Reaches

5, 4 and 3, 1993 – 1997

81 Summer and autumn abundance (reaches combined) 146

of fishes in San Juan River secondary channels,

1993 – 1997

82 Total reach abundance (seasons combined) of fishes 146

in San Juan River secondary channels, 1993 – 1997

83 Summer and autumn abundance (reaches combined) of 147

red shiner in San Juan River secondary channels, 1993 –

1997

84 Reach abundance (seasons combined) of red shiner in 147

San Juan River secondary channels, 1993 – 1997

85 Summer and autumn abundance (reaches combined) 148

of fathead minnow in San Juan River secondary

channels, 1993 – 1997
xxi

86 Reach abundance (seasons combined) of fathead 148

minnow in San Juan River secondary channels,

1993 – 1997

87 Summer and autumn abundance (reaches combined) 150

of speckled dace in San Juan River secondary channels,

1993 – 1997

88 Reach abundance (seasons combined) of speckled dace 150

in San Juan River secondary channels, 1993 – 1997

89 Summer and autumn abundance (reaches combined) of 151

flannelmouth sucker in San Juan River secondary

channels, 1993 – 1997

90 Reach abundance (seasons combined) of flannelmouth 151

sucker in San Juan River secondary channels, 1993 –

1997

91 Summer and autumn abundance (reaches combined) of 152

bluehead sucker in San Juan River secondary channels,

1993 – 1997

92 Reach abundance (seasons combined) of bluehead 152

sucker in San Juan River secondary channels, 1993 –

1997

93 Summer and autumn abundance (reaches combined) 153

of western mosquitofish in San Juan River secondary

channels, 1993 – 1997

94 Reach abundance (seasons combined) of western 153

mosquitofish in San Juan River secondary channels,

1993 – 1997

95 Total summer versus total autumn abundance of fishes 154

in San Juan River secondary channels, 1993 – 1997

96 Summer versus autumn abundance of red shiner, 155

fathead minnow, and speckled dace in San Juan River

secondary channels, 1993 – 1997

97 Summer versus autumn abundance of flannelmouth 156

sucker, bluehead sucker, and western mosquitofish

in San Juan River secondary channels, 1993 – 1997
xxii

98 Summer versus autumn abundance of channel catfish 157

in San Juan River secondary channels, 1993 – 1997

99 Mean summer abundance of commonly collected fish 168

species in San Juan River secondary channels, 1993 – 

1997

100 Mean autumn abundance of commonly collected fish 171

species in San Juan River secondary channels, 1993 –

1997
SEASONAL ABUNDANCE, DISTRIBUTION,

 AND POPULATION SIZE-STRUCTURE

 OF FISHES IN SAN JUAN RIVER

SECONDARY CHANNELS,

1991 – 1997

David L. Propst and Amber L. Hobbes

Conservation Services Division

New Mexico Department of Game and Fish

Santa Fe, New Mexico
2

INTRODUCTION

For large portions of its course through northwestern New Mexico and across

southeastern Utah, the San Juan River is restricted to a single channel. The reach

between Shiprock, New Mexico and Chinle Creek, Utah is, however, characterized by

considerable braiding with much of the water in a primary channel and lesser amounts in

secondary channels. Some secondary channels carry water throughout the year,

regardless of discharge, but others are wetted mainly during spring runoff and following

summer storms. Secondary channels vary considerably in volume of water that passes

through each, their length, and structural complexity. As a result of constantly changing

physical attributes (particularly degree of inundation), the fish assemblages of secondary

channels may be expected to vary.

No historical ichthyofaunal inventories were made of the San Juan River in the

reach having extensive braiding (Shiprock to Chinle Creek), but the fish fauna consisted

of at least six warmwater species (Tyus et al., 1982; Platania, 1990). Two other native

San Juan River fishes (Colorado River cutthroat trout, Oncorhynchus clarki pleuriticus,

and mottled sculpin, Cottus bairdi) may have seasonally occurred in braided portions of

the river. Native fishes in the braided reach were three cyprinids (roundtail chub, Gila

robusta; Colorado pikeminnow, Ptychocheilus lucius; and speckled dace, Rhinichthys

osculus) and three catostomids (flannelmouth sucker, Catostomus latipinnis; bluehead

sucker, Catostomus discobolus; and razorback sucker, Xyrauchen texanus). Each of these

species presumably used habitats provided by secondary channels.

 Since settlement by Europeans of the San Juan basin, at least 19 nonnative fish

species have been collected in the San Juan River (Platania, 1990), and six (common

carp, Cyprinus carpio; red shiner, Cyprinella lutrensis; fathead minnow, Pimephales

promelas; channel catfish, Ictalurus punctatus; plains killifish, Fundulus zebrinus, and

western mosquitofish, Gambusia affinis) are seasonally common to abundant in the in

the San Juan River downstream of its confluence with the Animas River. Each of the

latter nonnative species is seasonally common in secondary channels and each may

negatively interact with native fishes. Interactions may be via predation (channel catfish,

red shiner, and western mosquitofish;), competition for habitat (fathead minnow and

plains killifish), or disturbance (common carp) (Gido and Propst, 1999; Brandenburg and

Gido, 1999; Brooks et al., 2000).

A key premise of the San Juan River Seven Year Research Program was that

mimicry of the natural hydrograph, including elevated spring flows, was essential to

recovery of federally protected Colorado pikeminnow and razorback sucker and

conservation of other native fish species in the San Juan River. This premise was based,

in part, on the hypothesis that a dynamic natural hydrograph with elevated spring flows

maintains essential habitats (e.g., spawning bars) for native fishes. The premise was also

based in the hypothesis that a natural hydrograph diminishes or suppresses the abundance

of nonnative fish species.
3

This study was undertaken to characterize the fish fauna of San Juan River

secondary channels, to discern seasonal-use patterns of secondary channels by common

fishes, to evaluate the effects of different flow regimes on common fish species, and to

characterize use of secondary channel habitats by rare fishes. Among the objectives of

the San Juan Recovery Implementation Program Long Range Plan, this study provides

information to achieve:

5.2.5. Determine and monitor habitat use of endangered and other native fishes.

5.3.1. Identify and characterize the historic and current fish species community

structure.

5.3.2. Determine the status and trends of the resident fish species.

5.3.3. Determine the life history of endangered and other native fish species and

relationships to all other resident fish species.

5.3.4. Characterize fish species community responses to different annual flow

regimes.

5.3.5. Identify limiting factors for the endangered and other native fishes.

5.4.1. Characterize distribution and abundance of nonnative fish species.

5.4.2. Identify and characterize habitats used by nonnative fish species and

effects on native fish species habitat use.

5.4.3. Characterize the response of nonnative fish species to varying flow

regimes and recommend flows that minimize or eliminate interactions

with native fish species.

5.7.2. Develop and maintain a standardized database for storage and retrieval of

biotic and abiotic data.

5.7.3. Review and revise research activities to further define needs of and threats

to endangered and other native fish species.

5.7.4. Evaluate and refine recovery actions, as necessary, to accomplish recovery

Goals.

STUDY AREA

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

km2

 in Colorado, Utah, Arizona, and New Mexico. 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 Navajo, Piedra, Los Pinos, Animas, LaPlata, 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 regulates downstream flows. The completion of Glen
4

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

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

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 confluence of the San

Juan River with Lake Powell and the confluence with Chinle Creek, about 20 km

downstream of Bluff, Utah, the river is canyon-bound and restricted to a single channel.

Upstream of Chinle Creek, the river is multi-channeled to varying degrees with highest

density of secondary channels occurring between Hogback Diversion, about 13 km east

of Shiprock, New Mexico, and Bluff, Utah. The reach of river between Navajo Dam and

Farmington, New Mexico is relatively stable with predominantly embedded cobble

substrate and few secondary channels. Below the confluence with Animas River, the

channels is less stable and more subject to floods from the unregulated Animas River.

Between Farmington and Shiprock cobble substrate becomes mixed with sand to an

increasing degree with distance downstream, resulting in decreasing channel stability.
FISH ASSEMBLAGES OF SAN JUAN RIVER

SECONDARY CHANNELS DURING SPRING

1993 – 1997
6

INTRODUCTION

During 1991 and 1992 spring ichthyofaunal inventories of the San Juan River between Shiprock and

Sand Island, no effort was made to segregate sampling of secondary channels from the overall sampling

effort. It was evident, however, there were substantial differences in the habitats provided by secondary and

primary channels. Many secondary channels were narrow, shallow, and shaded whereas the primary

channel was not shaded (except along some shorelines), often deep, and broad. The sampling protocol at

that time did not enable determination of differences, or lack, in species assemblages of secondary and

primary channels. Accordingly, in 1993 the adult sampling protocol was modified to segregate sampling of

primary and secondary channels. The New Mexico Department of Game and Fish assumed lead

responsibility for sampling secondary channels during spring ichthyofaunal surveys.

Objectives of the Secondary Channels Ichthyofaunal Inventory were:

1). Characterize the type of extent of secondary channels in the San Juan

River;

2). Characterize the faunal assemblages of secondary channels;

3). Determine seasonal use patterns of secondary channels by target species;

and

4). Relate habitat use and availability of secondary channels to flow levels.

This chapter addresses Objectives 1, 2 (in part), and 3 (in part) during spring.

STUDY AREA

Spring inventories of San Juan River secondary channels were conducted from near Hogback to

Chinle Creek (Figure 1). Attributes of some secondary channels during the spring were at least superficially

similar to those of the adjacent primary channel in that they were comparatively wide (>20 m), had a

mixture of general habitat types (e.g., runs, pools, and riffles), and moderately rapid water velocity (0.5 to

1.0 m/sec). Many secondary channels, however, were quite different in many attributes from the primary

channel. Secondary channels were often narrow with dense, overhanging vegetation (Russian olive and

tamarisk), mainly run habitat with pools around instream obstructions (root masses and boulders), and a few

shallow riffles. Water velocity was frequently less than that of the primary channel and undercut banks were

common. Average depths of most secondary channels were less than that of the primary channel and

maximum depths rarely were as great as depths commonly found in the primary channel. Substrates varied

among silt, sand, gravel, and cobble, with sand and cobble being the most common substrates. In lowgradient, shallow secondary channel reaches, silt was the predominant substrate. Near cliffs, large boulders

were often in the channel. Secondary channel terraces were typically vegetated (annuals and cottonwood

and salt cedar seedlings); during high flows these terraces were often inundated.

The mouths of secondary channels were typically narrow, steep gradient riffles, and surrounded by

large debris piles. Flow into some secondary channels was “controlled” by debris berms. After the initial

plunge, secondary channel gradient diminished, width increased, and water velocity slowed. The

debouchements of secondary channels were sometimes broad, shallow, and sand-bottomed but others were

8

narrow, deep cuts through floodplain terraces of mixed composition (typically sand and cobble).

Islands were present in some secondary channels.

At the time of spring inventories, most secondary channels had sufficient flow (minimum depth ca.

0.4 m) to enable passage with electrofishing rafts. Deposition of large woody debris, rocks, and sand during

flow recession periods choked the mouths of some secondary channels. Subsequent elevated flows

sometimes eroded the berms or, depending on flow volume and position of secondary channel mouth, added

to berms. Thus, some secondary channels that were sampled in one spring were impassable in a subsequent

year or years and were therefore not sampled.

During the five-year study, spring runoff varied considerably from a low in 1996 (peak never

exceeded 4000 cfs) to a high of about 11000 cfs in 1997 (Figure 2). Lowest flow during spring inventories

was in 1997 (about 1200 cfs) and the highest was in 1993 when discharge was about 6000 cfs.

Figure 2. Mean weekly discharge (cfs) of the San Juan River during spring runoff. 

 Horizonal lines with arrows indicate the dates of secondary channel 

 inventories each year. 

WEEK

1-5 MAR

6-10

11-15

16-20

21-25

26-31

1-5 APR

6-10

11-15

16-20

21-25

26-30

1-5 MAY

6-10

11-15

16-20

21-25

26-31

1-5 JUN

6-10

11-15

16-20

21-25

26-30

DISCHARGE (CFS)

0

2000

4000

6000

8000

10000

12000

1993 

1994 

1995 

1996 

1997 
9

METHODS

Initial identification of secondary channels was done by examination of aerial photographs (1:

12000) taken on 28 May 1988 by U.S. Bureau of Reclamation. Mean daily discharge at time of aerial

photography was 1610 cfs (Shiprock gage). The visual standard for classification as a secondary channel

was that in braided reaches, the channel with the greatest wetted width was the primary channel and all

others were secondary channels. It was assumed that the widest channel carried the greatest volume of

water; based on subsequent experience, this almost always the case. An arbitrary scheme was used to

classify secondary channels. Type I channel was < 1 km long and had > 25 and < 50 % of total discharge,

Type II was < 1 km long and had < 25 % of total discharge, Type III was > 1 km long and had > 25 and <

50 % of discharge, and Type IV was > 1 km long and had < 25 % of total discharge.

Sampling of San Juan River secondary channels occurred each May from 1993 through 1997.

Sampling was conducted in Geomorphic Reaches 5 (RM 154 through 131), 4 (RM 130 through RM 106),

and 3 (RM 105 through RM 68)(Bliesner and Lamarra, 2000). Channels < 100 meters long and carrying <

50% of the river’s discharge were not treated as secondary channels. Secondary channel flow volume was

visually estimated as a percent of total discharge. Sampling was conducted when flows were greater than

winter base flows (normally between 600 and 800 cfs) but less than the annual spring peak (usually > 5000

cfs). Peak spring runoff occurred about one month after spring sampling. Regardless of specific level,

flows were sufficient to allow passage of rafts with electrofishing gear (5000 watt generator, with bow

anode and stern cathode) through most San Juan River secondary channels between RM 154 and RM 68. In

secondary channels of sufficient width (about 4 m), the raft was positioned perpendicular (bow towards

shore) to the shore as the current carried it downstream. The particular shore sampled often changed within

a secondary channel because of instream obstructions and overhanging vegetation. In narrow channels (< 4

m), the raft was pointed downstream in mid-channel. The netter, on the bow deck, attempted to net all fish,

regardless of size or species, stunned by electrofishing gear. Electrical output was between 3 and 4 amps.

Captured fish were placed in a live well.

All fish captured were identified and counted. All specimens of commonly collected large-bodied

(common carp, flannelmouth sucker, bluehead sucker, and channel catfish) and rare fishes (roundtail chub,

Colorado pikeminnow, and razorback sucker) were weighed (+ 1 g if < 249 and + 5 g if > 250 mm TL), and

measured (+ 1 mm TL and SL) at the end of each sampled secondary channel. Native fishes were returned

to the river alive. Depending on other ongoing studies, nonnative fishes were returned alive to river,

retained as voucher specimens, sacrificed for food habits studies, or removed for nonnative suppression

studies. Elapsed time electrofishing (seconds) was recorded for each secondary channel. If a captured fish

had a Floy tag, the tag number and specimen TL, SL and weight were recorded.

San Juan River discharge data were obtained from the USGS Shiprock gage (# 09368000). Water

temperature (C°), dissolved oxygen (mg/l), conductivity (μmho/cm) were measured at the downstream end

of each sampled secondary channel. Notes on habitat, fish aggregations, and general conditions were

recorded for each sampled secondary channel. Although flow level determined, in part, which secondary

channels were sampled, the number sampled per Geomorphic Reach did not vary greatly from year to year.

Forty-four secondary channels were sampled in 1994, 1995, and 1996, 40 in 1993, and 36 in 1997. In

Geomorphic Reach 5, 9 to 12 secondary channels were sampled each year, 14 to 18 in Reach 4, and 11 to 21

in Reach 3.
10

Fish data were compiled by Geomorphic Reach. If a secondary channel was in two Geomorphic

Reaches, its data were included with that of the Reach in which a majority of its linear length occurred.

Abundance was defined as the number of fish (total or by species) captured per minute elapsed time

electrofishing. Six-letter codes (first three letters of genus and first three letters of species) were used to

identify species in tables and figures. Commonly collected species were aged following the classifications

of the Upper Basin (D.Ryden, pers. comm.), except that the Upper Basin juvenile age-class was divided into

juvenile and sub-adult classes for San Juan River secondary channel fishes. Thus, total-length ranges for

San Juan River fishes were Age 0 or young-of-year (YOY) < 75 mm (flannelmouth sucker, bluehead sucker,

common carp, and channel catfish), juvenile = 76 to 200 mm (flannelmouth sucker) or 76 to 175 mm

(bluehead sucker, common carp, and channel catfish), sub-adult = 201 to 400 mm (flannelmouth sucker) or

176 to 300 (bluehead sucker, common carp, and channel catfish), and adult = > 401 (flannelmouth sucker)

or >301 (bluehead sucker, common carp, and channel catfish).

All species collected were considered in characterizing overall changes, or lack, in secondary

channel fish assemblages. Only frequently and commonly collected fishes were used in detailed

comparisons among and within species by Geomorphic Reach and year. These comparisons were restricted

to flannelmouth sucker, bluehead sucker, common carp, and channel catfish. Several species, such as

speckled dace and red shiner, were frequently collected; however, their numbers were usually low and these

species were not used for most analyses. The sampling technique (boat-mounted electrofishing gear)

precluded unbiased sampling of these species.

Abundance (number of specimens per minute elapsed time electrofishing) and biomass data for

common carp, flannelmouth sucker, bluehead sucker, and channel catfish captured in the primary channel

during concurrent inventories were provided by the USFWS Grand Junction office. Only data from primary

channel designated miles (every fifth mile; see Ryden, 2000 for details) were used in comparisons with

secondary channels. Primary and secondary channels were grouped by Geomorphic Reach. Mean biomass

of each species was calculated by total weight of species/number of species specimens.

Linear regression analysis was used to determine if flow volume at time of sampling influenced

sampling efficiency. Coefficients of variation (CV) were calculated for several repeatedly measured

attributes (e.g., abundance). Friedman’s test and Kendall’s coefficient of concordance (Zar, 1984) were

used to evaluate the abundance rank of fishes (all species except those collected once or twice during the

study) in each Geomorphic Reach across years. Analysis of variance (ANOVA) was used to compare

differences in total abundance among years and Reaches. Changes in abundance, mean total length, total

biomass, and mean biomass (per year and Geomorphic Reach) of individual species were also evaluated

with ANOVA. Analysis of variance was used to compare primary and secondary channel data (abundance

and mean biomass). The Kolomogorov-Smirnov goodness of fit test was used to sequentially compare the

size-structure (25 mm length-classes) of commonly collected fishes. The significance threshold for all tests

was < 0.05.

RESULTS

Secondary Channel Classifications

The scheme to classify secondary channels by length and proportion of total discharge provided a

convenient means of generally describing secondary channels. However, for analytical purposes, the
11

scheme was not satisfactory. Few channels were classified as Type I or III. The rarity of these types

(typically fewer than five of either were present during any inventory) rendered comparisons of their fish

assemblages to those of common types (II and IV) problematic and statistically unsound. In addition,

comparison of fish assemblages among channel types did not help elucidate or clarify similarities and

dissimilarities. Therefore the Geomorphic Reaches of Bliesner and Lamarra (2000) were used to group data

for analyses.

Water Quality

During most years, measured water quality parameters were similar from the most-upstream through

the most-downstream secondary channels. Water temperature tended to increase slightly in a downstream

direction (Figure 3). Water temperature, at time of inventory, was highest in 1996 (a low spring runoff

year) and lowest in 1995 (a relatively high spring runoff year). Dissolved oxygen changed little among

secondary channels in all years except 1994 (Figure 4). Mean secondary channel dissolved oxygen was

lowest in 1996 and highest in 1993. From 1993 through 1996, specific conductance did not change

appreciably among secondary channels (except downstream of RM 95 in 1995) and mean specific

conductance was between 250 and 293 μmhos/cm (Figure 5). In 1997, specific conductance increased in a

downstream direction, varied among secondary channels, and generally was higher than during preceding

years.

Spring Secondary Channel Fish Assemblages

San Juan River secondary channel fish assemblages were inventoried in early to mid May from 1993

through 1997. Sampling was conducted in Geomorphic Reaches 5 through 3 (RM 154 – 68). A total of

seventeen fish species and one hybrid form (Table 1) was collected during the study period. The greatest

number of species was found in 1996 (four native and nine nonnative) and the fewest in 1993 and 1997

(three native, six nonnative and four native, five nonnative, respectively). Native flannelmouth sucker was

the most common fish species in secondary channels in all years (Table 2). The abundance of other species,

however, was variable among years. Bluehead sucker was the second-most common fish in 1993, but it was

less abundant in subsequent years. Common carp was third-most common in 1993 and 1997 and secondmost common in 1994 through 1996. Channel catfish was fourth and fifth-most common in 1993 and 1994,

but its abundance increased, relative to other species, from 1995 through 1997. Speckled dace varied from

the fourth to seventh most common species. Red shiner and fathead minnow abundance likewise varied

among years. One Colorado pikeminnow was
12

150

145

140

135

130

125

120

115

110

105

100

95

90

85

80

75

70

0

5

10

15

20

25

1993 MEAN = 14.4

SD = 1.9

CV = 13 %

150

145

140

135

130

125

120

115

110

105

100

95

90

85

80

75

70

0

5

10

15

20

25

1994 MEAN = 12.9

SD = 1.6

CV = 12 %

150

145

140

135

130

125

120

115

110

105

100

95

90

85

80

75

70

WATER TEMPERATURE (0C)

0

5

10

15

20

25

1995

MEAN = 12.1

SD = 1.2

CV = 10 %

150

145

140

135

130

125

120

115

110

105

100

95

90

85

80

75

70

0

5

10

15

20

25

1996 MEAN = 17.7

SD = 1.5

CV = 8 %

Figure 3. Temperature (0C) of San Juan River secondary channels during

 spring inventories, 1993 - 1997.

RIVER MILE

150

145

140

135

130

125

120

115

110

105

100

95

90

85

80

75

70

0

5

10

15

20

25

1997 MEAN = 13.4

SD = 2.1

CV = 16 %
13

150 145 140 135 130 125 120 115 110 105 100 95 90 85 80

0

2

4

6

8

10

12

14

1993

150 145 140 135 130 125 120 115 110 105 100 95 90 85 80 75 70

0

2

4

6

8

10

12

14

150 145 140 135 130 125 120 115 110 105 100 95 90 85 80 75 70

DISSOLVED OXYGEN (MG/L)

0

2

4

6

8

10

12

14

1994

1995

150 145 140 135 130 125 120 115 110 105 100 95 90 85 80 75 70

0

2

4

6

8

10

12

14

1996

Figure 4. Dissolved oxygen (mg/l) of San Juan River secondary channels 

 during spring inventories, 1993 - 1997.

RIVER MILE

150 145 140 135 130 125 120 115 110 105 100 95 90 85 80 75 70

0

2

4

6

8

10

12

14

1997

MEAN = 10.7

SD = 1.0

CV = 9%

MEAN = 8.7

SD = 1.4

CV = 16%

MEAN = 7.8

SD = 0.4

CV = 5%

MEAN = 6.7

SD = 0.4

CV = 6%

MEAN = 7.9

SD = 0.5

CV = 6%
14

150 145 140 135 130 125 120 115 110 105 100 95 90 85 80

0

100

200

300

400

500

600

150 145 140 135 130 125 120 115 110 105 100 95 90 85 80 75 70

0

100

200

300

400

500

600

1993

1994

150 145 140 135 130 125 120 115 110 105 100 95 90 85 80 75 70

CONDUCTIVITY (uMHOS/CM)

0

100

200

300

400

500

600

150 145 140 135 130 125 120 115 110 105 100 95 90 85 80 75 70

0

100

200

300

400

500

600

1995

1996

Figure 5. Conductivity (umhos/cm) of San Juan River secondary channels

 during spring inventories, 1993 - 1997.

RIVER MILE

150 145 140 135 130 125 120 115 110 105 100 95 90 85 80 75 70

0

100

200

300

400

500

600

1997

MEAN = 293

SD = 20.2

CV = 7%

MEAN = 254

SD = 10.9

CV = 4%

MEAN = 247

SD = 35.9

CV = 15%

MEAN = 250

SD = 19.8

CV = 8%

MEAN = 355

SD = 91.3

CV = 26%
15

Table 1. Occurrence of fishes in San Juan River secondary channels during spring, 1993 – 1997.Acronyms

for each species derived from first three letters of genus and first three letters of species. I = introduced and

N = native,

SPECIES

COMMON SCIENTIFIC ACRONYM STATUS 1993 1994 1995 1996 1997

Common carp Cyprinus carpio CYPCAR I X X X X X

Red shiner Cyprinella lutrensis CYPLUT I X X X X X

Fathead minnow Pimephales promelas PIMPRO I X X X X

Colorado pikeminnow Ptychocheilus lucius PTYLUC N X

Speckled dace Rhinichthys osculus RHIOSC N X X X X X

Flannelmouth sucker Catostomus latipinnis CATLAT N X X X X X

Bluehead sucker Catostomus discobolus CATDIS N X X X X X

Flannelmouth x

bluehead sucker

C. latipinnis x C.

discobolus

LATDIS X X X X

Razorback sucker Xyrauchen texanus XYRTEX N X X X

Black bullhead Ameiurus melas AMEMEL I X X X X

Yellow bullhead Ameiurus natalis AMENAT I X

Channel catfish Ictalurus punctatus ICTPUN I X X X X X

Rainbow trout Oncorhynchus mykiss ONCMYK I X X

Brown trout Salmo trutta SALTRU I X X

Plains killifish Fundulus zebrinus FUNZEB I X

Green sunfish Lepomis cyanellus LEPCYA I X X X

Smallmouth bass Micropterus dolomieu MICDOL I X

Largemouth bass Micropterus salmoides MICSAL I X X

Total Native1 5 34344

Total Nonnative 12 6 7 8 9 5

1

excluding flannelmouth x bluehead sucker

collected in 1994 and razorback suckers were collected in 1995, 1996, and 1997. Differences in among year

abundance rank of the eight most-commonly collected fish species, however, were not significant.

Kendall’s coefficient of concordance was 0.7995 (Friedman’s χ2

 = 27.98, p<0.0002).

The greatest number of fish specimens was collected in 1993 and the fewest in 1995. The highest

CPUE was in 1993 (3.21 fish/minute) and the lowest in 1995 (2.06 fish/minute). Stream discharge (at time

of sampling) did not affect CPUE (r2

 = 0.0013, p = .9543) or total number of specimens collected (r2 =

0.0296, p = .7822).

In Geomorphic Reach 5 (RM154 – RM131), the greatest number of fish and species were collected

in 1993 (Table 3). Abundance of fishes was also greatest in 1993; in subsequent years abundance did not

vary greatly (Figure 6). The fewest species were collected in 1997, but abundance that year was the secondhighest during the study in Geomorphic Reach 5. Flannelmouth sucker was the most abundant fish each

year, and was often twice or more common than the next most-common species. Common carp was the

second-most common species in all years except 1993 when bluehead sucker was second-most common.

The abundance rank of other species varied among years;
16

Table 2. Fish species collected in San Juan River secondary channels (RM 154 – RM 68) during spring

inventories, 1993 – 1997. Bold-lettered species were used to calculate Friedman’s χ2 and Kendall’s

coefficient of concordance (W).

1993 1994 1995 1996 1997

Species N Species N Species N Species N Species N

CATLAT 1127 CATLAT 1099 CATLAT 815 CATLAT 747 CATLAT 545

CATDIS 317 CYPCAR 158 CYPCAR 94 CYPCAR 312 ICTPUN 250

CYPCAR 123 CATDIS 66 ICTPUN 79 ICTPUN 155 CYPCAR 235

RHIOSC 111 PIMPRO 65 RHIOSC 54 CYPLUT 86 CATDIS 122

ICTPUN 92 CYPLUT 55 CATDIS 21 CATDIS 74 RHIOSC 22

CYPLUT 71 ICTPUN 33 CYPLUT 12 PIMPRO 67 AMENEB 5

PIMPRO 20 RHIOSC 28 CAT X DIS 4 RHIOSC 58 AMEMEL 4

CAT X DIS 9 CAT X DIS 6 PIMPRO 3 AMEMEL 4 CYPLUT 3

ONCMYK 2 AMEMEL 3 ONCMYK 1 XYRTEX 2 XYRTEX 1

SALTRU 1 PTYLUC 1 AMEMEL 1 CAT X DIS 1

SALTRU 1 LEPCYA 1 FUNZEB 1

LEPCYA 1 MICSAL 1 LEPCYA 1

TOTAL N 1873 1516 1086 1508 1187

ABUND. 3.21 2.63 2.06 2.84 2.36

however, changes in abundance rank among years were not significant (Kendall’s W = 0.9063; Friedman’s

χ2

 = 31.59, p<0.00005). Neither Colorado pikeminnow nor razorback sucker was collected in secondary

channels in Geomorphic Reach 5 during spring inventories.

Geomorphic Reach 4, in 1993, yielded the greatest abundance (4.087 fish/min) and numerically

largest (n = 803) secondary channel spring inventory fish collection during this study (Table 4). In

subsequent years, abundance ranged from 2.016 (1997) to 2.738 (1996) (Figure 6). Species richness was

greatest (11 species) in 1996 and least in 1995 (5 species). Flannelmouth sucker was the most abundant fish

in all years. In 1993 and 1994, bluehead sucker was the second-most abundant species, but nonnative

channel catfish was second-most common in 1995 and common carp was in 1996 and 1997. Flannelmouth

sucker was always at least three times as abundant as the next common-species. Although the abundance

rank of species was variable among years, the differences were not significant (Kendall’s W = 0.6114;

Friedman’s χ2

 = 24.20, p<0.001). One razorback sucker was collected from a Geomorphic Reach 4

secondary channel in 1996.

The greatest number of specimens collected in Geomorphic Reach 3 was obtained in 1994 (N =

649), but the greatest abundance was in 1996 (3.7803 fish/min) (Figure 6 and Table 5). Flannelmouth

sucker was numerically the most common fish in all years. Speckled dace was the second-most common

species in 1993, common carp in 1994 through 1996, and channel catfish in 1997. Eleven species were

collected in 1996, but only 6 in 1997. Rank abundance of species was not different among years of the

study (Kendall’s W = 0.6865; Friedman’s χ2

 = 24.03, p<0.001). One Colorado pikeminnow was collected

in a Geomorphic Reach 3 secondary channel in 1994 and one razorback sucker in each 1995, 1996, and

1997.
17

1993 1994 1995 1996 1997

0

1

2

3

4

5

1993 1994 1995 1996 1997

ABUNDANCE (FISH/MIN ELECTROFISHING)

0

1

2

3

4

5

Figure 6. Abundance of fishes in San Juan River secondary channels 

 during spring inventories, 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

0

1

2

3

4

5

REACH 5 MEAN = 2.464

REACH 4 MEAN = 2.736

REACH 3 MEAN = 2.710
18

Table 3. Number and abundance (number/minute elapsed electrofishing time) of fishes in San Juan River

secondary channels in Geomorphic Reach 5 (RM154 – RM131) during spring, 1993 – 1997.

1993 1994 1995 1996 1997

SPECIES N ABU SPECIES N ABU SPECIES N ABU SPECIES N ABU SPECIES N ABU

CATLAT 314 1.39CATLAT 258 1.71CATLAT 1771.57 CATLAT 186 1.08CATLAT 167 0.94

CATDIS 211 0.94CYPCAR 45 0.30CYPCAR 320.28 CYPCAR 79 0.46CYPCAR 123 0.69

CYPCAR 74 0.33CATDIS 19 0.13RHIOSC 160.14 CATDIS 43 0.25CATDIS 71 0.40

ICTPUN 42 0.19ICTPUN 14 0.09ICTPUN 140.12 PIMPRO 37 0.22ICTPUN 71 0.40

RHIOSC 22 0.10RHIOSC 9 0.06CATDIS 40.04 ICTPUN 18 0.10RHIOSC 9 0.05

CYPLUT 13 0.06PIMPRO 6 0.04CYPLUT 40.04 RHIOSC 6 0.03AMENEB 5 0.03

PIMPRO 4 0.02CYPLUT 4 0.03ONCMYK 10.01 CYPLUT 4 0.02CYPLUT 1 0.01

LAT x DIS 3 0.01LAT x DIS 2 0.01PIMPRO 10.01 LAT x DIS 1 0.01

ONCMYK 1 <0.01

SALTRU 1 <0.01

TOTAL N 685 357 249 374 447

EFFORT 13530 9055 6769 10303 10644

ABUND 3.04 2.37 2.21 2.18 2.52

Despite some variation in fish abundance among Geomorphic reaches and across years, these

differences were not significant. Two-way ANOVA yielded F = 0.322 (p = 0.7338) for among reach

comparisons and F = 1.645 (p = 0.2543) for across year comparisons.

During spring secondary channel inventories, four species were collected in sufficient numbers to

enable comparisons of abundance. Flannelmouth sucker was the most abundant species in all years in all

Geomorphic reaches (Table 6). It was most abundant in Geomorphic Reach 4 in all years, but 1997, and

least abundant in Geomorphic Reach 5 in all years except 1995. Two-way ANOVA indicated significant

differences among reaches (F = 5.669, p = 0.0292) and across years (F = 7.906, p = 0.007) in flannelmouth

sucker abundance.

Abundance of bluehead sucker decreased from Geomorphic Reach 5 through Reach 3 in 1993, 1996,

and 1997. Its abundance in Reach 3 was 80%+ less than that in Reach 5 in most years. These differences,

however, were not significant (F = 4.249, p = 0.0553). Although abundance of bluehead sucker was highest

in each reach in 1993, the across years change in its abundance was not significant (F = 3.314, p = 0.0701).

Common carp abundance did not vary greatly within each reach across years (F = 2.566, p = 0.1196)

nor was its abundance different among reaches (F = 1.3856, p = 0.3043). It was least common in Reaches 5

and 4 in 1995 and Reach 3 in 1993. In 1996, common carp abundance in Reach 3 was greater than channel

catfish and bluehead sucker abundance in all reaches.
19

Table 4. Number and abundance (number/minute elapsed electrofishing time) of fishes in San Juan River

secondary channels in Geomorphic Reach 4 (RM130 – RM106) during spring, 1993 – 1997.

1993 1994 1995 1996 1997

SPECIES N ABU SPECIES N ABU SPECIES N ABU SPECIES N ABU SPECIES N ABU

CATLAT 483 2.46 CATLAT 407 2.26 CATLAT 260 1.63 CATLAT 322 1.59 CATLAT 219 1.13

CATDIS 90 0.46 CATDIS 34 0.19 ICTPUN 23 0.14 CYPCAR 73 0.36 CYPCAR 68 0.35

RHIOSC 68 0.35 CYPLUT 23 0.13 CATDIS 17 0.11 CYPLUT 38 0.19 ICTPUN 47 0.24

CYPLUT 53 0.27 CYPCAR 21 0.12 RHIOSC 13 0.08 ICTPUN 38 0.19 CATDIS 43 0.22

CYPCAR 49 0.25 RHIOSC 14 0.08 CYPCAR 11 0.07 CATDIS 32 0.16 RHIOSC 9 0.05

ICTPUN 39 0.20 PIMPRO 7 0.04 LAT x DIS 2 0.01 RHIOSC 29 0.14 AMEMEL 4 0.02

PIMPRO 15 0.08 LAT x DIS 2 0.01 PIMPRO 10 0.05 CYPLUT 2 0.01

LAT x DIS 5 0.03 ICTPUN 1 0.01 AMEMEL 3 0.01

ONCMYK 1 0.01 SALTRU 1 0.01 MICSAL 3 0.01

XYRTEX 1 <0.01

MICDOL 1 <0.01

TOTAL N 803 500 326 550 392

EFFORT 11790 10813 9553 12164 11665

ABUND 4.09 2.77 2.05 2.74 2.02

Mean channel catfish abundance was greatest in Geomorphic Reach 3, mainly the consequence of

its high abundance in 1996 and 1997. The abundance of channel catfish in Reach 3 in 1997 was greater

than that of common carp and bluehead sucker in all reaches. However, neither among reach (F = 1.898, p

= 0.2115) nor across years (F = 2.653, p = 0.1120) differences in channel catfish abundance were

significant.

Among commonly-collected species, only flannelmouth sucker had a comparatively low abundance

coefficient of variation (< 30% in all reaches). All other commonly-collected species had high coefficients

of variation (> 50%) in most reaches. The abundance of flannelmouth sucker varied most in Reach 4,

bluehead sucker in Reach 5, and common carp and channel catfish in Reach 3.
20

Table 5. Number and abundance (number/minute elapsed time electrofishing) of fishes in San Juan River

secondary channels in Geomorphic Reach 3 (RM15 – RM68) during spring, 1993 – 1997.

1993 1994 1995 1996 1997

SPECIES N ABU SPECIES N ABU SPECIES N ABU SPECIES N ABU SPECIES N ABU

CATLAT 330 2.05 CATLAT 434 1.76 CATLAT 378 1.48 CATLAT 239 1.52 CATLAT 159 1.21

RHIOSC 21 0.13 CYPCAR 92 0.37 CYPCAR 51 0.20 CYPCAR 160 1.02 ICTPUN 132 1.01

CATDIS 16 0.10 PIMPRO 52 0.21 ICTPUN 42 0.16 ICTPUN 99 0.63 CYPCAR 44 0.34

CYPCAR 16 0.10 CYPLUT 28 0.11 RHIOSC 25 0.10 CYPLUT 44 0.28 CATDIS 8 0.06

ICTPUN 11 0.07 ICTPUN 18 0.07 CYPLUT 8 0.03 RHIOSC 23 0.15 RHIOSC 4 0.03

CYPLUT 5 0.03 CATDIS 13 0.05 LAT x DIS 2 0.01 PIMPRO 20 0.13 XYRTEX 1 0.01

LAT x DIS 1 0.01 RHIOSC 5 0.02 PIMPRO 2 0.01 CATDIS 4 0.03

PIMPRO 1 0.01 AMEMEL 3 0.01 XYRTEX 1 <0.01 XYRTEX 1 0.01

LAT x DIS 2 0.01 AMEMEL 1 <0.01 AMEMEL 1 0.01

PTYLUC 1 <0.01 LEPCYA 1 <0.01 FUNZEB 1 0.01

LEPCYA 1 <0.01 MICSAL LEPCYA 1 0.01

TOTAL N 401 649 512 593 348

EFFORT 9682 14775 15364 9412 7876

ABUND 2.49 2.64 2.00 3.78 2.65

Table 6. Abundance (fish/minute elapsed electrofishing time) of commonly collected fishes in San Juan

River secondary channels during spring 1993 – 1997, New Mexico, Colorado, and Utah. Number below

six-letter code indicates Geomorphic Reach. Coefficients of variation (CV) reported as percents.

SPECIES

CATLAT CATDIS CYPCAR ICTPUN

YEAR 5 4 3 5 4 3 5 4 3 5 4 3

1993 1.39 2.46 2.05 0.94 0.46 0.10 0.33 0.25 0.10 0.19 0.20 0.07

1994 1.71 2.26 1.76 0.13 0.19 0.05 0.30 0.12 0.37 0.09 0.01 0.07

1995 1.57 1.63 1.48 0.04 0.11 0.00 0.28 0.07 0.20 0.12 0.14 0.16

1996 1.08 1.59 1.52 0.25 0.16 0.03 0.46 0.36 1.02 0.10 0.19 0.63

1997 .94 1.13 1.21 0.40 0.22 0.06 0.69 0.35 0.34 0.40 0.24 1.01

MEAN 1.338 1.814 1.604 0.352 0.228 0.048 0.412 0.230 0.406 0.180 0.156 0.388

SD 0.324 0.540 0.317 0.355 0.136 0.037 0.171 0.132 0.360 0.129 0.089 0.418

CV 24.2 29.8 19.8 100.9 59.7 77.1 41.5 57.4 88.7 71.7 57.1 107.7
21

Population dynamics

Flannelmouth sucker—Size-structure of the flannelmouth sucker population in Geomorphic Reach

5 did not vary greatly among years (Figure 7). Sequential comparison of the size-structure of specimens in

annual Reach 5 collections did not yield any significant differences (Table 7). The spring sampling

methodology precluded efficient collection of young-of-year or Age-1 (YOY, < 120 mm TL) specimens and

few were taken. Sub-adults (200 to 399 mm TL) were typically the most common age-class and adults (>

400 mm TL) were usually the second-most common (Figure 8). Although the absolute number and

abundance of flannelmouth suckers collected declined from 1993 through 1997, mean total length remained

about the same (Figure 9).

In Geomorphic Reach 4, the size-structure of flannelmouth sucker samples did not vary greatly from

year-to-year, until 1997 (Figure 10). Prior to 1997, fish between 225 and 299 mm TL were comparatively

common, but in 1997 few fish in this size-range were collected. Observed differences, however, were not

significant (Table 7). Age-class abundance varied substantially from year –to-year (Figure 11). For

example, juveniles were 27 % of the collection in 1995, but only 7 % in 1997. In most years, sub-adults

were the numerically largest age-class but in 1997 adults were the largest age-class

in the collection. Mean total length varied slightly from 1993 through 1996, but increased substantially in

1997 (Figure 9). While mean total length was similar for most years, density of flannelmouth sucker

steadily declined from 1993 through 1997.

Table 7. Results of Kolomogorov-Smirov (Dmax) sequential comparisons of size-structure of flannelmouth

suckers in San Juan River secondary channel collections,

spring 1993 – 1997.

YEARS DMAX SIGNIFICANCE

GEOMORPHIC REACH 5 93 – 94 0.1775 NS

94 – 95 0.1818 NS

95 – 96 0.1364 NS

96 – 97 -0.2273 NS

GEOMORPHIC REACH 4 93 – 94 0.2273 NS

94 – 95 0.1818 NS

95 – 96 -0.2473 NS

96 – 97 -0.1436 NS

GEOMORPHIC REACH 3 93 – 94 0.1364 NS

94 – 95 0.2273 NS

95 – 96 0.2745 NS

96 – 97 -0.1855 NS

Size-structure of flannelmouth sucker collections in Reach 3 varied from 1993 through 1997 (Figure

12). In 1995, for example, a comparatively large number of individuals (ca. 23 % of collection) in two

length-classes (150 to 200 mm) were collected. The 1997 collection, in contrast to all others, had a large

proportion (ca. 42 %) of individuals > 375 mm TL. These observed changes in size-structure, however,
22

25-4975-99

125-149175-199225-249275-299325-349375-399425-449

475-499525-549

0

5

10

15

20

25-4975-99

125-149175-199225-249275-299325-349375-399425-449

475-499525-549

25-4975-99

125-149175-199225-249275-299325-349375-399425-449475-499525-549

PERCENT FREQUENCY

0

5

10

15

20

25-4975-99

125-149175-199225-249275-299325-349375-399425-449475-499525-549

Figure 7. Size-structure of the flannelmouth sucker, Catostomus latipinnis, population 

 in Geomorphich Reach 5, San Juan River, 1993 - 1997.

LENGTH CLASS

25-4975-99

125-149175-199225-249275-299325-349375-399425-449475-499525-549

0

5

10

15

20

1993 N = 392

MEAN TL = 346.5 mm

1994 N = 283

MEAN TL = 359.6 mm

1995 N = 196

MEAN TL = 341.7 mm

1996 N = 182

MEAN TL = 364.2 mm

1997 N = 167

MEAN TL = 366.2 mm
23

AGE 0 JUVENILE SUB-ADULT ADULT

0

10

20

30

40

50

60

AGE 0 JUVENILE SUB-ADULT ADULT

PERCENT FREQUENCY

0

10

20

30

40

50

60

AGE 0 JUVENILE SUB-ADULT ADULT

AGE 0 JUVENILE SUB-ADULT ADULT

Figure 8. Age-structure of the flannelmouth sucker, Catostomus latipinnis, 

 population in Geomorphic Reach 5, San Juan River, 1993 - 1997.

AGE-CLASS

AGE 0 JUVENILE SUB-ADULT ADULT

0

10

20

30

40

50

60

1993

1994

1995

1996

1997
24

25-4975-99

125-149175-199225-249275-299325-349375-399425-449475-499525-549575-599625-649

0

4

8

12

16

20

25-4975-99

125-149175-199225-249275-299325-349375-399425-449475-499525-549575-599625-649

PERCENT FREQUENCY

0

4

8

12

16

20

25-4975-99

125-149175-199225-249275-299325-349375-399425-449475-499525-549575-599625-649

25-4975-99

125-149175-199225-249275-299325-349375-399425-449475-499525-549575-599625-649

Figure 9. Size-structure of the flannelmouth sucker, Catostomus latipinnis, 

 population in Geomorphic Reach 4, San Juan River, 1993 - 1997.

LENGTH CLASS

25-4975-99

125-149175-199225-249275-299325-349375-399425-449475-499525-549575-599625-649

0

4

8

12

16

20

1993 N = 505

MEAN TL = 327.1 mm

1994 N = 413

MEANT TL = 322.9 mm

1995 N = 269

MEAN TL = 329.7 mm

1996 N = 339

MEAN TL = 332.0 mm

1997 N = 218

MEAN TL = 388.2
25

AGE 0 JUVENILE SUB-ADULT ADULT

0

10

20

30

40

50

60

70

AGE 0 JUVENILE SUB-ADULT ADULT

PERCENT FREQUENCY

0

10

20

30

40

50

60

70

AGE 0 JUVENILE SUB-ADULT ADULT

AGE 0 JUVENILE SUB-ADULT ADULT

Figure 10. Age-structure of the flannelmouth sucker, Catostomus latipinnis,

 population in Geomorphic Reach 4, San Juan River, 1993 - 1997.

AGE CLASS

AGE 0 JUVENILE SUB-ADULT ADULT

0

10

20

30

40

50

60

70

1993

1994

1995

1996

1997
26

25-4975-99

125-149175-199225-249275-299325-349375-399425-449475-499525-549

0

5

10

15

20

25-4975-99

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25-4975-99

125-149175-199225-249275-299325-349375-399425-449475-499525-549

PERCENT FREQUENCY

0

5

10

15

20

25-4975-99

125-149175-199225-249275-299325-349375-399

425-449475-499

525-549

Figure 11. Size-structure of the flannelmouth sucker, Catostomus latipinnis, 

 population in Geomorphic Reach 3, San Juan River, 1993 - 1997.

LENGTH CLASS

25-4975-99

125-149175-199225-249275-299325-349375-399425-449

475-499

525-549

0

5

10

15

20

1993 N = 332

MEAN TL = 279.2 mm

1994 N = 470

MEAN TL = 296.5 mm

1995 N = 392

MEAN TL = 293.6 mm

1996 N = 248

MEANT TL = 283.3

1997

N = 160

MEAN TL = 343.4 mm
27

were not significant (Table 7). Throughout the 5-year period, sub-adults were the most abundant age-class,

by a large margin in most years, in Reach 3 collections (Figure 13). Abundance of flannelmouth sucker in

Reach 3 declined from 1993 through 1997, but mean TL did not change substantially from year-to-year until

1997 when it increased markedly (Figure 9).

Among reaches and across years, significant differences in mean abundance of flannelmouth sucker

were noted. Two-way ANOVA yielded F = 5.67 (p = 0.029) for reach comparisons and F = 7.906 (p =

0.007) for year comparisons. Among reach comparisons of annual mean TL yielded significant differences

(F = 22.73, p = 0.015).

Total biomass of flannelmouth sucker was higher in Reaches 5 and 4 in 1993 and 1994 than in

subsequent years (Figure 14). In Reach 3, total biomass was greatest in 1994 and 1995. Between Reaches 5

and 4 differences in total biomass were slight. Total biomass in Reach 3 was substantially less, each year,

than in upstream reaches. These differences, however, were not significant (F = 2.02, p = 0.153). Mean

biomass in Reaches 5 and 4 varied considerably among years, but remained fairly constant in Reach 3.

Differences in mean biomass were significant (F = 6.65, p = 0.011) and post hoc tests indicated that mean

biomass in Reach 3 was statistically less than in Reach 5 (p = 0.011).

Bluehead sucker – Changes in the size-structure of the bluehead sucker population in Geomorphic

Reach 5 during the study was, in part, a function of differences in sample size. For example, in 1993 and

1997 moderate numbers (> 60) were collected and a variety of size-classes were present, with most

individuals between 300 and 375 mm TL (Figure 15). But in 1995 only 9 specimens were collected and all

were > 250 mm. In 1994 and 1996 intermediate numbers of bluehead sucker were collected, but a variety of

sizes were present. Observed size-structure differences, however, were not significant (Table 8). Four ageclasses were present in 1993, 1994 and 1996; only subadults were collected in 1995 and juveniles and

subadults in 1997 (Figure 16). Abundance of bluehead sucker in Reach 5 declined considerably from 1993

to 1995 and then increased through 1997 (Figure 17). Mean total length varied among years but was near

300 mm.

Bluehead suckers ranged in size from <100 to >400 mm in all years, except 1997, in Geomorphic

Reach 4; in 1997 the size range was more restricted and most individuals

were 275 to 349 mm (Figure 18). Differences were not significant (Table 8). Four age-classes were

collected in 1993 and 1994 and three in subsequent years (Figure 19). Age-0 specimens were collected only

in 1993 and 1994 and subadults numerically dominated collections each year except 1994. Abundance of

bluehead sucker in Reach 4 was similar to that in Reach 5, with abundance greatest in 1993, declining

through 1995, and increasing through 1997 (Figure 17). In each year, except 1995, abundance was less in

Reach 4 than Reach 5. Mean TL was about 275 mm in all years except 1994 when it was about 240 mm.

Few bluehead suckers were collected in Geomorphic Reach 3 in any year, and the species was not

found there in 1995. Specimens <150 mm were not collected and most were between 250 and 375 mm in

all years (Figure 20). Differences in size-structure were not significant for the years compared (Table 8).

No Age-0 and few juvenile specimens were captured in this reach; most (> 60%) were sub-
28

AGE 0 JUVENILE SUB-ADULT ADULT

0

10

20

30

40

50

60

70

AGE 0 JUVENILE SUB-ADULT ADULT

PERCENT FREQUENCY

0

10

20

30

40

50

60

70

AGE 0 JUVENILE SUB-ADULT ADULT

AGE 0 JUVENILE SUB-ADULT ADULT

Figure 12. Age-structure of the flannelmouth sucker, Catostomus latipinnis,

 population in Geomorphic Reach 3, San Juan River, 1993 - 1997.

AGE CLASS

AGE 0 JUVENILE SUB-ADULT ADULT

0

10

20

30

40

50

60

70

1993

1994

1995

1996

1997
29

1993 1994 1995 1996 1997

0

50

100

150

200

0

200

400

600

800

REACH 5

1993 1994 1995 1996 1997

TOTAL BIOMASS (KG)

0

50

100

150

200

MEAN BIOMASS (G)

0

200

400

600

800

REACH 4

Figure 13. Biomass of flannelmouth sucker, Catostomus latipinnis, in San Juan

 River secondary channels during spring inventories, 1993 - 1997. 

YEAR

1993 1994 1995 1996 1997

0

50

100

150

200

0

200

400

600

800

TOTAL BIOMASS

MEAN BIOMASS

REACH 3
30

50-7475-99

100-124125-149150-174175-199200-224225-249250-274275-299300-324325-349350-374375-399400-424425-449450-474

0

5

10

15

20

25

30

50-7475-99

100-124125-149150-174175-199200-224225-249250-274275-299300-324325-349350-374375-399400-424425-449450-474

PERCENT FREQUENCY

0

5

10

15

20

25

30

50-7475-99

100-124125-149150-174175-199200-224225-249250-274275-299300-324325-349350-374375-399400-424425-449450-474

50-7475-99

100-124125-149150-174175-199200-224225-249250-274275-299300-324325-349350-374375-399400-424425-449450-474

Figure 14. Size-structure of the bluehead sucker, Catostomus discobolus, 

 population in Geomorphic Reach 5, San Juan River, 1993 - 1997.

LENGTH CLASS 

50-7475-99

100-124125-149150-174175-199200-224225-249250-274275-299300-324325-349350-374375-399400-424425-449450-474

0

5

10

15

20

25

30

N = 69

MEAN TL = 306.7 mm

N = 21

MEAN TL = 280.6 mm

N = 9

MEAN TL = 332.1 mm

N = 39

MEAN TL = 279.8

N = 70

MEAN TL = 305.8 mm

1993

1994

1995

1996

1997
31

AGE 0 JUVENILE SUB-ADULT ADULT

0

20

40

60

80

100

AGE 0 JUVENILE SUB-ADULT ADULT

PERCENT FREQUENCY

0

20

40

60

80

100

AGE 0 JUVENILE SUB-ADULT ADULT

0

20

40

60

80

100

AGE 0 JUVENILE SUB-ADULT ADULT

0

20

40

60

80

100

Figure 15. Age-structure of the bluehead sucker, Catostomus discobolus,

 population in Geomorphic Reach 5, San Juan River, 1993 - 1997.

AGE CLASS

AGE 0 JUVENILE SUB-ADULT ADULT

0

20

40

60

80

100

1993

1994

1995

1996

1997
32

1993 1994 1995 1996 1997

0.0

0.2

0.4

0.6

0.8

1.0

200

225

250

275

300

325

350

375

400

1993 1994 1995 1996 1997

ABUNDANCE (N/MIN)

0.0

0.2

0.4

0.6

0.8

1.0

MEAN TL (mm)

200

225

250

275

300

325

350

375

400

Figure 16. Abundance and mean total length of bluehead sucker, Catostomus

 discobolus, in San Juan River secondary channels during spring, 

 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

0.0

0.2

0.4

0.6

0.8

1.0

200

225

250

275

300

325

350

375

400

ABUNDANCE

MEAN TL

Geomorphic Reach 5

Geomorphic Reach 4

Geomorphic Reach 3
33

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524

0

5

10

15

20

25

30

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524

PERCENT FREQUENCY

0

5

10

15

20

25

30

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524

Figure 17. Size-structure of the bluehead sucker, Catostomus discobolus,

 population in Geomorphic Reach 4, San Juan River, 1993 - 1997.

LENGTH CLASS

50-74

100-124150-174200-224

250-274

300-324350-374

400-424

450-474500-524

0

5

10

15

20

25

30

1993 N = 91

MEAN TL = 271.1 mm

1994 N = 26

MEAN TL = 235.8 mm

1995 N = 16

MEAN TL = 279.3 mm

1996 N = 43

MEAN TL = 272.9 mm

N = 43 1997

MEAN TL = 

 282.4 mm
34

AGE 0 JUVENILE SUB-ADULT ADULT

0

20

40

60

80

100

AGE 0 JUVENILE SUB-ADULT ADULT

PERCENT FREQUENCY

0

20

40

60

80

100

AGE 0 JUVENILE SUB-ADULT ADULT

AGE 0 JUVENILE SUB-ADULT ADULT

Figure 18. Age-structure of the bluehead sucker, Catostomus discobolus,

 population in Geomorphic Reach 4, San Juan River, 1993 - 1997.

AGE CLASS

AGE 0 JUVENILE SUB-ADULT ADULT

0

20

40

60

80

100

1993

1994

1995

1996

1997
35

50-74

100-124150-174200-224250-274300-324350-374400-424

0

5

10

15

20

25

30

35

40

45

50-74

100-124150-174200-224250-274300-324350-374400-424

50-74

100-124150-174200-224250-274300-324350-374400-424

PERCENT FREQUENCY

0

5

10

15

20

25

30

35

40

45

50-74

100-124150-174200-224250-274300-324350-374400-424

Figure 19. Size-structure of the bluehead sucker, Catostomus discobolus,

 population in Geomorphic Reach 3, San Juan River, 1993 - 1997.

LENGTH CLASS

50-74

100-124150-174

200-224

250-274

300-324350-374400-424

0

5

10

15

20

25

30

35

40

45

1993 N = 16

MEAN TL = 288.9 mm

1994 N = 13

MEAN TL = 279.5 mm

1995 N = 0

1996 N = 5

MEAN TL = 

 267.2 mm

1997 N = 8

MEAN TL = 264.9 mm
36

Table 8. Results of Kolomogorov-Smirov (Dmax) sequential comparisons of size-structure of bluehead

suckers in San Juan River secondary channel collections, spring 1993 – 1997.

YEARS DMAX SIGNIFICANCE

GEOMORPHIC REACH 5 93 – 94 -0.2273 NS

94 – 95 0.2727 NS

95 – 96 -0.2527 NS

96 – 97 -0.1800 NS

GEOMORPHIC REACH 4 93 – 94 0.1818 NS

94 – 95 0.1818 NS

95 – 96 0.1473 NS

96 - 97 0.1273 NS

GEOMORPHIC REACH 3 93 – 94 -0.1364 NS

94 – 951 -- --

95 – 961 -- --

96 – 97 -0.1527 NS

1

No bluehead sucker was collected in Geomorphic Reach 3 in 1995; therefore K-S Dmax was not calculated for 94 – 95 and 95 – 96

comparisons.

adults or adults (Figure 21). The decline in abundance from 1993 through 1995 and increase to 1997 was

like that noted in Reaches 5 and 4 (Figure 17). Unlike Reaches 5 and 4, however, mean TL decreased from

1993 through 1997 in Reach 3.

There were no significant differences in bluehead sucker abundance among years (F = 4.25, p =

0.055) or among reaches (F = 3.31, p = 0.070). Differences in mean TL among reaches were significant (F

= 4.93, p = 0.040).

Total biomass of bluehead sucker was least in all reaches in 1995 and greatest in 1993 (Figure 22).

Between 1993 and 1997, mean biomass increased in Reach 5, but was not substantially different in Reaches

4 and 3. In most years, total biomass was greater in Reach 5 than downstream reaches. Mean biomass in

Reach 5 was > 300 g in all years except 1993, in Reach 4 mean biomass exceeded 300 g only in 1996, and

never exceeded 300 g in Reach 3. Among reach comparisons did not yield significant differences for either

total or mean biomass (F = 3.51, p = 0.063 and F = 1.91, p = 0.191).

Common carp—Reach 5 secondary channel collections yielded only adult common carp in all

years, except 1994, and almost all individuals were > 400 mm TL (Figure 23). Sequential annual

comparisons did not yield significant differences (Table 9). From 1993 through 1995, there was a slight

decline in common carp abundance, but it increased in 1996 and 1997 (Figure 24). Abundance in 1997 was

almost twice that of 1993, 1994, and 1995. Mean length varied little among the years.

Individuals >400 mm TL numerically dominated collections of common carp in Reach 4 (Figure

25). In contrast to Reach 5, a few individuals <250 mm (juveniles and sub-adults) were collected in Reach

4. There were no differences in size-structure of common carp in Reach 4 (Table 9). Abundance, and

absolute numbers declined from 1993 through 1995, but increased in 1996 and 1997 (Figure 24).
37

AGE 0 JUVENILE SUB-ADULT ADULT

0

10

20

30

40

50

60

AGE 0 JUVENILE SUB-ADULT ADULT

PERCENT FREQUENCY

0

10

20

30

40

50

60

AGE 0 JUVENILE SUB-ADULT ADULT

AGE 0 JUVENILE SUB-ADULT ADULT

Figure 20. Age-structure of the bluehead sucker, Catostomus discobolus,

 population in Geomorphic Reach 3, San Juan River, 1993 - 1997.

AGE CLASS

AGE 0 JUVENILE SUB-ADULT ADULT

0

10

20

30

40

50

60

1993

1994

1995

1996

1997
38

1993 1994 1995 1996 1997

0

5

10

15

20

25

30

35

40

0

100

200

300

400

500

1993 1994 1995 1996 1997

TOTAL BIOMASS (KG)

0

5

10

15

20

25

30

35

40

MEAN BIOMASS (G)

0

100

200

300

400

500

Figure 21. Total and mean biomass of bluehead sucker, Catostomus discobolus,

 in San Juan River secondary channels during spring inventories, 

 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

0

5

10

15

20

25

30

35

40

0

100

200

300

400

500

TOTAL BIOMASS

MEAN BIOMASS

REACH 5

REACH 4

REACH 3
39

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574

0

10

20

30

40

50

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574

PERCENT FREQUENCY

0

10

20

30

40

50

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574

Figure 22. Size-structure of the common carp, Cyprinus carpio, population

 in Geomorphic Reach 5, San Juan River, 1993 - 1997.

LENGTH CLASS 

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574

0

10

20

30

40

50

1993 N = 69

MEAN TL = 422.8 mm

1994 N = 52

MEAN TL = 443.1 mm

1995 N = 25

MEAN TL = 449.2 mm

1996 N = 79

MEAN TL = 442.2

1997 N = 117

MEAN TL = 441.8 mm
40

1993 1994 1995 1996 1997

0.0

0.2

0.4

0.6

0.8

1.0

1.2

200

250

300

350

400

450

500

1993 1994 1995 1996 1997

ABUNDANCE (N/MIN)

0.0

0.2

0.4

0.6

0.8

1.0

1.2

MEAN TL (mm)

200

250

300

350

400

450

500

Figure 23. Abundance and mean total length of common carp, Cyprinus carpio,

 in San Juan River secondary channels during spring, 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

0.0

0.2

0.4

0.6

0.8

1.0

1.2

200

250

300

350

400

450

500

ABUNDANCE

MEAN TL

Reach 5

Reach 4

Reach 3
41

100-124150-174200-224250-274300-324350-374400-424450-474500-524

0

5

10

15

20

25

30

35

100-124150-174200-224250-274300-324350-374400-424450-474500-524

PERCENT FREQUENCY

0

5

10

15

20

25

30

35

100-124150-174200-224250-274300-324350-374400-424450-474500-524

100-124150-174200-224250-274300-324350-374400-424450-474500-524

Figure 24. Size-structure of the common carp, Cyprinus carpio, population

 in Geomorphic Reach 4, San Juan River, 1993 - 1997.

LENGTH CLASS

100-124150-174200-224250-274300-324350-374400-424450-474500-524

0

5

10

15

20

25

30

35

1993 N = 47

MEAN TL = 412.7 mm

1994

N = 22

MEAN TL = 409.5 mm

1995 N = 11

MEAN TL = 463.5 mm

1996

N = 86

MEAN TL = 424.2 mm

1997

N = 75

MEAN TL = 433.9 mm
42

The Reach 4 decline in abundance was greater than in Reach 5 and the 1996 and 1997 Reach 4 increase was

less. Except for 1995, mean TL was between 410 and 434 mm.

Table 9. Results of Kolomogorov-Smirnov (Dmax) sequential comparisons of size-structure of

common carp in San Juan River secondary channel collections, spring 1993 – 1997.

YEARS DMAX SIGNIFICANCE

GEOMORPHIC REACH 5 93 – 94 -0.1364 NS

94 – 95 0.1364 NS

95 – 96 -0.1127 NS

96 – 97 -0.0781 NS

GEOMORPHIC REACH 4 93 – 94 -0.1364 NS

94 – 95 -0.0909 NS

95 – 96 0.1527 NS

96 – 97 0.1691 NS

GEOMORPHIC REACH 3 93 – 94 -0.3636 NS

94 – 95 0.2727 NS

95 – 96 0.3564 NS

96 – 97 -0.2418 NS

Although most individuals collected were >400 mm TL, a larger proportion of common carp

specimens were <250 mm, in several years, in Reach 3 than either upstream Reach (Figure 26). Annual

differences in the size-structure of the common carp population in Reach 3 were not significant (Table 9).

Abundance and absolute numbers of common carp collected varied considerably among years in Reach 3

(Figure 24). In 1996, abundance exceeded 1.0 fish/minute, but in 1993 it was <0.1 fish/minute. Mean TL

was about 400 mm and changed little among years.

No among-year or among reach abundance differences were noted for common carp (F = 2.57, p =

0.120; F = 1.39, p = 0.304). Among-reach differences in mean TL were significant (F = 5.76, p = 0.028).

In each reach, total biomass of common carp varied among years (Figure 27). In Reaches 5 and 4, it

was least in 1995 and least in Reach 3 in 1993. Common carp biomass was greatest in 1996 or 1997 in all

reaches. Mean biomass varied less than total biomass; in average, Reach 4 had the largest common carp and

Reach 3 the smallest. In Reaches 4 and 3, mean biomass was greater in 1997 than 1993. Neither total nor

mean biomass of common carp was significantly different among Reaches (F = 0.417, p = 0.668 and F =

3.198, p = 0.077).

Channel catfish—Between 1993 and 1995, most channel catfish collected in Reach 5 were between

400 and 575 mm TL, but in 1996 and 1997 a substantial proportion of the samples were 250 to 375 mm

(Figure 28). Size-structure differences were not significantly different (Table 10). From 1993 through

1996, channel catfish abundance in Reach 5 was <0.2 fish/min, but in 1997 abundance was near 0.4 fish/min

(Figure 29). Mean TL generally declined from 1993 through 1996 and increased, slightly, in 1997. In

1993, almost all channel catfish captured in Reach 5 were adults (>301 mm TL),
43

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574

0

10

20

30

40

50

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574

PERCENT FREQUENCY

0

10

20

30

40

50

Figure 25. Size-structure of the common carp, Cyprinus carpio, population

 in Geomorphic Reach 3, San Juan River, 1993 - 1997.

LENGTH CLASS

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574

0

10

20

30

40

50

1993

N = 15

MEAN TL = 404.7 mm

1994 N = 64

MEAN TL = 406.7 mm

1995 N = 44

MEAN TL = 380.9 mm

1996 N = 168

MEAN TL = 402.6 mm

1997 N = 43

MEAN TL = 423.0 mm
44

1993 1994 1995 1996 1997

0

20

40

60

80

100

120

140

160

0

400

800

1200

1600

2000

1993 1994 1995 1996 1997

TOTAL BIOMASS (KG)

0

20

40

60

80

100

120

140

160

MEAN BIOMASS (G)

0

400

800

1200

1600

2000

Figure 26. Total and mean biomass of common carp, Cyprinus carpio, in San

 Juan River secondary channels during spring inventories, 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

0

20

40

60

80

100

120

140

160

0

400

800

1200

1600

2000

TOTAL BIOMASS

MEAN BIOMASS

REACH 5

REACH 4

REACH 3
45

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574600-624

0

5

10

15

20

25

30

35

40

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574600-624

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574600-624

PERCENT FREQUENCY

0

5

10

15

20

25

30

35

40

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574600-624

Figure 27. Size-structure of the channel catfish, Ictalurus punctatus,

 population in Geomorphic Reach 5, San Juan River, 1993 - 1997.

LENGTH CLASS 

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574600-624

0

5

10

15

20

25

30

35

40

1993 N = 46

MEAN TL = 449.4 mm

1994 N = 18

MEAN TL = 467.6 mm

1995 N = 12

MEAN TL = 434.3 mm

1996 N = 16

MEAN TL = 357.3 mm

1997 N = 68

MEAN TL = 370.4 mm
46

1993 1994 1995 1996 1997

0.0

0.2

0.4

0.6

0.8

1.0

1.2

200

250

300

350

400

450

500

1993 1994 1995 1996 1997

ABUNDANCE (N/MIN)

0.0

0.2

0.4

0.6

0.8

1.0

1.2

MEAN TL

200

250

300

350

400

450

500

Figure 28. Abundance and mean total length of channel catfish, Ictalurus punctatus,

 in San Juan River secondary channels during spring, 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

0.0

0.2

0.4

0.6

0.8

1.0

1.2

200

250

300

350

400

450

500

ABUNDANCE

MEAN TL

Reach 5

Reach 4

Reach 3
47

but by 1997 their abundance declined to about 60% of the collection (Figure 30). Sub-adult (176 to 300

mm) abundance peaked in 1996.

In Reach 4, size-structure of the channel catfish population varied substantially from year-to-year

(Figure 31). In addition to capture of more very large individuals (>550 mm TL) in this reach than other

reaches, several fish <200 mm were captured in most years.

Table 10. Results of Kolomogorov-Smirnov (Dmax) sequential comparisons of size-structure of channel

catfish in San Juan River secondary channel collections, spring 1993 – 1997.

YEARS DMAX SIGNIFICANCE

GEOMORPHIC REACH 5 93 – 94 -0.2095 NS

94 – 95 -0.1245 NS

95 – 96 0.2436 NS

96 – 97 0.2487 NS

GEOMORPHIC REACH 4 93 – 94 0.5929 <0.001

94 – 95 -0.3656 NS

95 – 96 0.3109 NS

96 – 97 0.2417 NS

GEOMORPHIC REACH 3 93 – 94 -0.2036 NS

94 – 95 -0.2174 NS

95 – 96 0.1757 NS

96 – 97 0.1739 NS

In 1994 only one channel catfish was collected. The size-structure of the 1993 sample was

significantly different from the 1994 collection (Table 10), but the 1994 collection was not different from

that of 1995. Abundance of channel catfish in Reach 4 varied little, excluding the 1994 collection, from

year-to-year. Mean TL of channel catfish declined from 1993 through 1996 (again, excepting the 1994

collection), and increased slightly in 1997 (Figure 29). Adults were the most abundant age-class in all

years, except 1996 when their abundance equaled that of sub-adults (Figure 32). Juveniles were found in

more years in Reach 4 than 5.

Collections in Reach 3 yielded a higher proportion of small (<200 mm TL) catfish than were found

in either upstream Reach, and abundance of large specimens (>400 mm) was typically less (Figure 33) than

upstream reaches. In 1997, the 100 to 225 mm size-group represented over 50% of the collection.

Sequential between-year comparisons of size-structure did not indicate significant differences (Table 10).

Abundance of channel catfish in Reaches 5 and 4 remained fairly constant over the years of study, but

steadily increased in Reach 3 (Figure 29). Abundance was <0.1 fish/min in 1993, but was slightly greater

than 1.0 in 1997. While not as dramatic as abundance, changes in mean TL of channel catfish in Reach 3

were different from that observed in Reaches 5 and 4. Mean TL increased from 1993 through 1995 but

declined from 1995 through 1997. By 1997, mean TL (233 mm) in Reach 3 was substantially less than in

Reaches 5 and 4 (370 and 330 mm). Adults were the numerically dominant age-class in 1993 through 1995

(Figure 34), but juveniles and sub-adults were over 60% of the collections in 1996 and 1997.
48

AGE 0 JUVENILE SUBADULT ADULT

0

20

40

60

80

100

AGE 0 JUVENILE SUBADULT ADULT

ABUNDANCE (FISH/MIN)

0

20

40

60

80

100

AGE 0 JUVENILE SUBADULT ADULT

AGE 0 JUVENILE SUBADULT ADULT

Figure 29. Age-structure of the channel catfish, Ictalurus punctatus, 

 population in Geomorphic Reach 5, San Juan River, 1993 - 1997.

AGE CLASS

AGE 0 JUVENILE SUBADULT ADULT

0

20

40

60

80

100

1993

1994

1995

1996

1997
49

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574600-624

PERCENT FREQUENCY

0

5

10

15

20

25

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574600-624

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574600-624

PERCENT FREQUENCY

0

20

80

100

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574600-624

Figure 30. Size-structure of the channel catfish, Ictalurus punctatus,

 population in Geomorphic Reach 4, San Juan River, 1993 - 1997.

LENGTH CLASS

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574600-624

PERCENT FREQUENCY

0

5

10

15

20

25

N = 40 1993

MEAN TL = 389.3 mm

N = 1 1994

TL = 490.0 mm

N = 24 1995

MEAN TL = 391.0 mm

N = 42 1996

MEAN TL = 305.2

1997 N = 47

MEAN TL = 329.8 mm
50

AGE 0 JUVENILE SUBADULT ADULT

ABUNDANCE (FISH/MIN)

0

20

40

60

80

100

AGE 0 JUVENILE SUBADULT ADULT

ABUNDANCE (FISH/MIN)

0

20

40

60

80

100

AGE 0 JUVENILE SUBADULT ADULT

AGE 0 JUVENILE SUBADULT ADULT

Figure 31. Age-structure of the channel catfish, Ictalurus punctatus, 

 population in Geomorphic Reach 4, San Juan River, 1993 - 1997.

AGE CLASS

AGE 0 JUVENILE SUBADULT ADULT

ABUNDANCE (FISH/MIN)

0

20

40

60

80

100

1993

1994

1995

1996

1997
51

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574

0

5

10

15

20

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574

Figure 32. Size-structure of the channel catfish, Ictalurus punctatus,

 population in Geomorphic Reach 3, San Juan River, 1993 - 1997.

LENGTH CLASS

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574

0

5

10

15

20

50-74

100-124150-174200-224250-274300-324350-374400-424450-474500-524550-574

PERCENT FREQUENCY

0

5

10

15

20

1993 N = 11

MEAN TL =

295.0 mm

1994

N = 22

MEAN TL = 334.7 mm

1995 N = 42

MEAN TL =360.3 mm

1996 N = 97

MEAN TL = 253.6 mm

1997 N = 136

MEAN TL = 232.8 mm
52

AGE 0 JUVENILE SUBADULT ADULT

0

20

40

60

80

100

AGE 0 JUVENILE SUBADULT ADULT

ABUNDANCE (FISH/MIN)

0

20

40

60

80

100

AGE 0 JUVENILE SUBADULT ADULT

AGE 0 JUVENILE SUBADULT ADULT

Figure 33. Age-structure of the channel catfish, Ictalurus punctatus,

 population in Geomorphic Reach 3, San Juan River, 1993 - 1997.

AGE CLASS

AGE 0 JUVENILE SUBADULT ADULT

0

20

40

60

80

100

1993

1994

1995

1996

1997
53

Channel catfish abundance did not differ significantly among-years or reaches (F = 2.65, p = 0.112 and F =

1.90, p = 0.212). Among-reach differences in mean TL were significant (F = 26.25, p = 0.0003).

In Reach 5, channel catfish total biomass declined substantially from 1993 through 1996, but

increased in 1997 (Figure 35). In Reaches 4 and 3, total biomass was fairly similar among most years.

Mean biomass declined considerably from 1993 (1048 g) through 1997 (466 g) in Reach 5, noticeably in

Reach 4 (688 to 378 g) and Reach 3 (261 to 161 g). Neither total nor mean biomass of channel catfish was

significantly different among reaches (F = 0.74, p = 0.498 and F = 3.148, p = 0.080).

Within Reach Species Biomass Comparisons.

Significant differences in total biomass of species were found in all reaches. In Reach 5, total

flannelmouth sucker biomass was greater than other species (F = 14.437, p = 0.0008). Post hoc tests

indicated it was significantly greater than that of bluehead sucker and channel catfish, but not common carp

(Table 11). Total biomass of common carp was significantly greater than bluehead sucker. Significant

differences in total biomass also were found in Reach 4 (F = 35.865, p < 0.0001). Total biomass of

flannelmouth sucker was significantly greater than other species, but differences among the latter were not

significant. Differences in total biomass in Reach 3 were significant (F = 10.445, p = 0.0004) and similar to

those found in Reach 5. Flannelmouth sucker total biomass was significantly greater than bluehead sucker

and channel catfish, but not common carp. Common carp total biomass was significantly greater than

bluehead sucker, but not channel catfish.

Mean biomass of common carp was greater than that of other species in all reaches. In Reach 5

differences in mean biomass were significant (F = 8.401, p = 0.001). Mean biomass of common carp was

significantly greater than that of flannelmouth sucker and bluehead sucker, but not channel catfish. Mean

biomass of channel catfish was significantly greater than bluehead sucker, but not flannelmouth sucker.

Significant differences in mean biomass were also found in Reach 4 (F = 28.358, p < 0.0001); common carp

was significantly larger than flannelmouth sucker, bluehead sucker, and channel catfish. Channel catfish

mean biomass was significantly greater than that of bluehead sucker. Reach 3 mean biomass relationships

(F = 19.887, p < 0.0001) were similar to those of Reach 4 with mean biomass of common carp being greater

than that of bluehead sucker, flannelmouth sucker, and channel catfish. There were no significant

differences among the latter three species.

Differences in abundance of species were significant for all reaches (Reach 5 F = 19.698, p <

0.0001; Reach 4 F = 40.963, p < 0.0001; and Reach 3 F = 23.019, p < 0.0001). Flannelmouth sucker was

the most abundant species in all reaches. Its abundance was significantly greater than that of other species

in all reaches (all p < 0.004). Abundance of other species was not significantly different.
54

1993 1994 1995 1996 1997

0

10

20

30

40

50

0

400

800

1200

1600

REACH 5

1993 1994 1995 1996 1997

TOTAL BIOMASS (KG)

0

10

20

30

40

50

MEAN BIOMASS (G)

0

400

800

1200

1600

REACH 4

Figure 34. Biomass of channel catfish, Ictalurus punctatus, in San Juan River

 secondary channels during spring inventories, 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

0

10

20

30

40

50

0

400

800

1200

1600

REACH 3
55

Table 11. Post hoc comparisons from ANOVA of total biomass (right of diagonal) and mean biomass (left

of diagonal) of commonly collected fishes in San Juan River secondary channels during spring inventories.

NS = not significant, * = p < 0.05, ** = p < 0.01, and *** = p < 0.001.

REACH 5

SPECIES CATLAT CATDIS CYPCAR ICTPUN

CATLAT ----- *** NS ***

CATDIS NS ----- * NS

CYPCAR * *** ----- NS

ICTPUN NS * NS -----

REACH 4

CATLAT ----- *** *** ***

CATDIS NS ----- NS NS

CYPCAR *** *** ----- NS

ICTPUN NS * *** -----

REACH 3

CATLAT ----- *** NS **

CATDIS NS ----- * NS

CYPCAR *** *** ----- NS

ICTPUN NS NS *** -----

Secondary and Primary Channel Comparisons

Between 1994 and 1997, spring inventories of primary and secondary channels were done

concurrently, using the same sampling techniques (raft-mounted electrofishing). Data from primary and

secondary channels were grouped by Geomorphic Reach; only primary channel data from designated miles

were used while all data from all sampled secondary channels were used.

Mean biomass of flannelmouth sucker in primary and secondary channels was similar in all years

and all reaches (F = 0.294, p = 0.593; reaches and years combined) (Figure 36). Flannelmouth sucker mean

biomass (primary and secondary combined) was greater in Reach 5 than 4 and Reach 4 than 3 (F = 26.052, p

< 0.001). Among year comparisons (primary and secondary combined), however, were not significantly

different (F = 0.869, p = 0.474).

Abundance of flannelmouth sucker was significantly greater in secondary channels than the primary

channel (Figure 37; F = 5.570, p = 0.028; years and reaches combined). Significant differences were also

found for among year comparisons (F = 5.342, p = 0.007; reaches and channels combined). Post hoc tests

indicated that the only significant yearly comparison was that between 1994 and 1997 (p = 0.005).
56

1994 1995 1996 1997

0

200

400

600

800

1994 1995 1996 1997

MEAN BIOMASS (G)

0

200

400

600

800

Figure 35. Mean biomass (g) of flannelmouth sucker, Catostomus latipinnis, in

 primary and secondary channels of the San Juan River, 1994 - 1997.

YEAR

1994 1995 1996 1997

0

200

400

600

800

PRIMARY CHANNEL

SECONDARY CHANNEL

REACH 5

REACH 4

REACH 3
57

1994 1995 1996 1997

0.0

0.5

1.0

1.5

2.0

2.5

3.0

1994 1995 1996 1997

ABUNDANCE (FISH/MIN)

0.0

0.5

1.0

1.5

2.0

2.5

3.0

Figure 36. Abundance (fish/min) of flannelmouth sucker, Catostomus latipinnis,

 in San Juan River primary and secondary channels during spring

 inventories, 1994 - 1997.

YEAR

1994 1995 1996 1997

0.0

0.5

1.0

1.5

2.0

2.5

3.0

PRIMARY CHANNEL

SECONDARY CHANNEL

REACH 5

REACH 4

REACH 3
58

 Among reach differences (years and channels combined) were not significant (F = 1.300, p = 0.294).

Between 1994 and 1997, mean biomass of bluehead sucker increased in the primary but remained

fairly constant in secondary channels in Reach 5. In Reaches 4 and 3, both primary and secondary channels

mean biomass remained fairly constant (Figure 38). Between channel (years and reaches combined) and

among years (channels and reaches combined) mean biomass differences were not significant (F = 0.230, p

= 0.636 and F = 0.533, p = 0.665) but reach (channels and years combined) differences were (F = 7.862, p =

0.003). Post hoc tests revealed that mean biomass in Reach 5 was significantly greater than in Reach 4 (p =

0.003) and 3 (p = 0.003).

In Reach 5, abundance of bluehead sucker was usually greater in the primary than secondary

channels. Generally, the differences in Reaches 4 and 3 were not great (Figure 39). Abundance was

significantly greater in Reach 5 than Reach 4 than Reach 3 (F = 10.976, p = 0.0005). Between channel

(years and reaches combined) and among year (channels and reaches combined) differences were not

significant (F = 0.599, p = 0.447 and F = 1.428, p = 0.264).

There were no differences between primary and secondary channels in mean biomass of common

carp (F = 3.632, p = 0.070; reaches and years combined), among reaches (F = 3.379, p = 0.053; channels

and years combined), or among years (F = 0.114, p = 0.951; channels and reaches combined) comparisons

(Figure 40). Of the abundance comparisons, only that among years yielded significant differences (F =

4.403, p = 0.016; channels and reaches combined). Abundance differences between channels (reaches and

years combined) were apparent (Figure 41), but not significant (F = 3.656, p = 0.069). Abundance among

reaches was similar (F = 0.817, p = 0.455).

Differences in mean biomass of channel catfish when compared among years and between channels

were not significant (F = 3.013, p = 0.054 and F = 0.030, p = 0.865), but those among reaches were (F =

6.546, p = 0.006) (Figure 42). Post hoc tests indicated that mean biomass in Reach 5 (years and reaches

combined) was significantly greater than in Reach 3 (p = 0.005). Abundance of channel catfish was not

different in between channel (F = 1.071, p = 0.312) or among reaches (F = 3.019, p = 0.070) comparisons

(Figure 43). Among year differences were significant (F = 4.937, p = 0.010); post hoc tests indicated that

abundance (reaches and channels combined) in 1997 was greater than in 1994 and 1995 (p = 0.008 and

0.042).

Rare Fish Occurrence in Secondary Channels

Between 1993 and 1997, five specimens of rare fish were captured during spring inventories in

secondary channels (Table 12). One Colorado pikeminnow was captured in 1994 in a secondary

downstream of Sand Island, Utah. Four razorback suckers (all presumably stocked individuals) were

captured in secondary channels between 1995 and 1997. All captures were between RM 95 and 108. No

specimen of roundtail chub was captured in secondary channels during spring inventories between 1993 and

1997.
59

Table 12. Rare fishes captured in San Juan River secondary channels during spring inventories, 1993 –

1997.

SPECIES DATE RM TL SL WT SEX TAG NUMBER

Ptychocheilus lucius 16 May 94 76.0 759 630 4000 F 7F7D075651

Xyrauchen texanus 13 May 95 87.0 372 600 F 1F404E666D

Xyrauchen texanus 17 May 96 107.8 420 340 910 M 1F40464E0D

Xyrauchen texanus 17 May 96 101.0 450 361 980 F 1F43670136

Xyrauchen texanus 4 May 97 95.8 434 345 850 M 1F40464E0D

 
60

1994 1995 1996 1997

0

200

400

600

1994 1995 1996 1997

MEAN BIOMASS (G)

0

200

400

600

Figure 37 . Mean biomass (g) of bluehead sucker, Catostomus discobolus, in

 primary and secondary channels of the San Juan River, 1994 - 1997. 

YEAR

1994 1995 1996 1997

0

200

400

600

PRIMARY CHANNEL

SECONDARY CHANNEL

REACH 5

REACH 4

REACH 3
61

1994 1995 1996 1997

0.0

0.1

0.2

0.3

0.4

0.5

1994 1995 1996 1997

ABUNDANCE (FISH/MIN)

0.0

0.1

0.2

0.3

0.4

0.5

Figure 38. Abundance (fish/min) of bluehead sucker, Catostomus discobolus, in

 San Juan River primary and secondary channels during spring

 inventories, 1994 - 1997.

YEAR

1994 1995 1996 1997

0.0

0.1

0.2

0.3

0.4

0.5

PRIMARY CHANNEL

SECONDARY CHANNEL

REACH 5

REACH 4

REACH 3
62

1994 1995 1996 1997

0

400

800

1200

1600

1994 1995 1996 1997

MEAN BIOMASS (G)

0

400

800

1200

1600

Figure 39 . Mean biomass (g) of common carp, Cyprinus carpio, in

 primary and secondary channels of the San Juan River,

 1994 - 1997. 

YEAR

1994 1995 1996 1997

0

400

800

1200

1600

PRIMARY CHANNEL

SECONDARY CHANNEL

REACH 5

REACH 4

REACH 3
63

1994 1995 1996 1997

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1994 1995 1996 1997

ABUNDANCE (FISH/MIN)

0.0

0.2

0.4

0.6

0.8

1.0

1.2

Figure 40. Abundance (fish/min) of common carp, Cyprinus carpis,

 in San Juan River primary and secondary channels 

 during spring inventories, 1994 - 1997.

YEAR

1994 1995 1996 1997

0.0

0.2

0.4

0.6

0.8

1.0

1.2

PRIMARY CHANNEL

SECONDARY CHANNEL

REACH 5

REACH 4

REACH 3
64

1994 1995 1996 1997

0

400

800

1200

1600

1994 1995 1996 1997

MEAN BIOMASS (G)

0

400

800

1200

1600

Figure 41. Mean biomass (g) of channel catfish, Ictalurus punctatus,

 primary and secondary channels of the San Juan River, 1994 -

 1997.

YEAR

1994 1995 1996 1997

0

400

800

1200

1600

PRIMARY CHANNEL

SECONDARY CHANNEL

REACH 5

REACH 4

REACH 3
65

1994 1995 1996 1997

0.0

0.4

0.8

1.2

1994 1995 1996 1997

ABUNDANCE (FISH/MIN)

0.0

0.4

0.8

1.2

Figure 42. Abundance (fish/min) of channel catfish, Ictalurus punctatus, in

 San Juan River primary and secondary channels during spring 

 inventories, 1994 - 1997. 

YEAR

1994 1995 1996 1997

0.0

0.4

0.8

1.2

PRIMARY CHANNEL

SECONDARY CHANNEL

REACH 5

REACH 4

REACH 3
FISH ASSEMBLAGES OF SAN JUAN RIVER

SECONDARY CHANNELS DURING SUMMER

1991 -- 1997
67

INTRODUCTION

During summer, San Juan River secondary channels do not have any habitat type

that is absent in the primary channel, but some habitats that are relatively rare in the

primary channel are fairly common in secondary channels. For example, during summer

low- and zero-velocity pool habitats are common in many secondary channels. Habitat

quantity and quality in secondary channels are dependent on flow levels, perhaps more so

than in the primary channel. When flows are < 500 cfs, only about 50 % of the secondary

channels are wetted (R. Bliesner, pers. comm.). During such periods, isolated pools with

elevated water temperature and depressed dissolved oxygen are among the most abundant

habitats available. Presumably, daily and seasonal changes in availability and quality of

habitats have a strong influence on fish assemblages of secondary channels.

Objectives of the Secondary Channels Ichthyofaunal Inventory were:

1) Characterize the type of secondary channels in the San Juan River;

2) Characterize the faunal assemblages of secondary channels;

3) Determine seasonal use patterns of secondary channels by target species;

and

4) Relate habitat use and availability of secondary channels to flow levels.

This phase of the Secondary Channels Study was designed to document the

species occupying San Juan River secondary channels during summer low-flow periods

and to characterize the effect of spring flow attributes on summer fish assemblages and

abundance of individual species. This chapter specifically addresses study objectives 2

(in part), 3 (in part), and 4 (in part).

STUDY AREA

Summer sampling of San Juan River secondary channels occurred between RM

149.5 (Shiprock) and RM 76.5 (Sand Island). During summer low-flow periods, some

secondary channels were dry for much of their lengths, others had scattered pools,

sometimes connected by shallow rivulets, and a few had continuous surface flow for their

entire lengths. Summer convectional storms sometimes raised water levels shortly before

or during sampling and briefly inundated dry channels and connected pools in others.

Some had inflow at their mouths and water persisted for variable distances downstream.

Isolated pools in some were maintained by extrusion of subsurface water. About 50 % of

the secondary channels in the study area had surface water at flows of 500 cfs and about

78 % were watered at 1500 cfs (R. Bliesner, pers. comm.). Summer flows during each

year of study averaged from about 280 to 2010 cfs (Figure 44).
68

Figure 43. Mean weekly discharge of San Juan River, 1 July through 31 October, 1991 - 1997. 

 Horizonal lines indicate time of summer sampling trips.

WEEK

1-5 JUL

6-10

11-15

16-20

21-25

26-31

1-5 AUG

6-10

11-15

16-20

21-25

26-31

1-5 SEP

6-10

11-15

16-20

21-25

26-30

1-5 OCT

6-10

11-15

16-20

21-25

26-31

DISCHARGE (CFS)

0

2000

4000

6000

8000

1991 

1992 

1993 

1994 

1995 

1996 

1997 
69

During summer, base substrates (cobble, gravel, and sand) were typically overlain

with a silt layer of varying thickness (1 or 2 mm to 20 cm) in low-velocity areas. Riffles

were usually the only silt-free habitats in secondary channels. Riparian vegetation

shaded some secondary channels but others were completely exposed to sunlight.

Secondary channels having surface water one year were sometimes dry in

subsequent years. Deposition of organic debris, along with silt and sand, during high

flow periods precluded inflow to some channels and low flows resulted in drying of

others. Within each secondary channel, the mix of habitats varied among years. A

secondary channel with riffles, pools, and runs, all having silt-free substrates, might have

only a few silt-bottomed isolated pools the next year.

METHODS

Summer sampling of San Juan River secondary channels between Shiprock 9RM

147.9) and Sand Island (RM 76.5) occurred during late-July through August, 1991

through 1997. In 1991 and 1992, only secondaries with surface inflow at their mouths

were sampled. In subsequent years, the inflow requirement was discontinued and all

secondary channels that had surface water, regardless of extent, were sampled. If surface

water was limited to the embayment or backwater associated with the secondary

channel’s debouchement, it was not sampled as part of the secondary channel studies;

these habitats were sampled under auspices of the Early Life History Studies portion of

the San Juan River Seven-Year Research program (E. Archer, pers. comm).

Location of sample sites within secondary channels depended upon extent of

surface water. If a secondary channel had surface flow throughout, the middle portion of

it was sampled. If surface water consisted of scattered pools and short-flowing areas,

collections were made wherever there was water. Regardless of the extent of surface

water, all habitat types (e.g., pool, run, riffle, and backwater) present within the

secondary channel were sampled.

Drag seines (3.1 x 1.8 m and 1.6 or 3.2 mm mesh) were used to collect fishes. In

riffles, the seine was anchored across the wetted perimeter (or portion, depending upon

width), perpendicular to direction of flow, and held by one individual. A second worker

agitated the substrate from about 4 m upstream of the seine into the seine. Pools with

debris piles were sampled by encircling the instream cover with the seine, agitating the

cover, and lifting the seine. Other areas were sampled by dragging the seine parallel or

diagonal to the shore; specific angle of the drag depended upon flow and substrate. In

any case, the goal was to maximize efficiency of the drag. Area of each haul and kick

effort was determined and recorded.

Large-bodied (> 150 mm Total Length [TL]) native fish were weighed (+ 1.0 g),

measured (+ 1 mm TL), and released alive. All specimens in each seine haul were
70

examined to determine if roundtail chub, Colorado pikeminnow, or razorback sucker was

present. If any of these was present, (individuals of these species < 75 mm TL were

occasionally overlooked), it was weighed, measured, and released. All other specimens

were preserved in 10 % formalin and returned to the laboratory for identification and

enumeration. All specimens that could not be readily identified were sent to the Museum

of Southwestern Biology (UNM) for identification. All retained specimens were

accessioned to the NMGF Collection of Fishes. Six-letter codes (first 3 letters of genus

and first 3 letters of species) were used to identify species in tables.

Following specimen collection, water quality was determined at a location not

disturbed by specimen collection. Such areas were also a sufficient distance from the

mouth of a secondary channel that primary channel influences were minimized. At each

sampled secondary channel, water temperature (°C), dissolved oxygen (mg/l), and

specific conductance (μmho/cm) were determined. General notes on habitat conditions

for each sampled secondary channel were recorded.

Data from the USGS gage at Shiprock (#09368000) were used to characterize five

attributes of spring runoff. The period of spring runoff was defined as 1 March through

31 July (R. Bliesner, pers. comm.). Mean spring runoff discharge (cfs) data for each year

were provided by Keller-Bliesner Engineering, Inc. Monthly discharge data , spring

runoff volume (ac-ft), days discharge > 3,000, 5,000, and 8,000 cfs were obtained from

USGS Water Resources (New Mexico) Data Report (USGS, 1991 et seq.; Table 13).

Although these attributes were covariant, each nonetheless provided slightly different

metrics for assessing flow-related responses of fish populations.

For most analyses, the Geomorphic Reaches of Bliesner and Lamarra (2000) were

used to group secondary channel data. Abundance was estimated as the number of

individuals (total, by Geomorphic Reach, or species) captured per m2

 sampled. The

Shannon-Wiener Diversity Index (H = ΣpIlnpI, where pI = proportion of species i in the

sample) was used to evaluate changes in assemblage structure (Ricklefs, 1979) among

years and Geomorphic Reaches. Friedman’s χ2 and Kendall’s coefficient of concordance

(W; Zar, 1984) were used to evaluate changes in rank abundance of species; only those

species collected in at least 5 of 7 years in each Geomorphic Reach were used.

Regression analysis was used to assess the relationship between spring runoff attributes

and summer abundance of six commonly collected species. These were native speckled

dace, flannelmouth sucker, and bluehead sucker and nonnative red shiner, fathead

minnow, and channel catfish. Although western mosquitofish was occasionally collected

in large numbers, its occurrence was irregular and not deemed sufficient for meaningful

analyses. Analysis of Variance (ANOVA) was used to evaluate differences in abundance

and Shannon-Wiener Diversity Index values (Sokal and Rohlf, 1981) within Geomorphic

Reaches (across years) and within a year (across reaches). The Tukey Honest Significant

Difference test was used to determine which comparisons were different if ANOVA

yielded significant results.
71

Table 13. Attributes of spring runoff, San Juan River, 1991 – 1997. Data from USGS

Shiprock gage (#09368000).

MONTH 1991 1992 1993 1994 1995 1996 1997

MARCH1 1029 1258 5099 886 2777 700 2057

APRIL1 1750 3329 5970 868 3472 532 2295

MAY1 3515 6403 6387 4779 6108 1997 5703

JUNE1 2443 4757 6816 6563 9351 2661 8286

JULY1 885 1763 2438 3000 7193 789 3249

MEAN (CFS)2 2279 4083 6646 3592 5440 1607 4805

VOLUME (AC-FT) 555,308 1,004,618 1,539,529 790,550 1,523,378 355,850 1,203,366

DAYS > 3000 CFS 26 74 126 62 109 16 75

DAYS > 5000 CFS 0 45 101 43 72 0 44

DAYS > 8000 CFS 0 4 11 7 27 0 24

1

Mean monthly discharge determined from USGS Water Year reports.

2

Mean annual spring runoff discharge provided by Keller-Bliesner Engineering, Inc.

RESULTS

Summer secondary channel sampling occurred between RM 147.9 (Shiprock) and

RM 76.5 (Sand Island) in all years except 1997 when secondary channels downstream to

RM 68.7 (Chinle Creek) were sampled. All summer inventories were conducted during

mid to late August, except 1992 when sampling as done in late July through early

August. Sampling was post-spawning for native fishes (speckled dace, flannelmouth

sucker, and bluehead sucker), but overlapped, in part, spawning by red shiner and fathead

minnow. Comparatively few secondary channels were sampled in 1991 and 1992 (n = 21

and 13). In those years, inflow at top of secondary channel was required to sample it. In

addition, flows were low (< 300 cfs) in 1991 at time of sampling and comparatively few

secondary channels had water. Beginning in 1993, inflow at the mouth of a secondary

channel was not required for it to be sampled. From 1993 through 1997, 33 to 45

secondary channels were sampled each year. Mean daily discharge during summer

inventories varied from 278 (1991) to 2011 (1997) cfs.

Water Quality

Water temperature at time of summer inventories did not change appreciably from

upstream to downstream in primary or secondary channels (Figure 45).
72

150

145

140

135

130

125

120

115

110

105

100

95

90

85

80

75

WATER TEMPERATURE (C)

0

6

12

18

24

30

36

150

145

140

135

130

125

120

115

110

105

100

95

90

85

80

75

0

6

12

18

24

30

36

1992

1993

150

145

140

135130

125

120

115

110

105

100

9590

85

80

75

0

6

12

18

24

30

36

1994

150

145

140

135

130

125

120

115

110

105

100

95

90

85

80

75

0

6

12

18

24

30

36

150

145

140

135130

125

120

115

110

105

100

9590

85

80

75

0

6

12

18

24

30

36

1991

1995

150

145

140

135

130

125

120

115

110

105

100

95

90

85

80

75

0

6

12

18

24

30

36

1996

Figure 44. Water temperature (Co ) of San Juan River secondary and primary channels during

 summer inventories, 1991 - 1997.

RIVER MILE

150

145

140

135

130

125

120

115

110

105

100

95

90

85

80

75

70

0

6

12

18

24

30

36

SECONDARY

PRIMARY

1997
73

Secondary channel water temperature was usually similar to that of the adjacent primary

channel; if different, temperature was greater in the secondary channel in most instances.

Mean water temperature was > 21.0 and < 27.0° C in all years (Table 14). Dissolved

oxygen generally declined from upstream to downstream in 1994, 1995, and 1996 in

primary and secondary channels (Figure 46). Dissolved oxygen varied more among

secondary channels than in the primary channel, particularly in 1993, 1994, and 1996.

From 1991 through 1997, mean dissolved oxygen declined in both the primary and

secondary channels (Table 14). In most years, differences in specific conductance

between secondary and primary channels were negligible (Figure 47). Most differences

occurred in 1994 and 1996; two differences in 1996 were considerable. The 1996 spikes

were near Aneth and Montezuma Creek. Specific conductance tended to be lower in

years of high summer flows and higher in years of low summer flows (Table 14). In

1991 and 1997, there was a slight increase in specific conductance from upstream to

downstream, in 1993 an almost imperceptible decline, and no evident pattern in other

years.

Table 14. Mean water quality parameters of San Juan River primary and secondary

channels during summer inventories, 1991 – 1997. Parenthetic values are standard

deviations.

WATER TEMPERATURE

(Co)

DISSOLVED OXYGEN

(mg.l)

CONDUCTIVITY

(μmho/cm)

YEAR 1o 2o 1o 2o 1o 2o

1991 25.6 (2.1) 26.5 (3.2) 10.4 (0.9) 11.4 (2.1) 833 (134) 962 (362)

1992 25.2 (1.6) 26.5 (3.0) 10.6 (0.6) 11.0 (1.1)

1993 23.8 (1.8) 24.4 (2.7) 8.9 (0.7) 8.3 (1.2) 722 (113) 783 (183)

1994 22.7 (1.8) 23.0 (1.8) 8.5 (1.6) 7.8 (2.4) 903 (110) 957 (127)

1995 23.9 (1.2) 24.4 (2.0) 6.4 (0.7) 6.3 (1.0) 586 (69) 601 (79)

1996 23.5 (1.9) 24.2 (3.2) 7.0 (0.7) 7.0 (1.1) 682 (72) 1230 (2190)

1997 21.9 (1.6) 22.2 (1.9) 6.2 (0.3) 6.2 (0.5) 432 (79) 448 (110)

Summer Fish Assemblages

A total of 14 species (five native and nine nonnative) were collected during

summer inventories (Table 15). The greatest number of species (n = 11) was collected in

1991 and 1995 and the fewest (n = 9) in 1993). Number of native species (n = 5) was

greatest in 1997 and fewest nonnative species (n = 6) were found in 1993 and 1997. The

increase in number of native species in 1997 was the result of capture of rare roundtail

chub and stocked Colorado pikeminnow. Five nonnative species (common carp, red

shiner, fathead minnow, channel catfish, and western mosquitofish) and three native

species (speckled dace, flannelmouth sucker, and bluehead sucker) were captured in all

years of study. Few sub-adult or adult flannelmouth sucker, bluehead sucker, common

carp, or channel catfish were collected. All age-classes (young-of-year, juvenile, subadult, and adult) of red shiner, fathead minnow, and speckled dace were collected; YOY
74

150145140135130125120115110105100 95 90 85 80 75

0

5

10

15

20

1991

150145140135130125120115110105100 95 90 85 80 75

DISSOLVED OXYGEN (MG/L)

0

5

10

15

20

1992

150145140135130125120115110105100 95 90 85 80 75

0

5

10

15

20

1993

150145140135130125120115110105100 95 90 85 80 75

0

5

10

15

20

1994

150145140135130125120115110105100 95 90 85 80 75

0

5

10

15

20

1995

150145140135130125120115110105100 95 90 85 80 75

0

5

10

15

20

Figure 45. Dissolved oxygen (mg/l) of San Juan River secondary and primary channels during

 summer inventories, 1991 - 1997.

RIVER MILE

150145140135130125120115110105100 95 90 85 80 75

0

5

10

15

20

SECONDARY

PRIMARY

1996

1997
75

150145140135130125120115110105100 95 90 85 80 75

0

500

1000

1500

2000

2500

150145140135130125120115110105100 95 90 85 80 75

CONDUCTIVITY (MICROMHOS/CM)

0

500

1000

1500

2000

2500

1991

1992

150145140135130125120115110105100 95 90 85 80 75

0

500

1000

1500

2000

2500

1993

150145140135130125120115110105100 95 90 85 80 75

0

500

1000

1500

2000

2500

1994

150145140135130125120115110105100 95 90 85 80 75

0

500

1000

1500

2000

2500

1995

150145140135130125120115110105100 95 90 85 80 75

0

500

1000

1500

2000

4000

6000

8000

10000

12000

14000

Figure 46. Specific conductance (micromhos/cm) of San Juan River secondary and primary

 channels during summer inventories, 1991 - 1997. 

RIVER MILE

150145140135130125120115110105100 95 90 85 80 75

0

500

1000

1500

2000

2500

SECONDARY

PRIMARY

1996

1997
76

Table 15. Occurrence of fishes in San Juan River secondary channels during summer, 1991 – 1997. I =

introduced and N = native. Six letter species codes derived from first three letters of genus and first three

of species.

COMMON SCIENTIFIC ACRONYM STATUS 1991 1992 1993 1994 1995 1996 1997

Common carp Cyprinus carpio CYPCAR I X X X X X X X

Red shiner Cyprinus lutrensis CYPLUT I X X X X X X X

Roundtail chub Gila robusta GILROB N X

Fathead minnow Pimephales promelas PIMPRO I X X X X X X X

Colorado pikeminnow Ptychocheilus lucius PTYLUC N X

Speckled dace Rhinichthys osculus RHIOSC N X X X X X X X

Flannelmouth sucker Catostomus latipinnis CATLAT N X X X X X X X

Bluehead sucker Catostomus discobolus CATDIS N X X X X X X X

Black bullhead Ameiurus melas AMEMEL I X X

Channel catfish Ictalurus punctatus ICTPUN I X X X X X X X

Plains killifish Fundulus zebrinus FUNZEB I X X X X X

Western mosquitofish Gambusia affinis GAMAFF I X X X X X X X

Green sunfish Lepomis cyanellus LEPCYA I X X X X

Largemouth bass Micropterus salmoides MICSAL I X X X X X

Total Native 5 3 3 3 3 3 3 5

Total Nonnative 9 8 7 6 7 8 9 6

individuals were typically the most abundant age-class of these species. Most captured

flannelmouth sucker and bluehead sucker were juveniles (25 to 100 mm TL).

Nonnative red shiner was the most abundant species in secondary channels in all

years except 1994 and 1996 when nonnative fathead minnow was most common (Table

16). Abundance of other nonnative species was low in most years; however, channel

catfish was moderately abundant in 1994 and western mosquitofish was common in

1996. Native speckled dace was the second- or third-most abundant species in all years.

In 1991 and 1992, flannelmouth sucker was moderately common, but in subsequent years

it was a relatively small proportion of the total collection (Figure 48). Bluehead sucker

abundance was comparatively high in 1993 and 1995. Roundtail chub and Colorado

pikeminnow were collected in 1997. Despite some shifts in the abundance rank of

species, there was a high degree of concordance in ranks among years (W = 0.849, p <

0.001).

Among years, total abundance varied considerably. Total abundance was high in

1993 and 1995 (> 12 fish/m2

), but was only 0.74 fish/m2 in 1997 (Figure 49). The

restriction of sampling to only those secondary channels with inflow in 1991 and 1992

may have contributed to the comparatively low fish abundance (< 3.0 fish/m2

) in those

years. Shannon-Wiener Diversity Index values varied little from year to year (Figure 49).

The highest values were in 1992 and 1994. There was no relationship between discharge

during sampling periods and total fish abundance per sampling period (r2 = 0.079, p =

0.541).
77

Figure 47. Relative abundance of commonly collected fishes in San Juan River

secondary channels (Reaches combined) during summer 1991 – 1997.

RHIOSC

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

PIMPRO CYPLUT

CYPLUT

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

RHIOSC

PIMPRO

RHIOSC

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

CYPLUT

PIMPRO

CATLAT CYPLUT

CATDIS

ICTPUN

CYPCAR

OTHER

PIMPRO

RHIOSC

CYPLUT

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

RHIOSC

PIMPRO

CYPLUT

CYPCAR

OTHER

ICTPUN

CATDIS

CATLAT

RHIOSC

PIMPRO

RHIOSC

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

CYPLUT

PIMPRO

1991 1992 1993

1994 1995 1996

1997
78

Table 16. Fish species collected in San Juan River secondary channels (RM 149 – RM

76.5) during summer inventories, 1991 – 1997. Bold-lettered species were used to

calculate Kendall’s coefficient of concordance (W).

1991 1992 1993 1994

SPECIES N SPECIES N SPECIES N SPECIES N

CYPLUT 1373 CYPLUT 728 CYPLUT 14034 PIMPRO 3721

RHIOSC 228 RHIOSC 249 PIMPRO 5516 CYPLUT 3073

PIMPRO 221 CATLAT 239 RHIOSC 4957 RHIOSC 2852

CATLAT 163 PIMPRO 166 CATDIS 1529 ICTPUN 830

GAMAFF 84 CATDIS 88 CATLAT 701 CYPCAR 210

ICTPUN 66 GAMAFF 47 ICTPUN 248 CATLAT 203

CATDIS 34 FUNZEB 15 CYPCAR 170 GAMAFF 171

CYPCAR 10 ICTPUN 7 GAMAFF 115 CATDIS 166

FUNZEB 3 CYPCAR 5 MICSAL 3 FUNZEB 16

MICSAL 3 LEPCYA 2 MICSAL 2

LEPCYA 2

TOTAL N 2187 1546 27273 11244

AREA 928 680 1456 1344

ABUND 2.357 2.274 15.297 8.366

1995 1996 1997

SPECIES N SPECIES N SPECIES N

CYPLUT 12841 PIMPRO 2985 CYPLUT 1335

RHIOSC 5725 CYPLUT 3243 RHIOSC 751

PIMPRO 4218 GAMAFF 946 PIMPRO 215

CATDIS 3262 AMEMEL 192 ICTPUN 57

ICTPUN 692 RHIOSC 178 GAMAFF 56

CATLAT 366 CATLAT 108 CATLAT 50

GAMAFF 168 ICTPUN 63 AMEMEL 8

CYPCAR 18 FUNZEB 30 GILROB 5

MICSAL 11 CATDIS 28 CATDIS 4

FUNZEB 6 CYPCAR 5 CYPCAR 2

LEPCYA 2 MICSAL 3 PTYLUC 1

LEPCYA 1

TOTAL N 27309 8782 2484

AREA 2240 1296 3355

ABUND 12.195 6.776 0.740

Geomorphic Reach 5

Eleven species, eight nonnative and three native, were collected from secondary

channels in Reach 5 between 1991 and 1997. Neither Colorado pikeminnow nor

razorback sucker was collected. Total abundance and abundance of each species varied
79

Figure 48. Abundance of fishes and Shannon-Wiener Diversity

 Index values of fish assemblages in San Juan River 

 secondary channels (Geomorphic Reaches combined)

 during summer, 1991 - 1997. 

YEAR

1991 1992 1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

)

0

2

4

6

8

10

12

14

16

SHANNON-WIENER INDEX (H)

0.0

0.4

0.8

1.2

1.6

2.0

ABUNDANCE 

H 
80

considerably (Table 17). Total abundance peaked in 1993 at 25.2 fish/m2 and thereafter

declined to the Reach low of 1.26 fish/m2 in 1997. Although abundance varied

considerably, little change was noted in Shannon-Wiener Diversity Index values (Figure

50). There was no correlation between discharge at time of sampling and total abundance

(r2 = 0.141, p = 0.407).

Table 17. Number and abundance (fish/m2) of fishes in San Juan River secondary

channels in Geomorphic Reach 5 (RM 154 – RM 131) during summer, 1991 – 1997.

Bold-lettered species used to calculate Kendall’s coefficient of concordance (W).

1991 1992 1993 1994

SPECIES N ABUN SPECIES N ABUN SPECIES N ABUN SPECIES N ABUN

CYPLUT 997 2.44 CYPLUT 316 1.32 CYPLUT 5448 11.16 PIMPRO 2387 5.14

PIMPRO 13 0.32 CATLAT 123 0.51 PIMPRO 3546 7.27 RHIOSC 1777 3.83

RHIOSC 103 0.25 CATDIS 88 0.37 RHIOSC 1765 3.62 CYPLUT 445 0.96

GAMAFF 77 0.19 PIMPRO 64 0.27 CATDIS 1159 2.38 ICTPUN 287 0.62

CATLAT 71 0.17 RHIOSC 61 0.25 CATLAT 234 0.48 CATDIS 151 0.33

CATDIS 31 0.08 GAMAFF 12 0.05 GAMAFF 104 0.21 GAMAFF 127 0.27

CYPCAR 7 0.02 FUNZEB 8 0.03 ICTPUN 29 0.06 CATLAT 83 0.18

FUNZEB 3 0.01 ICTPUN 2 0.01 CYPCAR 19 0.04 CYPCAR 75 0.16

MICSAL 3 0.01 LEPCYA 2 0.01 MICSAL 3 0.01 FIMZEB 8 0.02

LEPCYA 1 <0.01 CYPCAR 1 <0.01 MICSAL 1 <0.01

TOTAL N 1423 677 12307 5341

AREA 408 340 488 464

ABUND 3.488 2.821 25.219 11.511

1995 1996 1997

SPECIES N ABUN SPECIES N ABUN SPECIES N ABUN

CATDIS 1981 3.30 PIMPRO 1045 2.90 CYPLUT 359 0.50

CYPLUT 1209 2.02 CYPLUT 830 2.31 RHIOSC 316 0.44

RHIOSC 853 1.42 GAMAFF 586 1.63 PIMPRO 161 0.22

PIMPRO 436 0.73 RHIOSC 117 0.33 GAMAFF 43 0.06

GAMAFF 131 0.22 CATLAT 54 0.15 CATLAT 23 0.03

CATLAT 81 0.14 CATDIS 28 0.08 AMEMEL 3 <0.01

CYPCAR 8 0.01 FUNZEB 19 0.05 CYPCAR 2 <0.01

MICSAL 8 0.01 ICTPUN 10 0.03 ICTPUN 1 <0.01

LEPCYA 2 <0.01 AMEMEL 4 0.01

CYPCAR 3 0.01

LEPCYA 1 <0.01

TOTAL N 4709 2697 908

AREA 600 360 720

ABUND 7.848 7.492 1.261

Red shiner was the most abundant species in 1991, 1992, 1993, and 1997.

Fathead minnow was most abundant in 1994 and 1996 and bluehead sucker was most
81

Figure 49. Abundance of fishes and Shannon-Wiener Diversity Index 

 values of fish assemblages in Geomorphic Reach 5 secondary 

 channels, San Juan River, 1991 - 1997.

YEAR

1991 1992 1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

)

0

5

10

15

20

25

30

SHANNON-WIENER INDEX (H)

0.0

0.5

1.0

1.5

2.0

ABUNDANCE

H 
82

 abundant in 1995. Speckled dace varied from the second- to fifth-most common species

and flannelmouth sucker varied from second- to seventh-most abundant. Common carp

and channel catfish, both common during spring inventories, were rare in most years.

Despite some variation in abundance rank, concordance of ranks among years was high

(W = 0.7551, p < 0.001). Expressed as a proportion, red shiner represented 25 to 75 % of

each year’s collection in all years except 1994 (Figure 51). Relative abundance of

speckled dace, usually the most common native species, varied from 4 (1996, a low flow

year) to 35 % (1997, a high flow spring runoff year with high summer flows). In 1995, a

high spring runoff year, bluehead sucker was 42 % of the collection.

No attribute of spring runoff was significantly related to summer abundance of

red shiner (Table 18), fathead minnow (Table 19), speckled dace (Table 20),

flannelmouth sucker (Table 21) or channel catfish (Table 23). Number of days spring

runoff > 5000 cfs had the strongest relationship with red shiner, fathead minnow,

speckled dace, and flannelmouth sucker (Figure 52). Summer abundance of bluehead

sucker was significantly related to several attributes of spring runoff (Table 22); the

strongest was with days discharge > 3000 cfs (Figure 52).

Table 18. Results of linear regression analysis of relationship between spring runoff

attributes and summer secondary channel abundance of red shiner, Cyprinella lutrensis,

in Geomorphic Reach 5, San Juan River, 1991 – 1997.

RUNOFF ATTRIBUTE r2 r p

Runoff volume (ac.ft.) 0.1310 0.3619 0.42

Runoff mean (ac. ft) 0.1796 0.4238 0.34

Days discharge > 3000 cfs 0.2585 0.5085 0.24

Days discharge > 5000 cfs 0.3813 0.6175 0.14

Days discharge > 8000 cfs 0.0144 0.1202 0.78

Table 19. Results of linear regression analysis of relationship between spring runoff

attributes and summer secondary channel abundance of fathead minnow, Pimephales

promelas, in Geomorphic Reach 5, San Juan River, 1991 – 1997.

RUNOFF ATTRIBUTE r2 r p

Runoff volume (ac.ft.) 0.0292 0.1710 0.71

Runoff mean (ac. ft) 0.0608 0.2466 0.59

Days discharge > 3000 cfs 0.1157 0.3402 0.46

Days discharge > 5000 cfs 0.2307 0.4803 0.28

Days discharge > 8000 cfs 0.0325 0.1803 0.70
83

Figure 50. Relative abundance of commonly collected fishes in Geomorphic Reach 5,

San Juan River, 1991 – 1997.

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

CYPLUT

RHIOSC

PIMPRO

CYPLUT

CATDIS

ICTPUN

CYPCAR

OTHER

CATLAT

RHIOSC

PIMPRO

CYPLUT

RHIOSC

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

PIMPRO

CYPLUT

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

RHIOSC PIMPRO

CYPLUT

CATDIS

ICTPUN

CYPCAR

OTHER

PIMPRO

CATLAT RHIOSC

CYPLUT

CATDIS

ICTPUN

CYPCAR

OTHER

CATLAT

RHIOSC

PIMPRO

CYPLUT

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

PIMPRO

RHIOSC

1991 1992 1993

1994 1995 1996

1997
84

 Table 20. Results of linear regression analysis of relationship between spring runoff

attributes and summer abundance of speckled dace, Rhinichthys osculus, in Geomorphic

Reach 5, San Juan River, 1991 – 1997.

RUNOFF ATTRIBUTE r2 r p

Runoff volume (ac.ft.) 0.1475 0.3840 0.40

Runoff mean (ac. ft) 0.2094 0.4576 0.30

Days discharge > 3000 cfs 0.2808 0.5299 0.22

Days discharge > 5000 cfs 0.3991 0.6317 0.13

Days discharge > 8000 cfs 0.0103 0.1013 0.83

Table 21. Results of linear regression analysis of relationship between spring runoff

attributes and summer abundance of flannelmouth sucker, Catostomus latipinnis, in

Geomorphic Reach 5, San Juan River, 1991 – 1997.

RUNOFF ATTRIBUTE r2 r p

Runoff volume (ac.ft.) 0.0742 0.2724 0.56

Runoff mean (ac. ft) 0.0843 0.2903 0.53

Days discharge > 3000 cfs 0.1673 0.4090 0.36

Days discharge > 5000 cfs 0.2093 0.4574 0.30

Days discharge > 8000 cfs 0.1220 0.3493 0.44

Table 22. Results of linear regression analysis of relationship between spring runoff

attributes and summer abundance of bluehead sucker, Catostomus discobolus, in

Geomorphic Reach 5, San Juan River, 1991 – 1997.

RUNOFF ATTRIBUTE r2 r p

Runoff volume (ac.ft.) 0.6147* 0.7840 0.04

Runoff mean (ac. ft) 0.6175* 0.7858 0.04

Days discharge > 3000 cfs 0.6312* 0.7945 0.03

Days discharge > 5000 cfs 0.5923* 0.7696 0.04

Days discharge > 8000 cfs 0.3310 0.5759 0.18
85

DAYS DISCHARGE > 5000 CFS

0 20 40 60 80 100 120

0

2

4

6

8

10

12

Red Shiner

r

2

 = 0.3813, p = 0.14

DAYS DISCHARGE > 5000 CFS

0 20 40 60 80 100 120

0

1

2

3

4

Fathead minnow

r

2

 = 0.2307, p = 0.28

DAYS DISCHARGE > 5000 CFS

0 20 40 60 80 100 120

ABUNDANCE (FISH/M2

)

0

1

2

3

4

5

Speckled dace

r

2

 = 0.3991, p = 0.13

DAYS DISCHARGE > 5000 CFS

0 20 40 60 80 100 120

0.00

0.25

0.50

0.75

1.00

Flannelmouth sucker

r

2

 = 0.2093, p = 0.30

DAYS DISCHARGE > 3000 CFS

0 20 40 60 80 100 120 140

0

1

2

3

4

Bluehead sucker

r

2

 = 0.6312, p = 0.03

Figure 51. Secondary channel abundance of red shiner, fathead minnow, speckled dace, 

 flannelmouth sucker, bluehead sucker, and channel catfish versus attributes of 

 spring discharge, Geomorphic Reach 5, San Juan River, 1991 - 1997.

RUNOFF VOLUME (AC.FT.)

2.0e+5 4.0e+5 6.0e+5 8.0e+5 1.0e+6 1.2e+6 1.4e+6 1.6e+6

0.00

0.25

0.50

0.75

1.00

Channel catfish

r

2

 = 0.0317, p = 0.70
86

Table 23. Results of linear regression analysis of relationship between spring runoff

attributes and summer abundance of channel catfish, Ictalurus punctatus, in Geomorphic

Reach 5, San Juan River, 1991 – 1997.

RUNOFF ATTRIBUTE r2 r p

Runoff volume (ac.ft.) 0.0317 0.1780 0.70

Runoff mean (ac. ft) 0.0125 0.1160 0.81

Days discharge > 3000 cfs 0.0028 0.0533 0.91

Days discharge > 5000 cfs 0.0013 0.0362 0.94

Days discharge > 8000 cfs 0.0238 0.1544 0.74

Geomorphic Reach 4

Twelve fish species, four native and eight nonnative, were collected in

Geomorphic Reach 4 secondary channels between 1991 and 1997 (Table 24). Ten

species were collected in each 1994 and 1996. Only three native species (speckled dace,

flannelmouth sucker, and bluehead sucker) were regularly collected in Reach 4 secondary

channels and roundtail chub was collected in 1997. Red shiner was the most abundant

species in all years except 1996, when fathead minnow was most common. Speckled

dace was always the second-most common species, except in 1994 and 1996 when it was

third- and sixth-most common. Abundance rank of flannelmouth and bluehead suckers

varied from year to year and bluehead sucker was absent from Reach 4 collections in

1992. Despite variation, overall abundance rank of species was fairly similar among

years (W = 0.767, p < 0.001). Red shiner was at least 42 % of each summer collection,

except 1997 (Figure 53). In 1996, nonnative fishes represented over 95 % of the

collection.

Abundance of fishes in Reach 4 secondary channels peaked at about 17 fish/m2 in

1993 and 1995, years of high spring runoff and moderately high summer flows.

Abundance of fishes was lowest in 1991 (0.83/m2) and 1997 (0.44/m2). There was no

relationship between discharge at time of sampling and abundance of fishes (r2

 = 0.058, p

= 0.72). Assemblage diversity generally declined from 1991 through 1997 (Figure 54).

In 1991, 1992, and 1994, years of comparatively high H values, the two most-abundant

species represented about 70 % of the specimens. In years of comparatively low H

values (1995, 1996, and 1997), the two most abundant species were 84 to 91 % of the

collections.

The relationship between spring runoff attributes and species abundance was

fairly strong for several attributes in Reach 4. Abundance of red shiner was positively

related to all attributes of spring runoff and significantly related to days discharge > 5,000

cfs (Table 25 and Figure 55). Speckled dace abundance was significantly related to all

spring runoff attributes except days discharge > 8,000 cfs (Table 26) and most strongly

with days discharge > 5,000 cfs (Figure 55). The abundance of flannelmouth sucker and
87

Figure 52. Relative abundance of commonly collected fishes in Geomorphic Reach 4

during summer, San Juan River, 1991 – 1997.

CYPLUT

RHIOSC

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

PIMPRO

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

CYPLUT

RHIOSC

PIMPRO

RHIOSC

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

CYPLUT PIMPRO

CYPLUT

RHIOSC

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

PIMPRO

RHIOSC

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

CYPLUT

PIMPRO

CYPLUT

RHIOSC

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

PIMPRO

RHIOSC

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

CYPLUT PIMPRO

1991 1992 1993

1994 1995 1996

1997
88

Table 24. Number and abundance (fish/m2) of fishes in San Juan River secondary

channels in Geomorphic Reach 4 (RM 130 – RM 106) during summer, 1991 – 1997.

Bold-lettered species were used to calculate Kendall’s coefficient of concordance (W).

1991 1992 1993 1994

SPECIES N ABUN SPECIES N ABU

N

SPECIES N ABUN SPECIES N ABUN

CYPLUT 65 0.41 CYPLUT 358 1.32 CYPLUT 6969 10.62 CYPLUT 2212 4.01

RHIOSC 28 0.18 RHIOSC 139 0.51 RHIOSC 2099 3.20 PIMPRO 1206 2.18

PIMPRO 25 0.16 CATLAT 98 0.36 PIMPRO 1600 2.44 RHIOSC 854 1.55

CATLAT 11 0.07 PIMPRO 72 0.26 CATLAT 262 0.40 ICTPUN 289 0.52

ICTPUN 2 0.01 GAMAFF 23 0.08 CATDIS 182 0.28 CYPCAR 134 0.24

CATDIS 1 0.01 CYPCAR 3 0.01 ICTPUN 177 0.27 GAMAFF 28 0.05

CYPCAR 1 0.01 FUNZEB 2 0.01 CYPCAR 147 0.22 CATLAT 25 0.05

ICTPUN 1 <0.01 GAMAFF 9 0.01 CATDIS 9 0.02

FUNZEB 8 0.01

MICSAL 1 <0.01

TOTAL N 133 696 11445 4766

AREA 160 272 656 552

ABUN 0.831 2.559 17.447 8.634

1995 1996 1997

SPECIES N ABUN SPECIES N ABU

N

SPECIES N ABUN

CYPLUT 10642 11.88 PIMPRO 2068 3.98 CYPLUT 40 0.29

RHIOSC 2362 2.64 CYPLUT 1809 3.48 RHIOSC 147 0.11

CATDIS 993 1.11 AMEMEL 188 0.36 CATLAT 14 0.01

PIMPRO 993 1.11 GAMAFF 107 0.21 PIMPRO 14 0.01

ICTPUN 346 0.39 CATLAT 35 0.07 GILROB 9 0.01

CATLAT 119 0.13 RHIOSC 33 0.06 ICTPUN 9 0.01

GAMAFF 22 0.02 ICTPUN 26 0.05 GAMAFF 6 <0.01

CYPCAR 3 <0.01 CYPCAR 2 <0.01 AMEMEL 5 <0.01

MICSAL 2 <0.01 MICSAL 2 <0.01 CATDIS 3 <0.01

FUNZEB 1 <0.01

TOTAL N 15482 4271 607

AREA 896 520 1371

ABUN 17.279 8.214 0.443

bluehead sucker was not significantly related to any flow attribute (Tables 27 and 28), but

was moderately strong for days discharge > 5,000 cfs (flannelmouth sucker, Figure 55)

and days discharge > 8,000 cfs (bluehead sucker, Figure 55). Summer abundance of

fathead minnow and channel catfish in Reach 4 did not appear to be related to spring

runoff attributes (Tables 29 and 30, Figure 55).
89

Figure 53. Abundance of fishes and Shannon-Wiener Diversity Index 

 values of fish assemblages in Geomorphic Reach 4 secondary 

 channels, San Juan River, 1991 - 1997.

YEAR

1991 1992 1993 1994 1995 1996 1997

ABUNDANCE (FISH/M 2

)

0

2

4

6

8

10

12

14

16

18

20

SHANNON-WIENER INDEX (H)

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

2.0

ABUNDANCE 

H 
90

DAYS DISCHARGE > 5000 CFS

0 20 40 60 80 100

ABUNDANCE (FISH/M 2

) 0

4

8

12

Red shiner

r

2

 = 0.5557, p = 0.05 

Figure 54. Secondary channel abundance of red shiner, speckled dace, bluehead sucker,

 fathead minnow, flannelmouth sucker, and channel catfish versus spring 

 discharge attributes, Geomorphic Reach 4, San Juan River, 1991 - 1997.

DAYS DISCHARGE > 5000 CFS

0 20 40 60 80 100

0

1

2

3

4

Speckled dace

r

2

 = 0.7645, p = 0.01

DAYS DISCHARGE > 5000 CFS

0 20 40 60 80 100

0.0

0.1

0.2

0.3

0.4

0.5

Flannelmouth sucker

r

2

 = 0.4554, p = 0.09

DAYS DISCHARGE > 8000 CFS

0 5 10 15 20 25 30

0

1

2

3

4

5

Fathead minnow

r

2

 = 0.1091, p = 0.47

DAYS DISCHARGE > 8000 CFS

0 5 10 15 20 25 30

0

1

2

Bluehead sucker

r

2 = 0.4611, p = 0.09

DAYS DISCHARGE > 5000 CFS

0 20 40 60 80 100 120

0.0

0.1

0.2

0.3

0.4

0.5

0.6

Channel catfish

r

2

 = 0.2618, p = 0.24
91

Table 25. Results of linear regression analysis of relationship between spring runoff

attributes and summer secondary channel abundance of red shiner, Cyprinella lutrensis,

in Geomorphic Reach 4, San Juan River, 1991 – 1997.

RUNOFF ATTRIBUTE r2 r p

Runoff volume (ac.ft.) 0.4528 .6729 0.10

Runoff mean (ac.ft.) 0.4822 .6944 0.08

Days discharge > 3000 cfs 0.5227 .7264 0.06

Days discharge > 5000 cfs 0.5557 .7454 0.05

Days discharge > 8000 cfs 0.2065 .4545 0.31

Table 26. Results of linear regression analysis of relationship between spring runoff

attributes and summer secondary channel abundance of fathead minnow, Pimephales

promelas, in Geomorphic Reach 4, San Juan River, 1991 – 1997.

RUNOFF ATTRIBUTE r2 r p

Runoff volume (ac.ft.) 0.0800 0.2821 0.54

Runoff mean (ac.ft.) 0.0540 0.2324 0.62

Days discharge > 3000 cfs 0.0243 0.1559 0.74

Days discharge > 5000 cfs 0.0009 0.0297 0.95

Days discharge > 8000 cfs 0.1091 0.3303 0.47

Table 27. Results of linear regression analysis of relationship between spring runoff

attributes and summer secondary channel abundance of speckled dace, Rhinichthys

osculus, in Geomorphic Reach 4, San Juan River, 1991 – 1997.

RUNOFF ATTRIBUTE r2 r p

Runoff volume (ac.ft.) 0.5753* 0.7585 0.05

Runoff mean (ac.ft.) 0.6311* 0.7944 0.03

Days discharge > 3000 cfs 0.7085* 0.8417 0.02

Days discharge > 5000 cfs 0.7645* 0.8423 0.01

Days discharge > 8000 cfs 0.1739 0.4170 0.35

Table 28. Results of linear regression analysis of relationship between spring runoff

attributes and summer secondary channel abundance of flannelmouth sucker, Catostomus

latipinnis, in Geomorphic Reach 4, San Juan River, 1991 – 1997.

RUNOFF ATTRIBUTE r2 r p

Runoff volume (ac.ft.) 0.2857 0.5345 0.22

Runoff mean (ac.ft.) 0.3259 0.5708 0.18

Days discharge > 3000 cfs 0.3851 0.6206 0.14

Days discharge > 5000 cfs 0.4554 0.6868 0.09

Days discharge > 8000 cfs 0.0095 0.0976 0.84
92

Table 29. Results of linear regression analysis of relationship between spring runoff

attributes and summer secondary channel abundance of bluehead sucker, Catostomus

discobolus, in Geomorphic Reach 4, San Juan River, 1991 – 1997.

RUNOFF ATTRIBUTE r2 r p

Runoff volume (ac.ft.) 0.4153 0.6444 0.12

Runoff mean (ac.ft.) 0.3913 0.6256 0.13

Days discharge > 3000 cfs 0.3533 0.5944 0.16

Days discharge > 5000 cfs 0.2765 0.5258 0.23

Days discharge > 8000 cfs 0.4611 0.6791 0.09

Table 30. Results of linear regression analysis of relationship between spring runoff

attributes and summer secondary channel abundance of channel catfish, Ictalurus

punctatus, in Geomorphic Reach 4, San Juan River, 1991 – 1997.

RUNOFF ATTRIBUTE r2 r p

Runoff volume (ac.ft.) 0.1686 0.4106 0.36

Runoff mean (ac.af.) 0.1450 0.3808 0.40

Days discharge > 3000 cfs 0.2113 0.4157 0.30

Days discharge > 5000 cfs 0.2618 0.5116 0.24

Days discharge > 8000 cfs 0.0925 0.3041 0.51

Geomorphic Reach 3

Between 1991 and 1997, 13 species of fish were captured in Reach 3 (Table 31).

Red shiner was the most abundant species in all years, except 1995 and 1996 when

fathead minnow was the most abundant. Speckled dace was the second-most abundant

species in 1991 through 1993, 1995, and 1997. In 1994 and 1996, comparatively low

flow years, it was third- and fourth-most abundant. Flannelmouth sucker was never

particularly abundant, but was found each year. Bluehead sucker abundance was low (<

0.05/m2

) or it was absent (1992 and 1996) in all years except 1993 and 1995. In the latter

years, high spring runoff years, its abundance was comparatively high (> 0.3/m2).

Roundtail chub and Colorado pikeminnow were collected in 1997. The abundance rank

of species was similar among years (W = 0.749, p < 0.001). Relative abundance of

speckled dace varied from less than 5 % (1996, a low flow year) to more than 30 % of the

collection (1993 and 1995, high spring runoff years; Figure 56). Fathead minnow was a

comparatively large percent (> 10 %) of the collection in all years, except 1997. Red

shiner was the largest proportion of the collection in all years, except 1995 and 1996,

when fathead minnow was most common.

Overall abundance of fishes in Reach 3 secondary channels peaked in 1993 and

1995 (Figure 57). Between 1991 and 1997, Shannon-Wiener Diversity Index values

generally declined (Figure 57). From 1991 through 1995, the two most-abundant species
93

Figure 55. Relative abundance of commonly collected fishes in Geomorphic Reach 3

secondary channels, San Juan River, 1991 – 1997.

CYPLUT

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

RHIOSC

PIMPRO

CYPLUT CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

PIMPRO RHIOSC

CYPLUT

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

RHIOSC

PIMPRO

CYPLUT

CATDIS

ICTPUN

CYPCAR

OTHER

PIMPRO

CATLAT

RHIOSC

CYPLUT CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

PIMPRO

RHIOSC

CYPLUT RHIOSC

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

PIMPRO

RHIOSC

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

CYPLUT

PIMPRO

1991 1992 1993

1994 1995 1996

1997
94

Figure 56. Abundance of fishes and Shannon-Wiener Diversity

 Index values of fish assemblages in Geomorphic Reach 3 

 secondary channels, San Juan River, 1991 - 1997.

YEAR

1991 1992 1993 1994 1995 1996 1997

ABUNDANCE (FISH/M 2

)

0

2

4

6

8

10

12

SHANNON-WIENER INDEX (H)

0.0

0.5

1.0

1.5

2.0

ABUNDANCE 

H 
95

Table 31. Number and abundance (fish/m2) of fishes in San Juan River secondary

channels in Geomorphic Reach 3 (RM 105 – RM 68) during summer, 1991 – 1997.

Bold-lettered species were used to calculate Kendall’s coefficient of concordance (W).

1991 1992 1993 1994

SPECIES N ABUN SPECIES N ABUN SPECIES N ABUN SPECIES N ABUN

CYPLUT 311 0.86 CYPLUT 54 0.32 CYPLUT 1617 5.18 CYPLUT 416 1.27

RHIOSC 97 0.27 RHIOSC 49 0.29 RHIOSC 1093 3.50 ICTPUN 254 0.77

CATLAT 81 0.23 PIMPRO 30 0.18 PIMPRO 370 1.19 RHIOSC 221 0.67

PIMPRO 66 0.18 CATLAT 18 0.11 CATLAT 205 0.66 PIMPRO 128 0.39

ICTPUN 64 0.18 GAMAFF 12 0.07 CATDIS 188 0.60 CATLAT 95 0.29

GAMAFF 7 0.02 FUNZEB 5 0.03 ICTPUN 42 0.13 GAMAFF 16 0.05

CATDIS 2 0.01 ICTPUN 4 0.02 CYPCAR 4 0.01 CATDIS 6 0.02

CYPCAR 2 0.01 CYPCAR 1 0.01 GAMAFF 2 0.01 CYPCAR 1 <0.01

LEPCYA 1 <0.01

TOTAL N 631 173 3521 1137

AREA 360 168 312 328

ABUN 1.753 1.030 11.285 3.467

1995 1996 1997

SPECIES N ABUN SPECOES N ABUN SPECIES N ABUN

PIMPRO 2789 3.75 PIMPRO 872 2.10 CYPLUT 576 0.46

RHIOSC 2510 3.37 CYPLUT 604 1.45 RHIOSC 288 0.23

CYPLUT 990 1.33 GAMAFF 253 0.61 ICTPUN 47 0.04

ICTPUN 346 0.47 RHIOSC 28 0.07 PIMPRO 40 0.03

CATDIS 288 0.39 ICTPUN 27 0.06 CATLAT 13 0.01

CATLAT 166 0.22 CATLAT 19 0.05 GAMAFF 7 0.01

GAMAFF 15 0.02 FUNZEB 11 0.03 GILROB 5 <0.01

CYPCAR 7 0.01 MICSAL 1 <0.01 CATDIS 1 <0.01

FUNZEB 6 0.01 PYTLUC 1 <0.01

MICSAL 1 <0.01

TOTAL N 7118 1815 978

AREA 744 416 1264

ABUN 9.567 4.363 0.774

represented 59 to 74 % of the collection, but in 1996 and 1997 the two-most abundant

species accounted for > 80 % of the collection. There was no relationship between fish

abundance and discharge at time of sampling (r2 = 0.039, p = 0.67).

Attributes of spring runoff were significantly related to the abundance of three

species commonly collected in Reach 3. Red shiner abundance was significantly related

to days discharge > 5,000 cfs (Table 32, Figure 58). Four of five spring runoff attributes

were related to speckled dace and bluehead sucker abundance (Tables 34 and 36, Figure

58); only days discharge > 8,000 cfs was not related to their abundance. Abundance of

flannelmouth sucker was positively related to all attributes of spring runoff, except days

discharge > 8,000 cfs (no relationship), but none was significant (Table 35, Figure 58).
96

There was no relationship between any spring runoff attribute and abundance of fathead

minnow and channel catfish (Tables 33 and 37, Figure 58).

Table 32. Results of linear regression analysis of relationship between attributes of

spring runoff and summer secondary channel abundance of red shiner, Cyprinella

lutrensis, in Geomorphic Reach 3, San Juan River, 1991 – 1997.

RUNOFF ATTRIBUTE R2 R P

Runoff volume (ac.ft.) 0.4227 0.6540 0.11

Runoff mean (cfs) 0.4646 0.6816 0.09

Days discharge > 3000 cfs 0.5129 0.7162 0.07

Days discharge > 5000 cfs 0.5697* 0.7548 0.05

Days discharge > 8000 cfs 0.1119 0.3345 0.46

*significant relationship (P < 0.05)

Table 33. Results of linear regression analysis of relationship between attributes of

spring runoff and summer secondary channel abundance of fathead minnow, Pimephales

promelas, in Geomorphic Reach 3, San Juan River, 1991 – 1997.

RUNOFF ATTRIBUTE R2 R P

Runoff volume (ac.ft.) 0.0886 0.2976 0.52

Runoff mean (cfs) 0.0816 0.2857 0.54

Days runoff > 3000 cfs 0.767 0.2769 0.55

Days runoff > 5000 cfs 0.0637 0.2523 0.59

Days runoff > 8000 cfs 0.1646 0.4057 0.37

Table 34. Results of linear regression analysis of relationship between attributes of

spring runoff and summer secondary channel abundance of speckled dace, Rhinichthys

osculus, in Geomorphic Reach 3, San Juan River, 1991 – 1997.

RUNOFF ATTRIBUTE R2 R P

Runoff volume (ac.ft.) 0.6556* 0.8097 0.03

Runoff mean (cfs) 0.6799* 0.8246 0.02

Days runoff > 3000 cfs 0.7095* 0.8423 0.02

Days runoff > 5000 cfs 0.7095* 0.8423 0.02

Days runoff > 8000 cfs 0.2739 0.5234 0.23

*significant relationship (P < 0.05)
97

Table 35. Results of linear regression analysis of relationship between spring runoff

attributes and summer secondary channel abundance of flannelmouth sucker, Catostomus

latipinnis, in Geomorphic Reach 3, San Juan River, 1991 – 1997.

RUNOFF ATTRIBUTE R2 R P

Runoff volume (ac.ft.) 0.2263 0.4757 0.28

Runoff mean (cfs) 0.2772 0.5265 0.23

Days discharge > 3000 cfs 0.3603 0.6002 0.15

Days discharge > 5000 cfs 0.4554 0.6749 0.10

Days discharge > 8000 cfs 0.0010 0.0322 0.95

Table 36. Results of linear regression analysis of relationship between spring runoff

attributes and summer secondary channel abundance of bluehead sucker, Catostomus

discobolus, in Geomorphic Reach 3, San Juan River, 1991 – 1997.

RUNOFF ATTRIBUTE R2 R P

Runoff volume (ac.ft.) 0.6050* 0.7778 0.04

Runoff mean (cfs) 0.6360* 0.7975 0.03

Days discharge > 3000 cfs 0.6790* 0.8240 0.02

Days discharge > 5000 cfs 0.7125* 0.8441 0.02

Days discharge > 8000 cfs 0.1738 0.4169 0.35

*significant relationship (P < 0.05)

Table 37. Results of linear regression analysis of relationship between spring runoff

attributes and summer secondary channel abundance of channel catfish, Ictalurus

punctatus, in Geomorphic Reach 3, San Juan River, 1991 – 1997.

RUNOFF ATTRIBUTE R2 R P

Runoff volume (ac.ft.) 0.0044 0.0661 0.89

Runoff mean (cfs) 0.124 0.1113 0.81

Days discharge > 3000 cfs 0.0181 0.1346 0.77

Days discharge > 5000 cfs 0.0268 0.1636 0.73

Days discharge > 8000 cfs 0.0286 0.1692 0.72

Inter-Reach Comparisons

Over the course of the study, Shannon-Wiener Diversity Index values were

generally higher in Reach 5 than downstream reaches and lowest in Reach 4 (Figure 59).

The exceptions were 1993 when assemblage diversity was lowest in Reach 5 and 1994

when it was highest in Reach 3. Averaged over the years of study, assemblage diversity

was higher in Reach 5 (H = 1.3619, CV = 10.0 %) than Reach 3 (H = 1.3561, CV = 12.2

%). Mean assemblage diversity was 1.1891 (CV = 15.3 %) in Reach 4. Diversity,
98

DAYS DISCHARGE > 5000 CFS

0 20 40 60 80 100

ABUNDANCE (FISH/M 2

)

0

1

2

3

4

5

6

Red shiner

r

2

 = 0.5697, p = 0.05

DAYS DISCHARGE > 5000 CFS

0 20 40 60 80 100

0

1

2

3

4

Speckled dace

r

2

 = 0.7095, p = 0.02

Figure 57. Secondary channel abundance of red shiner, speckled dace, flannelmouth sucker,

 bluehead sucker, fathead minnow, and channel catfish versus attributes of

 spring discharge, Geomorphic Reach 3, San Juan River, 1991 - 1997.

DAYS DISCHARGE > 5000 CFS

0 20 40 60 80 100

0.0

0.2

0.4

0.6

0.8

1.0

Flannelmouth sucker

r

2

 = 0.4554, p = 0.10

DAYS DISCHARGE > 5000 CFS

0 20 40 60 80 100

0.0

0.2

0.4

0.6

0.8

1.0

Bluehead sucker

r

2

 = 0.7125, p = 0.02

DAYS DISCHARGE > 8000 CFS

0 5 10 15 20 25 30

0

1

2

3

4

Fathead minnow

r

2

 = 0.1646, p = 0.37

DAYS DISCHARGE > 8000 CFS

0 5 10 15 20 25 30

0.0

0.2

0.4

0.6

0.8

1.0

Channel catfish

r

2

 = 0.0286, p = 0.72
99

however, was not significantly different among years (F = 1.488, p = 0.25) or among

reaches (F = 2.068, p = 0.16).

Fish abundance varied considerably among reaches within years and particularly

among years within reaches (Figure 59). It was low (< 5 fish/m2) in 1991, 1992, and

1997, high (> 10 fish/m2) in all reaches in 1993, and intermediate (> 5 and < 10 fish/m2)

in most reaches in 1994 through 1996. From 1991 through 1994 and in 1997, total

abundance was highest in Reach 5. In 1995 and 1996, total abundance was greatest in

Reach 4. Total abundance was lowest in Reach 3 in all years except 1991 and 1997.

Among reach differences in abundance were not significant ( F = 1.004, p = 0.39), but

among year differences were (F = 8.199, p = 0.0006). Post-hoc tests indicated that

abundance in 1993 was significantly greater than all years except 1994 and 1995 and that

abundance in 1995 was greater than in 1997.

Five secondary channels were sampled in 6 of 7 or 7 of 7 years. The most

upstream was at RM 144.0 to RM 143.8 and the most downstream was at RM 94.3 to RM

94.0. Two were in Reach 5, two in Reach 4, and one in Reach 3. Abundance varied

considerably from year to year in each secondary channel (Figure 60). In the three mostupstream secondary channels, greatest abundance was in 1993. Highest abundance in the

most-downstream secondary channel was in 1995. There was no consistent pattern in

changes in assemblage diversity, it generally declined over time in three and was about

the same in two in 1991 or 1992 and 1997. Neither within-years nor within-secondary

channel differences were significant (F = 2.286, p 0.07 and F = 0.938, p = 0.49).

Although there was a large amount of variation in the abundance of each species across

years, rank abundance remained fairly constant. There was moderately high to high

concordance of abundance rank across years within each secondary channel except the

RM 144.0 to RM 143.8 secondary channel. There, Kendall’s W was 0.291 (p < 0.106);

Kendall’s W for all others was > 0.48 (p <0.008). Despite variation in abundance, neither

within-years nor within-secondary channel differences were significant (F = 1.643, p =

0.19 and F = 0.854, p = 0.50). In the secondary channel (RM 144.0 to RM 143.8) where

abundance rank changed considerably from year to year, red shiner was the most

abundant species in only one year (1996) of six years. Native speckled dace and

bluehead sucker were each the most abundant in two years (1991 and 1997; 1993 and

1995). In the sixth year (1994), channel catfish was the most abundant species. In each

of the other commonly sampled, and downstream, secondary channels red shiner was the

most abundant species in most years. Speckled dace was the most abundant species in

RM 132.2 to RM 131.05 (1994) and RM 116.55 to RM 115.6 (1994). Fathead minnow

was the most abundant species in RM 122.8 to RM 122.05 in 1993 and 1994 and in RM

94.3 to RM 94.0 in 1994.
100

1991 1992 1993 1994 1995 1996 1997

SHANNON-WIENER INDEX (H)

0.0

0.5

1.0

1.5

2.0

REACH 5

REACH 4

REACH 3

Figure 58. Shannon-Wiener Diversity Index values of fish assemblages 

 and abundance of fishes in San Juan River secondary 

 channels during summer, 1991 - 1997.

YEAR

1991 1992 1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

)

0

5

10

15

20

25

30

REACH 5

REACH 4

REACH 3
101

1991 1992 1993 1994 1995 1996 1997

0

2

4

6

8

10

12

14

0

1

2

3

ABUNDANCE

H

RM 144.0 - RM 143.8

1991 1992 1993 1994 1995 1996 1997

0

10

20

30

40

50

60

0

1

2

3

ABUNDANCE

H

RM 132.2 - RM 131.05

1991 1992 1993 1994 1995 1996 1997

ABUNDANCE (FISH/M 2

)

0

10

20

30

40

50

0

1

2

3

ABUNDANCE

H

RM 122.8 - RM 122.05

1991 1992 1993 1994 1995 1996 1997

0

1

2

3

4

5

SHANNON-WIENER INDEX (H)

0

1

2

3

ABUNDANCE

H

RM 116.55 - RM 115.6

Figure 59. Abundance of fishes and Shannon-Wiener Diversity Index values 

 of secondary channel fish assemblages for commonly sampled 

 San Juan River secondary channels during summer, 1991 - 1997. 

YEAR

1991 1992 1993 1994 1995 1996 1997

0

2

4

6

8

0

1

2

3

ABUNDANCE

H

RM 94.3 - RM 94.0
FISH ASSEMBLAGES OF SAN JUAN RIVER

SECONDARY CHANNELS DURING AUTUMN

1993 - 1997
103

INTRODUCTION

Autumn inventories of San Juan River secondary channels were initiated in 1993

to enable a more accurate and complete characterization of the fish assemblages of

secondary channels and dynamics of species populations within these habitats than could

be obtained from only spring and summer inventories. Overall objectives of the

Secondary Channel Ichthyofaunal Inventory were:

1) Characterize the type of secondary channels in the San Juan River;

2) Characterize the faunal assemblages of secondary channels;

3) Determine seasons use patterns of secondary channels by target species;

and

4) Relate habitat use and availability of secondary channels to flow levels.

Specifically, autumn inventories provided data necessary to meet and complete study

objectives 2, 3, and 4.

METHODS

The study area was the San Juan River from Shiprock (RM 147.9) to Chinle

Creek (RM 68.7), except 1993 when sampling was terminated at Sand Island (RM 76.5).

See Study Area description in preceding chapter for detailed description of study area.

Sampling methods during autumn inventories were the same as used during

summer inventories. Autumn inventories were initiated in 1993 and continued through

1997. Sampling was done during the first two weeks of October in all years, except 1996

when sampling occurred during the second and third week of October.

Kendall’s coefficient of concordance (W) was used to evaluate changes in the

abundance rank of fish species during autumn. Regression analysis was used to relate

attributes of summer discharge (Table 38) to autumn abundance (fish/m2) of each

commonly collected fish species. The Shannon-Wiener Diversity Index (where H =

Σpilnpi and pi is the proportion of the ith species in the collection) was calculated for each

year for each Geomorphic Reach. Coefficients of variation (CV = standard

deviation/mean) were calculated for the abundance (fish/m2) of each species each year in

each Geomorphic Reach. Analysis of variance (ANOVA) was used to assess changes in

abundance and Shannon-Wiener Diversity Index values within each Geomorphic Reach.

For multiple ANOVA, the Tukey Honest Significant Difference test was applied to

determine which comparisons were significantly different. The significance threshold

for all statistical comparisons was < 0.05.
104

Table 38. Attributes of summer discharge, San Juan River, 1993 – 1997.

 Data from USGS Shiprock gage (#09368000).

YEAR

MONTH 1993 1994 1995 1996 1997

JULY 922 1020 3282 563 2164

AUGUST 1346 534 1561 491 2306

SEPTEMBER 1432 1078 1193 891 2361

MEAN DISCHARGE (CFS)1 1518 1271 2660 697 2524

DISCHARGE VOLUME (AC-FT) 197,228 129,298 271,127 101,116 350,970

DISCHARGE SPIKE DATA

DAYS > 5000 CFS 0 0 0 0 4

DAYS > 4000 CFS 3 0 0 0 7

DAYS > 3000 CFS 4 0 0 0 18

DAYS > 2000 CFS 10 2 13 0 30

DAYS > 1000 CFS 35 15 53 22 66

DAYS < 1000 CFS 37 54 13 55 7

DAYS < 750 CFS 35 42 0 69 3

DAYS < 500 CFS 0 20 0 39 0

NUMBER DISCHARGE SPIKES 4 3 3 5 3

SPIKE DURATION (DAYS) 35 15 29 22 66

SPIKE MEAN (CFS) 1878 1437 1589 1253 2479

SPIKE VOLUME (AC-FT) 130,362 42,740 91,392 54,680 324,468

 1Mean discharge data provided by Keller-Bliesner Engineering.

RESULTS

San Juan River secondary channels from RM 147.9 (Shiprock) downstream to

RM 68.7 (Chinle Creek) were sampled during autumn from 1994 through 1997. In 1993,

secondary channel sampling stopped at RM 76.5 (Sand Island). Sampling was conducted

in the first two weeks of October in all years except 1996 when it was done in the second

and third weeks of October. Number of secondary channels sampled within each

Geomorphic Reach ranged from a low of 4 (Reach 3 in 1993) to a high of 20 (Reach 3 in

1994). Typically, 10 to 15 secondary channels were sampled in each Reach in all years.

Mean daily discharge during each annual effort ranged from 717 in 1993 to 1479 cfs in

1997. In all years, except 1997, flows were fairly constant from early September through

late October (Figure 61). Two flow spikes (> 3000 cfs) occurred in 1997 between early

and late September. Mean daily discharge during summer (1 July through 30 September)

was lower in 1996 (751 cfs) than in any other year (1993 through 1997), but mean

autumn (1 – 31 October) discharge in 1996 (1181 cfs) was not substantially different

from other years.
105

Figure 60. Mean weekly discharge (cfs) of San Juan River 1 July through 

 31 October, 1993-1997. Horizonal lines indicate time of 

 autumn sampling.

WEEK

1-5 JUL6-10

11-1516-2021-2526-31

1-5 AUG6-10

11-1516-2021-2526-31

1-5 SEP6-10

11-1516-2021-2526-30

1-5 OCT6-10

11-1516-2021-2526-31

DISCHARGE (CFS)

0

2000

4000

6000

8000

1993

1994

1995

1996

1997
106

Water Quality

During the study, mean autumn secondary channel water temperature varied from

10.2 in 1996 to 18.2°C in 1997. Water temperature was usually slightly higher in

secondary channels than it was in the adjacent primary channel (Figure 62 and Table 39).

Except for 1996, water temperature did not change longitudinally; in 1996 water

temperature was higher in upstream than downstream reaches. At most sample locations

there was negligible difference in secondary and primary channel dissolved oxygen levels

(Figure 63). In 1993, 1994, and 1996, mean dissolved oxygen (primary and secondary

channels) was comparatively high (> 9.0 mg/l), was near 8.0 mg/l in 1995, and only 6.7

mg/l in 1997. Considerable variation in dissolved oxygen was found in 1994, but little

variation was noted for 1993, 1995, and 1997. Mean annual specific conductance was

always greater in secondary channels than the primary channel. Spikes in specific

conductance were more frequently found in secondary channels than the primary channel

(Figure 64). In 1994, there was a slight downstream decreasing trend in specific

conductance, but in other years readings were similar throughout the study reach.

Table 39. Mean values of water quality parameters of San Juan River secondary and

primary channels during autumn inventories , 1993 – 1997. Values in parentheses are

standard deviations.

WATER TEMPERATURE DISSOLVED OXYGEN CONDUCTIVITY

(oC) (mg/l) (μmho/cm)

YEAR 1° 2° 1° 2° 1° 2°

1993 15.9 (1.6) 16.3 (2.0) 10.3 (1.1) 10.1 (1.1) 633 (109) 661 (121)

1994 13.8 (1.3) 14.2 (1.7) 11.6 (1.8) 11.6 (2.1) 643 (110) 676 (145)

1995 12.5 (1.4) 13.0 (2.4) 7.6 (1.3) 7.8 (1.2) 424 (56) 459 (130)

1996 9.8 (2.2) 10.2 (2.4) 9.9 (0.9) 10.0 (1.3) 411 (40) 445 (106)

1997 17.8 (1.2) 18.2 (1.7) 6.7 (0.3) 6.7 (0.7) 417 (57) 430 (114)

Autumn Fish Assemblages

 Fourteen species of fish, five native and nine nonnative, were collected in

secondary channels during autumn inventories (Table 40). The greatest number of

species was collected in 1997 (n = 13) and fewest (n = 9) in 1993. Abundance of fishes

was highest in 1993 and lowest in 1997 (Table 41). Only three native species (speckled

dace, flannelmouth sucker, and bluehead sucker) were collected each year of the study.

In 1997, five native species were collected. All Colorado pikeminnow specimens

collected in 1997 were likely stocked individuals. Roundtail chub was also found in

1997. Nonnative common carp, red shiner, fathead minnow, channel catfish, plains
107

150145140135130125120115110105100 95 90 85 80 75 70

0

5

10

15

20

25

1993

150145140135130125120115110105100 95 90 85 80 75 70

WATER TEMPERATURE (C)

0

5

10

15

20

25

1994

Figure 61. Water temperature of San Juan River secondary and primary channels during

 autumn inventories, 1993 - 1997. 

150145140135130125120115110105100 95 90 85 80 75 70

0

5

10

15

20

25

1995

150145140135130125120115110105100 95 90 85 80 75 70

0

5

10

15

20

25

1996

RIVER MILE

150145140135130125120115110105100 95 90 85 80 75 70

0

5

10

15

20

25

1997
108

150145140135130125120115110105100 95 90 85 80 75 70

0

4

8

12

16

1993

150145140135130125120115110105100

DISSOLVED OXYGEN (MG/L)

95 90 85 80 75 70

0

4

8

12

16

1994

Figure 62. Dissolved oxygen (mg/l) of San Juan River secondary and primary channels 

 during autumn inventories, 1993 - 1997.

150145140135130125120115110105100 95 90 85 80 75 70

0

4

8

12

16

1995

150145140135130125120115110105100 95 90 85 80 75 70

0

4

8

12

16

1996

RIVER MILE

150145140135130125120115110105100 95 90 85 80 75 70

0

4

8

12

16

SECONDARY

PRIMARY

1997
109

150145140135130125120115110105100 95 90 85 80 75 70

0

200

400

600

800

1000

1200

1993

150145140135130125120115110105100 95 90 85 80 75 70

CONDUCTIVITY (MICROMHO/CM)

0

200

400

600

800

1000

1200

1994

Figure 63. Conductivity (micromho/jcm) of San Juan River secondary and primary 

 channels during autumn inventories, 1993 - 1997.

150145140135130125120115110105100 95 90 85 80 75 70

0

200

400

600

800

1000

1200

1995

150145140135130125120115110105100 95 90 85 80 75 70

0

200

400

600

800

1000

1200

1996

RIVER MILE

150145140135130125120115110105100 95 90 85 80 75 70

0

200

400

600

800

1000

1200

SECONDARY

PRIMARY

1997
110

Table 40. Occurrence of fishes in San Juan River secondary channels during autumn,

1993 – 1997. I = introduced and N = native. Six-letter codes derived from first three

letters of genus and second three from species.

COMMON SCIENTIFIC CODE STATUS 1993 1994 1995 1996 1997

Common carp Cyprinus carpio CYPCAR I X X X X X

Red shiner Cyprinella lutrensis CYPLUT I X X X X X

Roundtail chub Gila robusta GILROB N X

Fathead minnow Pimephales promelas PIMPRO I X X X X X

Colorado squawfish Ptychocheilus lucius PTYLUC N X

Speckled dace Rhinichthys osculus RHIOSC N X X X X X

Flannelmouth sucker Catostomus latipinnis CATLAT N X X X X X

Bluehead sucker Catostomus discobolus CATDIS N X X X X X

Black bullhead Ameiurus melas AMEMEL I X X

Channel catfish Ictalurus punctatus ICTPUN I X X X X X

Plains killifish Fundulus zebrinus FUNZEB I X X X X X

Western mosquitofish Gambusia affinis GAMAFF I X X X X X

Green sunfish Lepomis cyanellus LEPCYA I X X X X

Largemouth bass Micropterus salmoides MICSAL I X X X X

TOTAL NATIVE 5 3 3 335

TOTAL NONNATIVE 9 6 9 988

killifish, and western mosquitofish were found in all years. Sub-adults and adults of

flannelmouth sucker, bluehead sucker, common carp, and channel catfish were rarely

collected during autumn secondary channel surveys; most collected specimens of each

species were 75 to 125 mm TL. Juveniles, sub-adults, and adults of red shiner, fathead

minnow, speckled dace, and western mosquitofish were uncommon to common in each

Geomorphic Reach. Age-0 (juveniles and sub-adults) of these species typically were

more common than adults. Although collected each autumn, plains killifish was

uncommon throughout the study reach in all years; most individuals were sub-adults or

adults. Autumn sampling occurred after most, if not all, spawning activity. Few

specimens of small-bodied species were < 35 mm TL (juveniles or younger).

Nonnative red shiner was the most common species in secondary channels in all

years; its abundance was 1.65 to 2.46 times greater than the next most-common species.

Native speckled dace was the second-most common species in 1993 and 1997 and was

never less than fourth-most common. Nonnative fathead minnow was second-most

common in 1994 and 1996 and, like speckled dace, was never less than fourth-most

common. Abundance rank of western mosquitofish varied considerably from year to

year, from third (1996) to ninth (1997). Abundance rank of native bluehead and

flannelmouth suckers was never greater than fourth or less than eighth. There was a high

level of concordance in abundance rank of species in autumn across years (Friedman’s χ2

= 33.94, p < 0.0001, W = 0.848).

Total abundance of fishes in secondary channels was relatively high from 1993

through 1995 (3.94 to 4.52 fish/m2

, but declined from 1996 (2.51 fish/m2) to an autumn

low in 1997 (0.76 fish/m2; Figure 65). Assemblage diversity was highest in 1993 and
111

Figure 64. Abundance of fishes and Shannon-Wiener Diversity Index values 

 of fish assemblages in San Juan River secondary channels 

 (Geomorphic Reaches combined) during autumn,1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

)

0

1

2

3

4

5

SHANNON-WIENER INDEX (H)

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

2.0

ABUNDANCE

H
112

Table 41. Fishes collected in San Juan River secondary channels (RM 149 – RM 68)

during autumn inventories, 1993 – 1997. Bold-lettered species were used to calculate

Kendall’s coefficient of concordance (W).

1993 1994 1995 1996 1997

SPECIES N SPECIES N SPECIES N SPECIES N SPECIES N

CYPLUT 2427 CYPLUT 5397 CYPLUT 4125 CYPLUT 3632 CYPLUT 1023

RHIOSC 1090 PIMPRO 2196 PIMPRO 2417 PIMPRO 2201 RHIOSC 564

PIMPRO 699 RHIOSC 967 RHIOSC 987 GAMAFF 716 PTYLUC 241

CATLAT 189 GAMAFF 643 GAMAFF 135 RHIOSC 127 PIMPRO 175

CATDIS 164 ICTPUN 204 ICTPUN 62 ICTPUN 57 CATLAT 75

ICTPUN 97 CATLAT 192 CATLAT 57 CATLAT 31 ICTPUN 68

FUNZEB 65 FUNZEB 43 CATDIS 42 CATDIS 29 CATDIS 45

GAMAFF 45 CATDIS 20 FUNZEB 18 FUNZEB 17 CYPCAR 18

CYPCAR 7 MICSAL 10 CYPCAR 9 CYPCAR 1 GAMAFF 15

CYPCAR 8 LEPCYA 2 LEPCYA 1 GILROB 11

AMEMEL 3 MICSAL 1 MICSAL 1 FUNZEB

LEPCYA 1 AMEMEL 1 LEPCYA 1

MICSAL 1

TOTAL N 4783 9684 7856 6813 2119

AREA 1058 2456 1758 2715 2681

ABUN 4.521 3.94 4.469 2.509 0.7904

H 1.8874 1.2844 1.1590 1.1173 1.558

lowest in 1996. In 1997, the year of lowest total abundance, diversity was the secondhighest (H = 1.5558) found in autumn. The three most-abundant species, red shiner,

fathead minnow, and speckled dace (all years except 1996 when western mosquitofish

was third-most common) represented > 82% of the total collection each year (Figure 66).

In 1996, nonnative species numerically dominated the collection (96% of total). Native

fishes were least common (2.8%) in 1996 and most common in 1997 (39.0%).

Abundance of red shiner was fairly constant from 1993 through 1995 (about 2.3/m2), but

diminished in 1996 and was lowest in 1997 (0.38/m2

). Speckled dace, flannelmouth

sucker, and bluehead sucker abundance was highest in 1993 and lowest in 1996 (speckled

dace and flannelmouth sucker) and 1994 (bluehead sucker). Total abundance was

negatively, but not significantly, related to discharge at time of sampling (r2

 = 0.768, p

<0.051).

Geomorphic Reach 5

Thirteen fish species, five native and eight nonnative, were collected in Reach 5

between 1993 and 1997 (Table 42). Colorado pikeminnow and roundtail chub were

found in 1997, but not in prior years. Total abundance was comparatively high (> 6.0

fish/m2

) in 1993 and 1996 and was lowest (1.3 fish/m2) in 1997. Red shiner was the most

abundant species in all years except 1997 when speckled dace was most abundant .

Fathead minnow and speckled dace were usually the second- or third-most abundant
113

Figure 65. Relative abundance of commonly collected fishes during autumn in secondary

channels, San Juan River, 1993 – 1997.

PIMPRO

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

CYPLUT

RHIOSC

PIMPRO

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

CYPLUT

RHIOSC

PIMPRO

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

CYPLUT

RHIOSC

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

CYPLUT PIMPRO

RHIOSC

CYPLUT

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

PIMPRO

RHIOSC

1993 1994

1995 1996

1997
114

species. In 1997, Colorado pikeminnow was the third-most abundant species.

Abundance rank of species did not change appreciably from year to year; concordance of

Table 42. Number and abundance (number/m2) of fishes in San Juan River secondary

channels in Geomorphic Reach 5 (RM 154 – RM 131) during autumn, 1993 – 1997.

Bold-lettered species used to calculate Kendall’s coefficient of concordance.

1993 1994 1995 1996 1997

SPECIES N ABU SPECIES N ABU SPECIES N ABU SPECIES N ABU SPECIES N ABU

CYPLUT 1028 2.62 CYPLUT 1066 1.16 CYPLUT 341 1.07 CYPLUT 1626 2.99 RHIOSC 292 0.40

PIMPRO 627 1.60 PIMPRO 695 0.76 RHIOSC 305 0.95 PIMPRO 1559 1.85 CYPLUT 292 0.40

RHIOSC 545 1.39 RHIOSC 541 0.59 PIMPRO 156 0.49 GAMAFF 501 0.92 PTYLUC 192 0.26

CATDIS 110 0.28 GAMAFF 268 0.29 GAMAFF 49 0.15 RHIOSC 63 0.12 PIMPRO 114 0.15

CATLAT 90 0.23 ICTPUN 74 0.08 CATLAT 35 0.11 ICTPUN 13 0.02 CATLAT 20 0.03

GAMAFF 44 0.11 CATLAT 50 0.05 CATDIS 26 0.08 FUNZEB 9 0.02 ICTPUN 16 0.02

FUNZEB 11 0.03 FUNZEB 26 0.03 CYPCAR 4 0.01 CATLAT 6 0.01 CYPCAR 16 0.02

ICTPUN 6 0.02 CATDIS 10 0.01 ICTPUN 2 0.01 CATDIS 4 0.01 GAMAFF 13 0.02

CYPCAR 3 0.01 MICSAL 9 0.01 LEPCYA 1 <0.01 CYPCAR 1 <0.01 CATDIS 12 0.02

CYPCAR 2 <0.01 MICSAL 1 <0.01 GILROB 2 <0.01

FUNZEB 2 <0.01

Lepcya 1 <0.01

Micsal 1 <0.01

TOTAL N 2464 2741 920 3782 971

AREA 392 920 320 544 738

ABU 6.286 2.979 2.875 6.952 1.316

H 1.425 1.521 1.468 1.118 1.650

rank was significant (Friedman’s χ2 = 31.68, p <0.0001, W = 0.792). From 1993 through

1995, assemblage diversity was essentially constant (H = 1.5), declined in 1996 (H =

1.1), and increased to the study high (H = 1.6) in 1997 (Figure 67). The relationship

between discharge at time of sampling and total fish abundance was negative, but not

significant (r2

 = 0.3899, p < 0.26).

As a proportion of the collections in Reach 5, red shiner was the most abundant species in

all years except 1997, and then it was only slightly less common than speckled dace

(Figure 68). Speckled dace was > 20% of the collection in all years except 1996, when it

was 1.7%. Fathead minnow relative abundance peaked (41%) in 1996. In 1997,

Colorado squawfish was 19.8% of the specimens collected in Reach 5.

The coefficient of variation (CV) of abundance (fish/m2) of fish species collected

each year in Reach 5 secondary channels was moderately high (0.50 to 0.75) to high (>

0.75). Abundant species had lower CVs than less abundant ones; there was a general

trend of increasing CV with decreasing abundance (Figure 69).
115

Figure 66. Abundance of fishes and Shannon-Wiener Diversity Index values 

 of fish assemblages during autumn in Geomorphic Reach 5, 

 San Juan River, 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

)

0

2

4

6

8

SHANNON-WIENER INDEX (H)

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

2.0

ABUNDANCE

H 
116

Figure 67. Relative abundance of commonly collected fishes during autumn in

Geomorphic Reach 5, San Juan River, 1993 – 1997.

CYPLUT

PIMPRO

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

RHIOSC

CYPLUT

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

RHIOSC

PIMPRO

CYPLUT

PIMPRO

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

RHIOSC

CYPLUT

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

RHIOSC

PIMPRO

CYPLUT

ICTPUN

CYPCAR

OTHER

RHIOSC

CATDIS

CATLAT

PIMPRO

1993 1994

1995 1996

1997
117

Figure 68. Mean abundance (1993 - 1997) and coefficient of variation (CV)

 in abundance of fish species commonly collected during autumn 

 in Geomorphic Reach 5, San Juan River, 1993 - 1997. 

SPECIES

CYPLUT

PIMPRO

RHIOSC

GAMAFF

CATLAT

CATDIS

ICTPUN

ABUNDANCE (FISH/M2

) 0.0

0.5

1.0

1.5

2.0

COEFFICIENT OF VARIATION

0.0

0.5

1.0

1.5

2.0

MEAN ABUNDANCE

CV 
118

Autumn abundance of red shiner, fathead minnow, speckled dace, flannelmouth

sucker, bluehead sucker, channel catfish, and western mosquitofish was compared to 10

attributes of summer discharge. Autumn abundance of red shiner was not significantly

related to any summer discharge attribute (Table 43). The general pattern was a negative

response in red shiner abundance to elevated summer flows (e.g., volume and days flow

Table 43. Results of linear regression analysis of relationship between summer discharge

Attributes and autumn secondary channel abundance of red shiner, Cyprinella lutrensis,

in Geomorphic Reach 5, San Juan River, 1993 – 1997.

SUMMER DISCHARGE ATTRIBUTE r2 r p

SUMMER DISCHARGE VOLUME (AC-FT) 0.5350 0.7314 0.16

SUMMER MEAN DISCHARGE (CFS) 0.5354 0.7317 0.16

DAYS >2000 CFS 0.4785 0.6918 0.20

DAYS >1000 CFS 0.3702 0.6084 0.28

DAYS <1000 CFS 0.4613 0.6792 0.21

DAYS <500 CFS 0.3038 0.5512 0.34

FLOW SPIKE DURATION (DAYS) 0.2480 0.4980 0.39

FLOW SPIKE MEAN (CFS) 0.3307 0.5751 0.31

FLOW SPIKE VOLUME (AC-FT) 0.3080 0.5549 0.33

1000 cfs) and a positive response to low summer flows (e.g., days flow < 500 cfs).

Figure 70 illustrates the relationship between red shiner abundance and one summer flow

attribute. The relationship of fathead minnow autumn abundance to summer flow

attributes was similar to that of red shiner (Table 44). Fathead minnow abundance was

less during in years with high summer flows than in years with low summer flows; the

strongest negative relationship was with mean summer discharge (Figure 70). Fathead

minnow autumn abundance was positively, but not significantly, related to days flow <

500 cfs.

Table 44. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of fathead minnow, Pimephales

promelas, in Geomorphic Reach 5, 1993 – 1997.

SUMMER DISCHARGE ATTRIBUTES r2 r p

SUMMER DISCHARGE VOLUME (AC-FT) 0.6022 0.7761 0.12

SUMMER MEAN DISCHARGE (CFS) 0.6026 0.7763 0.12

DAYS >2000 CFS 0.5178 0.7196 0.17

DAYS >1000 CFS 0.4467 0.6683 0.22

DAYS <1000 CFS 0.5481 0.7404 0.15

DAYS <500 CFS 0.3497 0.5913 0.29

FLOW SPIKE DURATION (DAYS) 0.2696 0.5192 0.37

FLOW SPIKE MEAN (CFS) 0.3393 0.5825 0.30

FLOW SPIKE VOLUME (AC-FT) 0.3195 0.5653 0.32
119

MEAN SUMMER DISCHARGE (CFS)

0 500 1000 1500 2000 2500 3000

0

1

2

3

4

MEAN SUMMER DISCHARGE (CFS)

0 500 1000 1500 2000 2500 3000

0

1

2

3

DAYS DISCHARGE < 500 CFS

ABUNDANCE (FISH/M

0 10 20 30 40 50

2

)

0

1

2

DAYS DISCHARGE < 500 CFS

0 10 20 30 40 50

0.00

0.05

0.10

0.15

0.20

0.25

DAYS DISCHARGE < 500 CFS

0 10 20 30 40 50

0.00

0.05

0.10

0.15

0.20

0.25

0.30

DAYS DISCHARGE > 1000 CFS

0 10 20 30 40 50 60 70

Y Data

0.00

0.02

0.04

0.06

0.08

0.10

Figure 69. Autumn abundance of commonly collected fish species in Geomorphic

 Reach 5 versus summer flow attributes, San Juan River, 1993 - 1997.

DAYS DISCHARGE < 500 CFS

0 10 20 30 40 50

0.0

0.2

0.4

0.6

0.8

1.0

r

2

 = 0.5354, p = 0.16 r

2

 = 0.6026, p = 0.12

r

2

 = 0.4831, p = 0.19

Red shiner Fathead minnow

Speckled dace Flannelmouth sucker r

2

 = 0.5342, p = 0.16

Bluehead sucker r2

 = 0.3249, p = 0.32 Channel catfish r2 = 0.2868, p = 0.35

Western mosquitofish

r

2

 = 0.9092, p = 0.01
120

There was essentially no relationship between speckled dace abundance and elevated

summer flows (Table 45). There was a negative, but not significant, relationship between

speckled dace abundance and days flow < 500 cfs (Figure 70). Overall, there was no

relationship between any attribute of summer discharge and flannelmouth sucker or

bluehead sucker autumn abundance (Tables 46 and 47). The strongest , and negative,

was with days flow < 500 cfs (Figure 70). Abundance of channel catfish was not related

to any attribute of summer discharge (Table 48 and Figure 70). Western mosquitofish

abundance was negatively, but not significantly, related to elevated summer flows (Table

49) and was significantly, and positively, related to days flow < 500 cfs (Figure 70).

Table 45. Results of linear regression analysis of relationship between summer discharge

Attributes and autumn secondary channel abundance of speckled dace, Rhinichthys

osculus, in Geomorphic Reach 5, San Juan River, 1993 – 1997.

SUMMER DISCHARGE ATTRIBUTES r2 r p

SUMMER DISCHARGE VOLUME (AC-FT) 0.0292 0.1710 0.78

SUMMER MEAN DISCHARGE (CFS) 0.0292 0.1708 0.78

DAYS >2000 CFS 0.0030 0.0546 0.93

DAYS >1000 CFS 0.0131 0.1146 0.85

DAYS <1000 CFS 0.0431 0.2075 0.74

DAYS <500 CFS 0.4831 0.6951 0.19

FLOW SPIKE DURATION (DAYS) 0.0014 0.0375 0.95

FLOW SPIKE MEAN (CFS) 0.0228 0.1511 0.81

FLOW SPIKE VOLUME (AC-FT) 0.0053 0.0725 0.91

Table 46. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of flannelmouth sucker, Catostomus

latipinnis, Geomorphic Reach 5, San Juan River, 1993 – 1997.

SUMMER DISCHARGE ATTRIBUTES r2 r p

SUMMER DISCHARGE VOLUME (AC-FT) 0.0844 0.2905 0.64

SUMMER MEAN DISCHARGE (CFS) 0.0842 0.2903 0.64

DAYS >2000 CFS 0.0569 0.2386 0.70

DAYS >1000 CFS 0.0639 0.2529 0.68

DAYS <1000 CFS 0.0849 0.2913 0.63

DAYS < 500 CFS 0.5342 0.7308 0.16

FLOW SPIKE DURATION (DAYS) 0.0490 0.2214 0.72

FLOW SPIKE MEAN (CFS) 0.1425 0.3775 0.53

FLOW SPIKE VOLUME (AC-FT) 0.0323 0.1798 0.77
121

Table 47. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of bluehead sucker, Catostomus

discobolus, Geomorphic Reach 5, San Juan River, 1993 – 1997.

SUMMER DISCHARGE ATTRIBUTE r2 r p

SUMMER DISCHARGE VOLUME (AC-FT) 0.0198 0.1406 0.82

SUMMER MEAN DISCHARGE (CFS) 0.0197 0.1403 0.82

DAYS >2000 CFS 0.0138 0.1196 0.85

DAYS >1000 CFS 0.0181 0.1345 0.83

DAYS <1000 CFS 0.0202 0.1423 0.82

DAYS < 500 CFS 0.3249 0.5700 0.32

FLOW SPIKE DURATION (DAYS) 0.0260 0.1612 0.80

FLOW SPIKE MEAN (CFS) 0.0807 0.2841 0.64

FLOW SPIKE VOLUME (AC-FT) 0.0120 0.1098 0.86

Table 48. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of channel catfish, Ictalurus

punctatus, Geomorphic Reach 5, San Juan River, 1993 – 1997.

SUMMER DISCHARGE ATTRIBUTES r2 r p

SUMMER DISCHARGE VOLUME (AC-FT) 0.1258 0.3547 0.56

SUMMER MEAN DISCHARGE (CFS) 0.1255 0.3543 0.56

DAYS >2000 CFS 0.0783 0.2797 0.65

DAYS >1000 CFS 0.2868 0.5356 0.35

DAYS <1000 CFS 0.2272 0.4767 0.42

DAYS < 500 CFS 0.0642 0.2533 0.68

FLOW SPIKE DURATION (DAYS) 0.1126 0.3356 0.58

FLOW SPIKE MEAN (CFS) 0.0257 0.1602 0.80

FLOW SPIKE VOLUME (AC-FT) 0.0494 0.2223 0.72

Table 49. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of western mosquitofish, Gambusia

affinis, Geomorphic Reach 5, San Juan River, 1993 – 1997.

SUMMER DISCHARGE ATTRIBUTE r2 r p

SUMMER DISCHARGE VOLUME (AC-FT) 0.5802 0.7617 0.14

SUMMER DISCHARGE MEAN (CFS) 0.5802 0.7617 0.14

DAYS > 2000 CFS 0.4992 0.7065 0.18

DAYS > 1000 CFS 0.3924 0.6265 0.26

DAYS < 1000 CFS 0.5009 0.7077 0.18

DAYS < 500 CFS 0.9092* 0.9535 0.01

FLOW SPIKE DURATION (DAYS) 0.3026 0.5501 0.34

FLOW SPIKE MEAN (CFS) 0.5434 0.7372 0.16

FLOW SPIKE VOLUME (AC-FT) 0.3261 0.5711 0.32
122

Geomorphic Reach 4

Between 1993 and 1997, 14 species of fish (five native and nine nonnative) were

found in Reach 4 (Table 50). Six species (red shiner, fathead minnow, speckled dace,

flannelmouth sucker, channel catfish, and western mosquitofish) were collected in all

years. Western mosquitofish was represented by single specimens in 1993 and 1997.

Bluehead sucker was not collected in 1996, plains killifish was absent in 1995 and 1997,

and common carp was not found in 1993 or 1996. Colorado pikeminnow and roundtail

chub were found in 1997. Red shiner was the most abundant species in all years.

Speckled dace was second-most abundant in 1993, 1995, and 1997 and fathead minnow

was second-most abundant in 1994 and 1996. The abundance rank of other species

varied from year to year. For example, western mosquitofish went from least abundant

species in 1993 to fourth-most abundant in 1994, was third or fourth through 1996, and

was again the least abundant in 1997. Despite some shifts in abundance rank of several

species, there was high concordance of rank among years (Friedman’s χ2 = 30.05, p <

0.0001, W = 0.776). From 1993 through 1996, total abundance of fishes in Reach 4

declined slightly, but was substantially less in 1997 than in preceding years (Figure 71).

Shannon-Wiener Diversity Index values changed little from year to year and was highest

in 1997. Discharge at time of sampling versus total abundance of fishes in Reach 4 was

not related (r2

 = 0.274, p = 0.468).

Table 50. Number and abundance (number/m2) of fishes in San Juan River

secondary channels in Geomorphic Reach 4 (RM 130 –RM 106) during autumn, 1993 –

1997. Bold-lettered species used to calculate Kendall’s coefficient of concordance.

1993 1994 1995 1996 1997

SPECIES N ABUN SPECIES N ABUN SPECIES N ABUN SPECIES N ABUN SPECIES N ABUN

CYPLUT 1084 2.34 CYPLUT 1459 1.96 CYPLUT 1340 1.51 CYPLUT 1046 1.87 CYPLUT 203 0.21

RHIOSC 472 1.02 PIMPRO 657 0.88 RHIOSC 479 0.54 PIMPRO 473 0.84 RHIOSC 114 0.12

CATLAT 68 0.15 RHIOSC 164 0.22 PIMPRO 220 0.25 GAMAFF 188 0.34 ICTPUN 20 0.02

CATDIS 54 0.12 GAMAFF 145 0.19 GAMAFF 66 0.07 RHIOSC 37 0.07 PIMPRO 14 0.01

PIMRPO 45 0.10 ICTPUN 50 0.07 ICTPUN 34 0.04 ICTPUN 25 0.05 PTYLUC 9 0.01

ICTPUN 24 0.05 CATLAT 20 0.03 CARLAT 15 0.02 CATLAT 4 0.01 CATLAT 7 0.01

FUNZEB 7 0.02 FUNZEB 9 0.01 CATDIS 6 0.01 FUNZEB 3 0.01 CATDIS 6 0.01

GAMAFF 1 <0.01 CATDIS 4 0.01 CYPCAR 1 <0.01 LEPCYA 1 <0.01 GILROB 5 0.01

CYPCAR 4 0.01 FUNZEB 1 <0.01 MICSAL 1 <0.01 CYPCAR 1 <0.01

AMEMEL 1 <0.01 GAMAFF 1 <0.01

LEPCYA 1 <0.01

MICSAL 1 <0.01

TOTAL N 1755 2515 2162 1778 380

AREA 464 744 888 560 960

ABUN 3.782 3.380 2.435 3.175 0.396

H 1.062 1.176 1.093 1.075 1.272

For most commonly collected species in Reach 4, there was an inverse

relationship between abundance of each and their respective coefficient of variation
123

Figure 70. Abundance of fishes and Shannon-Wiener Diversity Index values 

 of fish assemblages during autumn in Geomorphic Reach 4, San 

 Juan River, 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

)

0

1

2

3

4

SHANNON-WIENER INDEX (H)

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

2.0

ABUNDANCE 

H 
124

(Figure 72). Thus, the most abundant species had comparatively low CVs in contrast to

less abundant species with high CVs. The outstanding exception to this pattern was

channel catfish; both its abundance and CV were low.

In 1993, 1995, and 1997, native fishes were 23% or more of each year’s

collection in Reach 4 (Figure 73). In 1994 and 1996, native fishes were 7.5 and 2.3% of

the collections. Red shiner was the large majority of nonnative fishes collected in 1993,

1995, and 1997. In 1994 and 1996, fathead minnow was about 26% of each year’s

collection. Relative abundance of flannelmouth and bluehead suckers was highest in

1993 and 1997. Channel catfish generally represented a small proportion (< 2%) of each

year’s collection, but in 1997 was 5% of the total collection. Colorado pikeminnow was

2.4% of the 1997 collection.

The autumn abundance of several nonnative species was significantly related to

several attributes of summer discharge. Although none were significant, the autumn

abundance of red shiner in Reach 4 was fairly strongly, and negatively, related to several

summer discharge attributes (Table 51). The only summer discharge attribute not related

Table 51. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of red shiner, Cyprinella lutrensis, in

Geomorphic Reach 4, 1993 – 1997.

SUMMMER DISCHARGE ATTRIBUTES r2 r p

Summer discharge volume (ac.ft.) 0.6405 0.8004 0.10

Summer discharge mean (cfs) 0.6408 0.8005 0.10

Days >2000 cfs 0.7368 0.8584 0.06

Days >1000 cfs 0.6258 0.7911 0.11

Days <1000 cfs 0.5464 0.7392 0.15

Days < 500 cfs 0.1100 0.3316 0.59

Flow spiked duration (days) 0.6840 0.8270 0.08

Flow spike mean (cfs) 0.5403 0.7351 0.16

Flow spike volume (ac.ft.) 0.7175 0.8470 0.07

was days flow < 500 cfs. Most attributes were similar to that illustrated in Figure 74.

Fathead minnow abundance was negatively, but not significantly, related to most

attributes of summer discharge (Table 52). The outstanding exception was days flow <

500 cfs; it was positively, and significantly, related to autumn abundance (Figure 74).

Summer discharge attributes were generally not related to the three commonly collected

native fish species. The strongest relationship between autumn speckled dace abundance

and summer discharge was the negative relationship with days flow < 500 cfs (Table 53,

Figure 74). The relationships of flannelmouth and bluehead suckers abundance with

summer discharge (Tables 54 and 55) were similar to, but weaker than, those involving

speckled dace. Abundance of the two sucker species was negatively related to days flow
125

Figure 71. Mean abundance (1993 - 1997) and coefficient of variation (CV)

 of abundance of fish species commonly collected during autumn in 

 Geomorphic Reach 4, San Juan River, 1993 - 1997.

SPECIES

CYPLUT PIMPRO RHIOSC GAMAFF ICTPUN CATLAT CATDIS

ABUNDANCE (FISH/M2

) 0.0

0.5

1.0

1.5

2.0

COEFFICIENT OF VARIATION

0.0

0.5

1.0

1.5

2.0

ABUNDANCE 

CV 
126

Figure 72. Relative abundance of commonly collected fishes during autumn in

Geomorphic Reach 4, San Juan River, 1993 – 1997.

PIMPRO

CATLAT

CATDIS

ICTPUN

CYPCR

OTHER

CYPLUT

RHIOSC

PIMPRO

CATLAT

CATDIS

ICTPUN

CYPCR

OTHER

CYPLUT

RHIOSC

PIMPRO

CATLAT

CATDIS

ICTPUN

CYPCR

OTHER

CYPLUT

RHIOSC

CATLAT

CATDIS

ICTPUN

CYPCR

OTHER

CYPLUT

PIMPRO

RHIOSC

PIMPRO

CATLAT

CATDIS

ICTPUN

CYPCR

OTHER

CYPLUT

RHIOSC

1993 1994

1995 1996

1997
127

DAYS DISCHARGE > 2000 CFS

0 5 10 15 20 25 30 35

0

1

2

3

DAYS DISCHARGE < 500 CFS

0 10 20 30 40 50

0.0

0.5

1.0

1.5

2.0

DAYS DISCHARGE < 500 CFS

0 10 20 30 40 50

ABUNDANCE (FISH/M2

)

0

1

2

DAYS DISCHARGE < 500 CFS

0 10 20 30 40 50

0.00

0.05

0.10

0.15

0.20

0.25

DAYS DISCHARGE < 500 CFS

0 10 20 30 40 50

0.00

0.03

0.06

0.09

0.12

0.15

DAYS DISCHARGE > 1000 CFS

0 10 20 30 40 50 60 70

0.000

0.025

0.050

0.075

0.100

Figure 73. Autumn abundance of fishes in Geomorphic Reach 4 versus attributes

 of summer discharge, San Juan River, 1993 - 1997.

DAYS DISCHARGE < 500 CFS

0 10 20 30 40 50

0.0

0.1

0.2

0.3

0.4

Red shiner

r

2

 = 0.7368, p = 0.06 Fathead minnow r2 = 0.7917, p = 0.04

Speckled dace r2

 = 0.3401, p = 0.30 Flannelmouth sucker r2 = 0.1471, p = 0.52

Bluehead sucker r2

 = 0.1973, p = 0.45

Channel catfish

r

2

 = 0.8786, p = 0.02

Western mosquitofish

r

2

 = 0.9700, p = 0.002
128

Table 52. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of fathead minnow, Pimephales

promelas, in Geomorphic Reach 4, 1993 – 1997. An asterisk indicates a significant

relationship.

SUMMMER DISCHARGE ATTRIBUTES r2 r P

Summer discharge volume (ac.ft.) 0.7456 0.8635 0.06

Summer discharge mean (cfs) 0.7453 0.8633 0.06

Days >2000 cfs 0.7033 0.8386 0.08

Days >1000 cfs 0.7442 0.8+626 0.06

Days <1000 cfs 0.7242 0.8510 0.07

Days < 500 cfs 0.7917* 0.8898 0.04

Flow spiked duration (days) 0.6520 0.8074 0.10

Flow spike mean (cfs) 0.7037 0.8389 0.08

Flow spike volume (ac.ft.) 0.5824 0.7631 0.13

Table 53. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of speckled dace, Rhinichthys

osculus, in Geomorphic Reach 4, 1993 – 1997.

SUMMMER DISCHARGE ATTRIBUTES r2 r P

Summer discharge volume (ac.ft.) 0.0051 0.0717 0.91

Summer discharge mean (cfs) 0.0051 0.0714 0.91

Days >2000 cfs 0.0005 0.0218 0.97

Days >1000 cfs 0.0030 0.0545 0.93

Days <1000 cfs 0.0132 0.1149 0.85

Days < 500 cfs 0.3401 0.5832 0.30

Flow spiked duration (days) 0.0029 0.0539 0.93

Flow spike mean (cfs) 0.0092 0.0957 0.88

Flow spike volume (ac.ft.) 0.0111 0.1053 0.87

Table 54. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of flannelmouth sucker, Catostomus

latipinnis, Geomorphic Reach 4, San Juan River, 1993 – 1997.

SUMMER DISCHARGE ATTRIBUTE r2 r P

Summer discharge volume (ac.ft.) 0.0128 0.1132 0.86

Summer discharge mean (cfs) 0.0129 0.1135 0.86

Days > 2000 cfs 0.0111 0.1052 0.87

Days > 1000 cfs 0.0226 0.1504 0.81

Days < 1000 cfs 0.0193 0.1388 0.82

Days < 500 cfs 0.1471 0.3835 0.52

Flow spike duration (days) 0.0016 0.0399 0.95

Flow spike mean (cfs) 0.0148 0.1216 0.85

Flow spike volume (ac.ft.) 0.0046 0.0679 0.91
129

Table 55. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of bluehead sucker, Catostomus

discobolus, Geomorphic Reach 4, San Juan River, 1993 – 1997.

SUMMER DISCHARGE ATTRIBUTE r2 r P

Summer discharge volume (ac.ft.) 0.0002 0.0150 0.98

Summer discharge mean (cfs) 0.0002 0.0153 0.98

Days > 2000 cfs 0.0000 0.0000 1.00

Days > 1000 cfs 0.0020 0.0443 0.94

Days < 1000 cfs 0.0019 0.0441 0.94

Days < 500 cfs 0.1973 0.4442 0.45

Flow spike duration (days) 0.0053 0.0729 0.91

Flow spike mean (cfs) 0.0487 0.2207 0.72

Flow spike volume (ac.ft.) 0.0016 0.0397 0.95

< 500 cfs (Figure 74). There were strong negative, and in several instances, significant,

relationships between summer discharge and channel catfish abundance (Table 56). The

strongest was that with days discharge > 1000 cfs (Figure 74). There was a significant

positive relationship between western mosquitofish autumn abundance and days flow <

500 cfs (Figure 74); most other relationships were negative and fairly strong, but not

significant (Table 57).

Table 56. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of channel catfish, Ictalurus

punctatus, Geomorphic Reach 4, San Juan River, 1993 – 1997. An asterisk indicates a

significant relationship.

SUMMER DISCHARGE ATTRIBUTE r2 r p

Summer discharge volume (ac.ft.) 0.7492 0.8655 0.06

Summer discharge mean (cfs) 0.7490 0.8655 0.06

Days > 2000 cfs 0.7908* 0.8893 0.04

Days > 1000 cfs 0.8786* 0.9394 0.02

Days < 1000 cfs 0.7405 0.8605 0.06

Days < 500 cfs 0.2502 0.5002 0.39

Flow spike duration (days) 0.8268* 0.9093 0.03

Flow spike mean (cfs) 0.6018 0.7757 0.12

Flow spike volume (ac.ft.) 0.7507 0.8664 0.06
130

Table 57. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of western mosquitofish, Gambusia

affinis, Geomorphic Reach 4, 1993 – 1997. An asterisk indicates a significant

relationship.

SUMMER DISCHARGE ATTRIBUTE r2 r P

Summer discharge volume (ac.ft.) 0.6492 0.8058 0.10

Summer discharge mean (cfs) 0.6491 0.8057 0.10

Days flow > 2000 cfs 0.5797 0.7614 0.14

Days flow > 1000 cfs 0.5174 0.7193 0.17

Days flow < 1000 cfs 0.5869 0.7661 0.13

Days flow < 500 cfs 0.9700* 0.9849 0.01

Flow spike duration 9days) 0.4338 0.6586 0.23

Flow spike mean (cfs) 0.6432 0.8020 0.10

Flow spike volume (ac.ft.) 0.4228 0.6502 0.24

Geomorphic Reach 3

Thirteen species of fish were collected in Reach 3 between 1993 and 1997; five

were native and eight were nonnative (Table 58). Total abundance of fishes was greatest

in 1995 (8.68 fish/m2

) and least in 1997 (0.79 fish/m2). Red shiner was the most

Table 58. Number and abundance (number/m2

) of fishes in San Juan River secondary

channels in Geomorphic Reach 3 (RM 105 – RM 68) during autumn, 1993 – 1997. Boldlettered species were used to calculate Kendall’s coefficient of concordance.

1993 1994 1995 1996 1997

SPECIES N ABUN SPECIES N ABUN SPECIES N ABUN SPECIES N ABUN SPECIESs N ABUN

CYPLUT 315 1.58 CYPLUT 2872 3.63 CYPLUT 2444 4.44 CYPLUT 960 1.69 CYPLUT 527 0.54

RHIOSC 73 0.37 PIMPRO 844 1.07 PIMPRO 2041 3.71 PIMPRO 169 0.30 RHIOSC 151 0.15

ICTPUN 67 0.34 RHIOSC 262 0.33 RHIOSC 203 0.37 RHIOSC 27 0.05 PIMPRO 47 0.08

CATLAT 31 0.16 GAMAFF 230 0.29 ICTPUN 26 0.05 GAMAFF 27 0.05 ICTPUN 23 0.04

PIMPRO 27 0.14 CATLAT 122 0.15 GAMAFF 20 0.04 CATLAT 21 0.04 PTYLUC 13 0.02

CYPCAR 4 0.02 ICTPUN 80 0.10 FUNZEB 17 0.03 ICTPUN 19 0.03 CATLAT 10 0.02

FUNZEB 2 0.01 FUNZEB 8 0.01 CATDIS 10 0.02 CATDIS 7 0.01 GILROB 4 0.01

CATDIS 6 0.01 CATLAT 7 0.01 FUNZEB 5 0.01 CATDIS 2 <0.01

CYPCAR 2 <0.01 CYPCAR 4 0.01 CYPCAR 1 <0.01

AMEMEL 2 <0.01 AMEMEL 1 <0.01 FUNZEB 1 <0.01

LEPCYA 1 <0.01 GAMAFF 1 <0.01

TOTAL N 519 4428 4774 1235 780

AREA 200 792 550 568 983

ABUN 2.595 5.591 8.680 2.174 0.794

H 1.224 1.117 0.943 0.820 1.048
131

abundant species each year of the study. Its abundance and that of fathead minnow (the

second- or third-most abundant species each year) increased from 1993 through 1995 and

then declined to their Reach 3 lows in 1997. The abundance of speckled dace, the

second- or third-most abundant species, was fairly constant from 1993 through 1995,

decreased to its reach low in 1996, and then increased in 1997. Flannelmouth sucker

abundance was low throughout the study, and was lowest in 1997. Bluehead sucker was

not captured in Reach 3 in 1993, but was present in subsequent years, albeit in low

 numbers. Channel catfish abundance declined from 1993 through 1996 and increased

slightly in 1997. Colorado pikeminnow and roundtail chub were collected in 1997.

There was high concordance of species abundance rank across years in Reach 3

(Friedman’s χ2 = 31.56, p < 0.001, W = 0.7890). Assemblage diversity (H) decreased as

total abundance increased from 1993 through 1995 (Figure 75). Diversity was lowest in

1996 and slightly higher in 1997, when total abundance was lowest. Fish abundance in

Reach 3 was not related to discharge at time of sampling (r2

 = 0.112, p < 0.580).

Unlike in Reaches 5 and 4, the coefficient of variation for species abundance in

Reach 3 did not increase as abundance declined (Figure 76). Fathead minnow, a common

species, and western mosquitofish, an uncommon species, had the highest CVs.

As a proportion of the total collection, native fishes declined from about 20 to

4.5% from 1993 through 1996 (Figure 77). In 1997, native fishes were about 21 % of the

collection. Red shiner was 60% or more of each year’s collection in all years except

1995 when it was 51%. Fathead minnow relative abundance peaked at 43% in 1995.

Speckled dace steadily declined in relative abundance from 1993 through 1996, but

increased to its highest proportion in 1997.

Overall, abundance of fish species in Reach 3 was not related to any attribute of

summer discharge. The strongest relationship between red shiner abundance and summer

discharge attribute was that with spike duration (Table 59 and Figure 78). Fathead

Table 59. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of red shiner, Cyprinella lutrensis,

Geomorphic Reach 3, 1993 – 1997.

SUMMER DISCHARGE ATTRIBUTE r2 r p

Summer discharge volume (ac.ft.) 0.0511 0.2261 0.72

Summer discharge mean (cfs) 0.0511 0.2260 0.72

Days > 2000 cfs 0.1940 0.4404 0.46

Days > 1000 cfs 0.0695 0.2635 0.67

Days < 1000 cfs 0.0101 0.1007 0.87

Days < 500 cfs 0.0002 0.0149 0.98

Flow spike duration (days) 0.4562 0.6754 0.21

Flow spike mean (cfs) 0.3524 0.5936 029

Flow spike volume (ac.ft.) 0.4516 0.6720 0.21
132

Figure 74. Abundance of fishes and Shannon-Wiener Diversity Index

 values for fish assemblages during autumn in Geomorphic

 Reach 3, San Juan River, 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

)

0

1

2

3

4

5

6

7

8

9

10

SHANNON-WIENER INDEX (H)

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

2.0

ABUNDANCE 

H 
133

Figure 75. Mean abundance (1993 - 1997) and coefficient of variation (CV)

 of abundance of fish species commonly collected during autumn in 

 Geomorphic Reach 3, San Juan River, 1993 - 1997.

SPECIES

CYPLUT PIMPRO RHIOSC ICTPUN GAMAFF CATLAT CATDIS

ABUNDANCE (FISH/M2

) 0.0

0.5

1.0

1.5

2.0

2.5

3.0

COEFFICIENT OF VARIATION

0.0

0.5

1.0

1.5

2.0

2.5

3.0

ABUNDANCE 

CV 
134

Figure 76. Relative abundance of commonly collected fishes during autumn in

Geomorphic Reach 3, San Juan River, 1993 – 1997.

PIMPRO

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

CYPLUT RHIOSC

PIMPRO

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

RHIOSC CYPLUT

PIMPRO

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

CYPLUT

RHIOSC

RHIOSC

PIMPRO

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

CYPLUT

RHIOSC

PIMPRO

CATLAT

CATDIS

ICTPUN

CYPCAR

OTHER

CYPLUT

1993 1994

1995 1996

1997
135

minnow abundance was not related to any flow attribute (Table 60); Figure 77 illustrates

the typical relationship. With the exception of days flow < 500 cfs, there was no

relationship between summer discharge and speckled dace abundance (Table 61); days

flow < 500 cfs was weakly negative (Figure 77). Abundance of neither sucker species

was related to any flow attribute (Tables 62 and 63). Figure 77 illustrates the absence of

relationships. Channel catfish was negatively, but not significantly, related to days flow

< 1000 cfs (Figure 77), but was not related to other flow attributes (Table 64).

Abundance of western mosquitofish was not related to any flow attribute (Table 65 and

Figure 77).

Table 60. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of fathead minnow, Pimephales

promelas, Geomorphic Reach 3, 1993 – 1997.

SUMMER DISCHARGE ATTRIBUTE r2 r p

Summer discharge volume (ac.ft.) 0.0348 0.1867 0.76

Summer discharge mean (cfs) 0.0348 0.1866 0.76

Days > 2000 cfs 0.0032 0.0565 0.93

Days > 1000 cfs 0.0430 0.2073 0.74

Days < 1000 cfs 0.1200 0.3464 0.57

Days < 500 cfs 0.0752 0.2743 0.66

Flow spike duration (days) 0.0917 0.3028 0.62

Flow spike mean (cfs) 0.0907 0.3012 0.62

Flow spike volume (ac.ft.) 0.1134 0.3368 0.58

Table 61. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of speckled dace, Rhinichthys

osculus, Geomorphic Reach 3, 1993 – 1997.

SUMMER DISCHARGE ATTRIBUTE r2 r p

Summer discharge volume (ac.ft.) 0.0138 0.1173 0.85

Summer discharge mean (cfs) 0.0138 0.1173 0.85

Days > 2000 cfs 0.0019 0.0431 0.95

Days > 1000 cfs 0.0001 0.0003 1.00

Days < 1000 cfs 0.0243 0.1560 0.80

Days < 500 cfs 0.3973 0.6304 0.25

Flow spike duration (days) 0.0588 0.2425 0.69

Flow spike mean (cfs) 0.0001 0.0073 0.99

Flow spike volume (ac.ft.) 0.0567 0.2381 0.70
136

FLOW SPIKE DURATION (DAYS)

0 10 20 30 40 50 60 70

0

1

2

3

4

5

DAYS DISCHARGE < 1000 CFS

0 10 20 30 40 50 60

0

1

2

3

4

DAYS DISCHARGE < 500 CFS

ABUNDANCE (FISH/M

0 10 20 30 40 50

2

)

0.0

0.1

0.2

0.3

0.4

0.5

DAYS DISCHARGE > 1000 CFS

0 10 20 30 40 50 60 70

0.00

0.05

0.10

0.15

0.20

0.25

SUMMER FLOW SPIKE MEAN (CFS0

1000 1200 1400 1600 1800 2000 2200 2400 2600

0.00

0.01

0.02

0.03

0.04

0.05

DAYS DISCHARGE < 1000 CFS

0 10 20 30 40 50 60

0.0

0.1

0.2

0.3

0.4

Figure 77. Autumn abundance of fishes in Geomorphic Reach 3 versus attributes

 of summer discharge, San Juan River, 1993 - 1997. 

DAYS DISCHARGE > 1000 CFS

0 10 20 30 40 50 60 70

0.0

0.1

0.2

0.3

0.4

Red shiner

r

2

 = 0.4562, p = 0.21 Fathead minnow

r

2

 = 0.1200, p = 0.57

Speckled dace

r

2

 = 0.3973, p = 0.25 Flannelmouth sucker r

2

 = 0.4031, p = 0.25

Bluehead sucker r2

 = 0.3844, p = 0.27 Channel catfish

r

2

 = 0.1422, p = 0.53

Western mosquitofish

r

2

 = 0.4261, p = 0.23
137

Table 62. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of flannelmouth sucker, Catostomus

latipinnis, Geomorphic Reach 3, San Juan River, 1993 – 1997.

SUMMER DISCHARGE ATTRIBUTE r2 r p

Summer discharge volume (ac.ft) 0.2522 0.5022 0.39

Summer discharge mean (cfs) 0.2522 0.5022 0.39

Days flow > 2000 cfs 0.1984 0.4454 0.45

Days flow > 1000 cfs 0.4031 0.6349 0.25

Days flow < 1000 cfs 0.3490 0.5908 0.29

Days flow < 500 cfs 0.0002 0.0149 0.98

Flow spike duration (days) 0.1671 0.4087 0.49

Flow spike mean (cfs) 0.0313 0.1769 0.78

Flow spike volume (ac.ft) 0.1297 0.3601 0.55

Table 63. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of bluehead sucker, Catostomus

discobolus Geomorphic Reach 3, San Juan River, 1993 – 1997.

SUMMER DISCHARGE ATTRIBUTES r2 r p

Summer discharge volume (ac.ft) 0.0252 0.1587 0.80

Summer discharge mean (cfs) 0.0252 0.1587 0.80

Days flow > 2000 cfs 0.1322 0.3636 0.55

Days flow > 1000 cfs 0.0103 0.1016 0.87

Days flow < 1000 cfs 0.0001 0.0057 0.99

Days flow < 500 cfs 0.0348 0.1865 0.76

Flow spike duration (days) 0.3036 0.5511 0.34

Flow spike mean (cfs) 0.3844 0.6200 0.27

Flow spike volume (ac.ft) 0.3324 0.5765 0.31

Table 64. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of channel catfish, Ictalurus

punctatus, Geomorphic Reach 3, San Juan River, 1993 – 1997.

SUMMER DISCHARGE ATTRIBUTES r2 r p

Summer discharge volume (ac.ft) 0.0169 0.1300 0.84

Summer discharge mean (cfs) 0.0170 0.1302 0.84

Days flow > 2000 cfs 0.0131 0.1143 0.86

Days flow > 1000 cfs 0.0341 0.1846 0.77

Days flow < 1000 cfs 0.7405 0.8605 0.06

Days flow < 500 cfs 0.1422 0.3771 0.53

Flow spike duration (days) 0.0029 0.0540 0.93

Flow spike mean (cfs) 0.0156 0.1251 0.84

Flow spike volume (ac.ft) 0.0052 0.0720 0.91
138

Table 65. Results of linear regression analysis of relationship between summer discharge

attributes and autumn secondary channel abundance of western mosquitofish, Gambusis

affinis, Geomorphic Reach 3, San Juan River, 1993 – 1997

 

SUMMER DISCHARGE ATTRIBUTE r2 r p

Summer discharge volume (ac.ft) 0.2557 0.5056 0.39

Summer discharge mean (cfs) 0.2554 0.5053 0.39

Days > 2000 cfs 0.2540 0.5040 0.39

Days > 1000 cfs 0.4261 0.6528 0.23

Days < 1000 cfs 0.3138 0.5610 0.33

Days , 500 cfs 0.1398 0.3739 0.54

Flow spike duration (days) 0.3685 0.6071 0.28

Flow spike mean (cfs) 0.2114 0.4598 0.44

Flow spike volume (ac.ft) 0.2608 0.5107 0.38

Among Reach Comparisons

Abundance of fishes in secondary channels of each Geomorphic Reach varied

considerably from year to year. In Reach 5, abundance was comparatively high in 1993,

declined through 1995, increased in 1996, and declined again in 1997 (Figure 78).

Abundance in Reach 4 did not change greatly from 1993 through 1996, but dropped in

1997. Abundance in Reach 3 increased from 1993 through 1995 and then declined

through 1997. Despite these changes, differences were not significant for either across

years-within reach (F = 1.47, p < 0.28) or within-across reaches (F = 0.55, p < 0.59)

comparisons. Mean abundance (all years) was highest (4.08 fish/m2

) in Reach 5 and

lowest (2.63 fish/m2

) in Reach 4; that of Reach 3 was 3.97 fish/m2. Coefficients of

variation for abundance were moderately high (59 and 51 %) in Reaches 5 and 4 and high

(80 %) in Reach 3.

Within each reach, Shannon-Wiener Diversity Index values did not change

significantly from year to year (F = 0.84, p < 0.53). Diversity was highest in Reach 5 in

all years and usually lowest in Reach 3 (Figure 84). Among reach comparisons yielded

significant differences in Diversity Index values (F = 9.39, p < 0.004). Post hoc tests

indicated that diversity for Reach 5 was significantly greater than that of Reaches 4 and 3.

Mean assemblage diversity was 1.4367, 1.1361, and 1.0309 in Reaches 5, 4, and 3,

respectively. The CV for diversity was low (< 15 %) in all reaches.

Colorado Pikeminnow Captures

During 1997 autumn inventories, 206 specimens of Colorado squawfish were

captured in secondary channels. Most, and likely all, individuals were those released as

part of the studies being conducted by Utah Division of Wildlife Resources on survival of

young Colorado squawfish. Captures were primarily in the vicinity of RM 150 to RM
139

Figure 79. Abundance of fishes(fish/m2) in San Juan River secondary

 channels, 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

)

0

2

4

6

8

10

REACH 5 

REACH 4 

REACH 3 

Figure 78. Shannon-Wiener Diversity Index (H) values of fish assemblages

 in San Juan River secondary channels, 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

SHANNON-WIENER DIVERSITY INDEX (H)

0

1

2

REACH 5 

REACH 4 

REACH 3 
140

148 (n = 29), RM 131 to RM 138 (n = 147), and RM 103 (n = 8). Single individuals

were collected upstream, between, and downstream of these concentrations (Table 66).

Most specimens were captured in low-velocity habitats such as backwaters and pools, but

some were captured in habitats having comparatively rapid velocity water (e.g., runs and

riffles). A backwater pool in a secondary channel at RM 132.2 to RM 131.3 yielded 130

specimens.

Table 66. San Juan River secondary channel captures of Colorado squawfish,

Ptychocheilus lucius, during autumn inventories, 1993 – 1997. Parenthetic numbers with

TL indicate number of specimens captured in a mesohabitat if more than one.

DATE RM TL (mm) HABITAT

30 SEP 97 155.5 – 155.2 50 --

30 SEP 97 155.5 – 155.2 53 --

30 SEP 97 155.5 – 155.2 ca. 50 --

30 SEP 97 155.5 – 155.2 ca. 50 --

30 SEP 97 150.3 – 149.9 ca. 50 (4) EDDY POOL

30 SEP 97 150.3 – 149.9 ca. 50 (10) BACKWATER

30 SEP 97 148.5 – 148.3 ca. 50 (4) SHORE RUN

30 SEP 97 148.5 – 148.3 ca. 50 (7) SHORE RUN

30 SEP 97 148.5 – 148.3 ca. 50 SHORE RUN

30 SEP 97 148.5 – 148.3 ca. 50 (3) MID-CHANNEL RUN

1 OCT 97 144.0 – 143.8 ca. 50 POOL RUN

1 OCT 97 143.1 – 142.9 ca. 50 DEBRIS POOL-RUN

1 OCT 97 143.1 – 142.9 ca. 50 SHOAL-RUN

1 OCT 97 143.1 – 142.9 ca. 50 RIFFLE

1 OCT 97 141.4 – 141.05 ca. 50 SLACKWATER

1 OCT 97 140.6 – 140.0 ca. 50 EMBAYMENT

1 OCT 97 138.1 – 137.9 ca. 50 (14) POOL

1 OCT 97 136.6 – 134.6 ca. 50 (3) RIFFLE

2 OCT 97 132.2 – 131.3 ca. 50 (130) BACKWATER POOL

2 OCT 97 130.9 – 130.75 ca. 50 MID CHANNEL RUN

2 OCT 97 129.05 – 128.9 ca. 50 RUN

2 OCT 97 128.7 – 128.1 ca. 50 (3) SHOAL RUN

2 OCT 97 127.7 – 127.6 ca. 50 RUN-CHUTE

2 OCT 97 127.2 – 126.6 ca. 50 RIFFLE EDDY

2 OCT 97 127.2 – 126.6 ca. 50 EDDY

3 OCT 97 117.5 – 117.2 ca. 50 POOL

5 OCT 97 103.4 – 103.2 ca. 50 (2) DEBRIS POOL

5 OCT 97 103.4 – 103.2 ca. 50 (2) POOL

5 OCT 97 103.4 – 103.2 ca. 50 (2) SHOAL

5 OCT 97 103.4 – 103.2 ca. 50 (2) DEBRIS POOL

5 OCT 97 99.05 – 98.6 ca. 50 POOL

6 OCT 97 87.7 – 87.5 ca. 50 POOL

6 OCT 97 87.7 – 87.5 ca. 50 DEBRIS POOL
FISH ASSEMBLAGES OF SAN JUAN RIVER

SECONDARY CHANNELS

SEASONAL COMPARISONS

1993 – 1997
142

INTRODUCTION

During spring runoff (1 March through 1 July), San Juan River secondary

channels provided habitat for both large- and small-bodied fish species. Most individuals

captured during spring inventories were sub-adults and adults of large-bodied fish

species, particularly flannelmouth sucker, bluehead sucker, common carp, and channel

catfish. Speckled dace, red shiner, fathead minnow, common small-bodied fishes, were

captured but never were more than a small proportion of spring samples. Flow volume

(typically > 4000 cfs) and method of specimen collection (raft-mounted electrofishing)

precluded efficient sampling of small-bodied fishes; thus these species were likely underrepresented in spring inventories. Nonetheless, comparisons of primary and secondary

channel spring runoff collections indicted that the fish assemblages of both habitats were

similar in most respects. Reproduction by most native fishes, particularly large-bodied

species, occurred during spring runoff, and its recession (variable among years, but

normally late-June through mid- to late July).

During summer secondary channel inventories, discharge of the San Juan River

was normally less than 1200 cfs and surface water in many secondary channels was

limited to short flowing reaches and isolated pools; few had continuous surface flow for

their entire lengths. Under such conditions, few large-bodied specimens were collected,

but small-bodied fishes were common. Red shiner, fathead minnow, speckled dace, and

western mosquitofish were usually the most common fishes found, especially Age-0

individuals. Spawning of red shiner and fathead minnow peaked during summer lowflow periods, but speckled dace spawning was largely completed by early July. Age-0

individuals of flannelmouth sucker, bluehead sucker, and channel catfish were frequently

found in secondary channels but were rarely abundant.

Autumn inventories were conducted after all spawning activity when flows were,

in average, about the same as during summer but less variable. Available habitat in

secondary channels in autumn was not substantially different from that available in

summer. All species (except incidental species) collected in summer were also collected

in autumn.

Objectives of the Secondary Channel Ichthyological Inventory were:

1) Characterize the type of secondary channels in the San Juan River;

2) Characterize the faunal assemblages of secondary channels;

3) Determine seasonal use patterns of secondary channels by target species;

and
143

4) Relate habitat use and availability of secondary channels to flow levels.

This chapter compares the summer and autumn faunal assemblages of San Juan River

secondary channels and thus addresses Objectives 2 and 4 of the Secondary Channel

Studies.

METHODS

Summer and autumn comparisons were limited to total abundance and abundance

of species commonly collected in both seasons. Specific seasonal comparisons (by

Geomorphic Reach) included red shiner, fathead minnow, speckled dace, flannelmouth

sucker, bluehead sucker, and western mosquitofish. The statistical methods used were

the same as those for within season analyses. In addition, repeated measures ANOVA

was used to evaluate differences in total and species abundances between seasons

(reaches combined) and among reaches (years combined).

RESULTS

The abundance of fishes in secondary channels in each reach was usually greater,

often substantially, in summer than autumn (Figure 81). In Reach 5, total abundance

during summer declined from a high of 25.2 in 1993 to a low of 1.26 fish/m2

 in 1997

(Reach mean = 10.67). In contrast, total abundance during autumn was comparatively

constant during the study (Reach mean = 4.08). In Reach 4, summer abundance (Reach

mean = 10.41) also varied considerably from year to year, but autumn abundance was

fairly constant across years, except in 1997 (mean = 2.64). The year to year total

abundance changes (Reach mean = 5.89) in Reach 3 mirrored, but were lower than, those

found in Reach 4. Differences in the CV of summer and autumn abundance in Reaches 5

and 4 reflected the relative inconstancy of abundance during summer in these reaches and

its relative constancy in autumn (Table 67). The CVs for summer and autumn in Reach 3

were almost the same, and high.

Repeated-measures ANOVA yielded significant differences for between season

(Figure 82: F = 11.245, p < 0.02; Reaches combined) and among years (F = 8.605, p <

0.001) comparisons of total abundance. Reach comparisons (Figure 83; seasons

combined) did not yield significant differences in total abundance (F = 0.172, p < 0.85),

but year differences were significant (F = 4.433, p < 0.02).

Repeated-measures ANOVA was also applied to an assessment of speciesspecific differences in abundance. For red shiner, seasonal differences (Figure 84;

reaches combined) were not significant (F = 2.445, p < 0.193) , but differences among

years were (F = 5.53, p < 0.006). When seasons were combined (Figure 85), neither

reach (F = 0.393, p < 0.705) nor year (F = 3.189, p < 0.053) differences were significant.
144

1993 1994 1995 1996 1997

0

5

10

15

20

25

30

SUMMMER

AUTUMN

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

)

0

5

10

15

20

25

30

SUMMER

AUTUMN

Figure 80. Summer and autumn abundance of fishes in San Juan River

 secondary channels, Geomorphic Reaches 5, 4, and 

 3, 1993 - 1997.

 

YEAR

1993 1994 1995 1996 1997

0

5

10

15

20

25

30

SUMMER

AUTUMN

REACH 5

REACH 4

REACH 3
145

Table 67. Mean abundance (fish/m2), standard deviation (SD), and coefficient of

variation (CV, expressed as %) of fish abundance in San Juan River secondary channels

during summer and autumn, 1993 – 1997.

REACH 5 REACH 4 REACH 3

SUMMER AUTUMN SUMMER AUTUMN SUMMER AUTUMN

TOTAL

 MEAN 10.666 4.082 10.409 2.635 5.891 3.967

 SD 8.930 2.420 7.149 1.344 4.387 3.163

 CV 83.7 59.3 68.9 51.0 74.5 79.7

CYPLUT

 MEAN 3.390 1.648 6.056 1.578 1.938 2.376

 SD 4.047 1.104 4.970 0.820 1.584 1.605

 CV 130.0 67.0 82.1 52.0 95.7 67.6

PIMPRO

 MEAN 3.252 0.970 1.944 0.416 1.492 1.060

 SD 2.974 0.728 1.490 0.415 1.493 1.534

 CV 91.5 75.0 76.6 99.7 100.0 144.7

RHIOSC

 MEAN 1.928 0.690 1.620 0.394 1.568 0.254

 SD 1.696 0.494 1.310 0.395 1.719 0.146

 CV 88.0 71.6 80.9 100.2 109.6 57.4

CATLAT

 MEAN 0.196 0.086 0.132 0.044 0.246 0.076

 SD 0.169 0.089 0.156 0.060 0.259 0.073

 CV 86.0 103.2 118.1 136.0 105.2 96.1

CATDIS

 MEAN 1.218 0.080 0.284 0.030 0.204 0.010

 SD 1.521 0.116 0.476 0.051 0.276 0.007

 CV 124.9 194.4 167.7 168.3 135.3 70.7

GAMAFF

 MEAN 0.478 0.298 0.060 0.124 0.140 0.078

 SD 0.649 0.361 0.085 0.141 0.263 0.120

 CV 135.7 121.2 142.4 114.0 188.0 154.2

With reaches combined (Figure 86), abundance of fathead minnow was not significantly

different seasonally (F = 6.267, p < 0.067) or among years (F = 1.634, p < 0.214). Nor

were significant differences in abundance found with seasons combined (Figure 87);

among-reach F = 0.407, p < 0.698 and among-year F = 2.692, p < 0.082. Differences in

abundance of speckled dace were significant for three of four comparisons. Both
146

Figure 81. Summer and autumn abundance (fish/m2, reaches combined) of

 fishes in San Juan River secondary channels, 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

)

0

2

4

6

8

10

12

14

16

18

20

SUMMER 

AUTUMN 

Figure 82. Total reach abundance (fish/m2, seasons combined) of 

 fishes in San Juan River secondary channels, 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

)

0

5

10

15

20

25

30

35

REACH 5

REACH 4

REACH 3
147

Figure 83. Summer and autumn abundance (fish/m2, reaches combined) of 

 red shiner, Cypinella lutrensis, in San Juan River secondary

 channels, 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

)

0

2

4

6

8

10

12

SUMMER

AUTUMN

Figue 84. Reach abundance (fish/m2, seasons combined) of red shiner,

 Cyprinella lutrensis, in San Juan River secondary channels,

 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

)

0

2

4

6

8

10

12

14

16

REACH 5

REACH 4

REACH 3
148

Figure 85. Summer and autumn abundance (fish/m2, reaches combined) of

 fathead minnow, Pimephales promelas, in San Juan River 

 secondary channels, 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

)

0

1

2

3

4

SUMMER 

AUTUMN

Figure 86. Reach abundance (fish/m2, seasons combined) of fathead minnow,

 Pimephales promelas, in San Juan River secondary channels

 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

)

0

2

4

6

8

10

REACH 5

REACH 4

REACH 3
149

between-season (Figure 88; F = 54.43, p < 0.002) and among years (F = 3.658, p < 0.004)

differences were significant with reaches combined. With seasons combined (Figure 89)

among-year (F = 4.759, p < 0.016) differences were significant but among-reach

differences (F = 0.109, p < 0.90) were not. Results for flannelmouth sucker were similar

to those found for speckled dace. With reaches combined (Figure 90) seasonal and year

differences were significant (F = 12.048, p < 0.026 and F = 28.887, p < 0.001), but only

year differences were significant (F = 9.509, p < 0.001) when seasons were combined

(Figure 91). The only significant difference found for bluehead sucker comparisons was

that for year (F = 3.437, p < 0.032), with reaches combined (Figure 92). The

nonsignificant comparisons were season (F = 2.627, p < 0.18; reaches combined) and

reach (F = 0.771, p < 0.537) and year (F = 2.181, p < 0.133) when seasons were

combined (Figure 93). With reaches combined (Figure 94), differences in western

mosquitofish abundance were significant for year comparisons (F = 6.279, p < 0.003) but

not for season (F = 0.168, p < 0.702). The results obtained when seasons were combined

(Figure 95) were similar; reach differences were not significant (F = 8.217, p < 0.061) but

years were (F = 12.200, p < 0.001).

Total summer abundance was not a good predictor of total autumn abundance

(Figure 96). However, the summer abundance of several species was a fairly good

predictor of their autumn abundance. Summer abundance of fathead minnow, speckled

dace, flannelmouth sucker, bluehead sucker, and western mosquitofish were predictive of

their autumn abundance (Figures 97, 98, and 99). The summer abundance of red shiner

and channel catfish was not a good predictor of their autumn abundance (Figures 101 and

103).
150

Figure 87. Summer and autumn abundance (fish/m2, reaches combined) of

 speckled dace, Rhinichthys osculus, in San Juan River secondary

 channels, 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

) 0

1

2

3

4

SUMMER

AUTUMN

Figure 88. Reach abundance (fish/m2, seasons combined) of speckled dace,

 Rhinichthys osculus, in San Juan River secondary channels, 

 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

) 0

1

2

3

4

5

6

REACH 5

REACH 4

REACH 3
151

Figure 89. Summer and autumn abundance (fish/m2, reaches combined) of

 flannelmouth sucker, Catostomus latipinnis, in San Juan River

 secondary channels, 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

) 0.0

0.1

0.2

0.3

0.4

0.5

0.6

SUMMER

AUTUMN

Figure 90. Reach abundance (fish/m2, seasons combined) of flannelmouth sucker,

 Catostomus latipinnis, in San Juan River secondary channels,

 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

) 0.0

0.2

0.4

0.6

0.8

1.0

REACH 5

REACH 4

REACH 3
152

Figure 91. Summer and autumn abundance (fish/m2, reaches combined) of 

 bluehead sucker, Catostomus discobolus, in San Juan River 

 secondary channels, 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

) 0

1

2

SUMMER

AUTUMN

Figure 92. Reach abundance (fish/m2, seasons combined) of bluehead sucker,

 Catostomus discobolus, in San Juan River secondary channels,

 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

) 0

1

2

3

4

REACH 5

REACH 4

REACH 3
153

Figure 93. Summer and autumn abundance (fish/m2, reaches combined) of western

 mosquitofish, Gambusia affinis, in San Juan River secondary channels,

 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

) 0.00

0.05

0.10

0.15

0.20

0.25

0.30

SUMMER

AUTUMN

Figure 94. Reach abundance (fish/m2, seasons combined) of western

 mosquitofish, Gambusia affinis, in San Juan River secondary

 channels, 1993 - 1997.

YEAR

1993 1994 1995 1996 1997

ABUNDANCE (FISH/M2

) 0

1

2

3

REACH 5

REACH 4

REACH 3
154

Figure 95. Total summer versus total autumn abundance (fish/m2

) in San Juan River 

 secondary channels, 1993 - 1997.

SUMMER ABUNDANCE (FISH/M2

)

0 5 10 15 20 25 30

AUTUMN ABUNDANCE (FISH/M2

)

0

2

4

6

8

10

r

2

 = 0.1721, p < 0.12
155

0 2 4 6 8 10 12 14

0

1

2

3

4

5

RED SHINER

r

2

 = 0.0221, p < 0.60

02468

AUTUMN ABUNDANCE (FISH/M2

) 0

1

2

3

4

FATHEAD MINNOW

r

2

 = 0.2702, p < 0.047

Figure 96. Summer versus autumn abundance (fish/m2) of red shiner,

 fathead minnow, and speckled dace in San Juan River

 secondary channels, 1993 - 1997.

SUMMER ABUNDANCE (FISH/M2

)

012345

0

1

2

SPECKLED DACE

r

2

 = 0.4389, p < 0.007
156

0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7

0.00

0.05

0.10

0.15

0.20

0.25

FLANNELMOUTH SUCKER

r

2

 = 0.6952, p < 0.0001

01234

AUTUMN ABUNDANCE (FISH/M2

) 0.00

0.05

0.10

0.15

0.20

0.25

0.30

BLUEHEAD SUCKER

r

2

 = 0.3988, p < 0.012

Figure 97. Summer versus autumn abundance (fish/m2) of flannelmouth

 sucker, bluehead sucker, and western mosquitofish in San

 Juan River secondary channels, 1993 - 1997.

SUMMER ABUNDANCE (FISH/M2)

012

0

1

2

WESTERN MOSQUITOFISH

r

2

 = 0.7290, p < 0.0001
157

Figure 98. Summer versus autumn abundance (fish/m2) of channel

 catfish in San Juan River secondary channels, 1993 - 1997.

SUMMER ABUNDANCE

0.0 0.2 0.4 0.6 0.8 1.0

AUTUMN ABUNDANCE

0.0

0.1

0.2

0.3

0.4

0.5

r

2

 = 0.0327, p < 0.55
FISH ASSEMBLAGES OF SAN JUAN RIVER

SECONDARY CHANNELS

DISCUSSION

1991 – 1997
159

DISCUSSION

In the San Juan River between RM 155 and RM 68, secondary channels were

common and provided substantial habitat for resident fishes. The availability of

secondary channel habitats varied considerably with flow volume. During spring runoff

in most years, all secondary channels had surface flow and a range of habitats was

available to fishes. As flows receded with the end of spring runoff, the quantity of

secondary channel habitats diminished, and in some instances the quality of available

habitats may have decreased. For the remainder of the year, flows were fairly low,

typically less than 2000 cfs. During summer, convectional storms caused spikes in river

discharge and secondary channels that were dry or only had scattered pools and short

runs had surface flow for brief periods (normally less than one week) for their entire

lengths. Under these conditions, the fish assemblages of San Juan River secondary

channels varied considerably over the course of a year. During spring runoff, largebodied fishes numerically dominated collections, but by late summer most individuals

found in secondary channels were mainly representatives of small-bodied species.

During spring runoff, discharge in all years of the study was sufficient to inundate

all or most secondary channels associated with the primary channel of the San Juan

River. Secondary channels provided habitats for fishes during periods of elevated flow

(> 2500 cfs) that were unavailable or unsuitable for much of the year. When discharge

was < 1500 cfs (mid summer through winter) few secondary channels had sufficient

inflow to maintain flowing water throughout their courses, many had interrupted flow,

and some were completely dry except for their downstream confluence with the primary

channel. During low-flow periods , large-bodied fishes (> 200 mm TL) were rarely

collected in secondary channels and then only in those with surface flow throughout their

courses; native and nonnative small-bodied fishes (< 200 and most < 100 mm TL) were

common. However, when elevated flows flooded secondary channels, large-bodied

fishes quickly moved into secondary channels and were often common. For example,

sampling in spring 1996 occurred about 1 week after increasing discharge crossed the

1500 cfs threshold for inundation of 75% of the secondary channels and large-bodied

fishes were common in secondary channels.

There are at least three possible reasons for movement of large-bodied fishes into

secondary channels during spring runoff. Seasonally, secondary channels may provide

foraging areas for each of the commonly collected large-bodied fishes. Both sucker

species are benthic feeders; flannelmouth sucker consumes plant material (filamentous

algae and vascular plants) and aquatic macroinvertebrates (LaRivers, 1962; Greger and

Deacon, 1988) while bluehead sucker survives by scrapping vegetation (including

diatoms) from rocks (Baxter and Simon, 1970). Young of both sucker species consume

large numbers of aquatic insects, particularly chronomid larvae (Childs et al., 1998).

Common carp are omnivores, feeding on vegetation (algae and vascular plants), seeds,

and macroinvertebrates (Rehder, 1959; Eder and Carlson, 1977). Channel catfish are

largely insectivorous as smaller individuals (< 300 mm TL), but shift to piscivory as they

grow (Tyus and Nikirk, 1990; Marsh and Douglas, 1997; Larson and Propst, 1999;
160

Brooks et al., 2000). Food for each of these species was available, and often common, in

San Juan River secondary channels during spring runoff.

A second reason for the apparent high use of secondary channels is for spawning

by flannelmouth sucker, bluehead sucker, and common carp. Both sucker species spawn

during flow increases associated with spring runoff when water temperatures are 14 to

16°C (Muth and Nesler, 1993). Common carp also spawn in spring when water

temperatures are about 15°c (Rehder, 1959). Spawning aggregations of both sucker

species, but most frequently flannelmouth sucker, were found over cobble bars where

water velocity was rapid (> 1.0 m/s) in several secondary channels during most years.

Gravid females and ripe males of common carp were also common during spring in

secondary channels.

A third, but less likely, reason was avoidance of the higher velocity flows in the

primary channel. Flows at time of spring sampling were less than spring peaks and

would not seem sufficient to “force” fish into “protected” areas or channels. In addition,

both native sucker species are adapted to the characteristic high spring flows of the San

Juan River (Holden and Stalnaker, 1975) and avoidance of primary channel high velocity

flows does not therefore seem a reasonable explanation. Channel catfish, likewise, is a

riverine species (Pellett et al., 1998), but also inhabits lentic systems (Carlander, 1969).

Young channel catfish occur in a wide range of water velocities (Conklin et al., 1996)

whereas older individuals are often found in low-velocity areas. Common carp inhabits

lentic and lotic habitats and given its wide distribution and success in North American

(Moyle, 1976) elevated spring flows would not appear sufficient to prompt it to move to

lower velocity areas.

Any, and all, of the above reasons may have contributed to movement of largebodied fishes into secondary channels as they became inundated or fish simply moved

into secondary channels because access was possible. Comparison of primary and

secondary channel data for spring 1994 through 1997 indicated some differences in largebodied fish assemblages. For example, flannelmouth sucker was more common in

secondary than the primary channels, but mean biomass of individuals captured was not.

Bluehead sucker was more common in secondary channels in Reach 5, but there were no

significant differences in abundance in downstream Reaches 4 and 3. Several differences

(biomass and abundance) were noted for common carp and channel catfish, but most

comparisons indicated about equal usage of primary and secondary habitats by these two

species. These comparisons suggested that native suckers, at least smaller individuals,

may “seek” secondary channels during spring runoff, but no “preference” for them was

indicated by common carp and channel catfish comparisons.

The spring abundance trend of commonly collected species varied. Between 1993

and 1997, abundance of flannelmouth sucker declined in secondary channels in Reaches

5, 4, and 3. The abundance of bluehead sucker initially declined (1993 through 1995),

but then increased, in each Reach, from the 1995 low though 1997. The abundance trend

of common carp was not consistent among reaches; it generally increased in Reach 5,

decreased and then increased in Reach 4, and reversed abundance each year in Reach 3.
161

Abundance of channel catfish was lowest in all reaches in 1994 and increased in all

through the end of the study. The abundance of native flannelmouth and bluehead

suckers was lower in 1997 than 1993 in all reaches but that of nonnative common carp

and channel catfish was higher in all reaches in 1997 than 1993. There is no obvious

explanation for these observed changes. Changes may be related to reproductive success

in preceding years (prior to and during study), which, in turn, was influenced by annual

discharge patterns (see below). For most fish species, but particularly large-bodied

species, seven years was probably too brief to precisely determine patterns, or lack, in

abundance as a response to mimicry of a natural hydrograph. Large-bodied species are

long-lived (> 7 years) and perceived changes in abundance may be a reflection of cohort

abundance rather than total abundance. For example, the comparatively high abundance

of flannelmouth sucker in spring 1993 and 1994 may have been a reflection of elevated

reproductive success and recruitment of the 1987 year class (a high spring runoff year).

Its comparatively low abundance in 1995 and 1996 may have been a consequence of low

reproductive success and recruitment of the 1989 and 1990 year classes (both low spring

runoff years).

Similar to temporal changes in abundance, each commonly collected species had

spatial trends in abundance. Flannelmouth sucker abundance was greatest in Reach 4 and

least in Reach 5. Bluehead sucker abundance decreased from Reach 5 through Reach 3,

where it was incidental in spring collections. Common carp abundance was lowest in

Reach 4 and almost equal in Reaches 5 and 3. Channel catfish was most abundant in

Reach 3 and least in Reach 4. These overall patterns were generally consistent with that

noted for each year. The spatial abundance patterns of flannelmouth and bluehead

suckers are likely related, at least in part, to the habitat preferences of each. Because

bluehead sucker obtains much of its sustenance by scrapping rocks for vegetation, its

distribution in the San Juan River system was partially influenced by the relative

abundance of habitats with cobble substrates; such areas were more common in Reach 5

than Reach 4 and Reach 4 than Reach 3 (Bliesner and Lamarra, 1996). The generalist,

bottom-feeding habits of flannelmouth sucker may explain its higher abundance in Reach

4. There the abundance of mixed-bottom types were high (Bliesner and Lamarra, 1996).

The high island count (an indicator of habitat complexity) of Reach 4 may have

contributed to the high abundance of common carp. During spring inventories, common

carp were frequently captured in shallow, recently-flooded terraces associated with

secondary channels. From 1993 through 1996, abundance of channel catfish was low (<

0.20 fish/min) in all reaches (except Reach 3 in 1996). The 1997 increase in channel

catfish abundance in Reaches 4 and 3 was, in part, the consequence of relatively high

numbers of younger and smaller individuals (< 225 mm TL). These fish were likely

spawned in 1995 or 1994, years of high and average spring runoff.

Although some inter-year changes in the size-structure of flannelmouth sucker

populations were discerned from length-frequency histograms, none were significant.

Within each reach, the age-structure of flannelmouth sucker remained similar from year

to year. In Reaches 5 and 4, sub-adults were the most abundant age-class in all years

except 1997 when adults were most abundant. In Reach 3, sub-adults were always the

most abundant age-class and more abundant by a large margin in most years. Mean total
162

length of flannelmouth sucker did not change from year to year until 1997 when it

increased in Reaches 4 and 3. The increases in mean TL may be a reflection of reduced

spawning success and recruitment of the 1996 cohort and survival of the 1995 cohort.

Prior to 1997, juveniles (Ages 1 and 2; 76 to 200 mm TL) were at least 12% of annual

collections in Reach 4 and at least 20% of the annual Reach 3 collections. In 1997,

abundance of juveniles was markedly lower in both reaches. Flows during 1996 were the

lowest of the study period and likely contributed to increased mortality of young

flannelmouth sucker or reduced spawning success. Thus, paucity of young (and short)

individuals in the 1997 collections resulted in an increase in mean length. In Reach 5,

juveniles were a large proportion of the 1997 sample and mean length for 1997 was

therefore not substantially different than in preceding years. Survival of juveniles may

have been enhanced by greater availability of juvenile habitats in Reach 5 than

downstream reaches.

Although they were never abundant in secondary channel collections, juvenile,

sub-adult, and adult bluehead suckers were present in all reaches in most years. In Reach

5, adults were usually the most numerous age-class while sub-adults were typically more

common in Reaches 4 and 3. Mean length of bluehead sucker varied from year to year in

Reach 5, but mean TL in 1993 was almost the same as in 1997. Except for a decrease in

length in 1994, mean TL was almost identical from year to year in Reach 4. There was a

slight decrease in mean TL in Reach 3 during the study. Although there was a marked

decline in bluehead sucker abundance between 1993 and 1994 in Reaches 5 and 4, the

age- and size-structure data suggest a relative “stability” of bluehead sucker secondary

channels populations in each reach.

The size- and age-structure (not plotted in Results as almost all specimens in all

reaches in all years were adults) and mean length of common carp remained almost

constant throughout the study. Between 1993 and 1997, abundance of common carp

increased in Reach 5, remained fairly constant in Reach 4, and varied in Reach 3.

Greater numbers of small (< 400 mm TL) common carp were captured in Reach 3 than in

Reaches 5 and 4. This may indicate that habitat for juveniles and sub-adults was most

common in Reach 3. However, the high abundance of the species in Reach 3 in 1996

was the result of high numbers of adults, not juveniles or sub-adults.

Channel catfish abundance increased in all reaches over the course of the study,

but its mean length decreased markedly in all reaches. The decrease in mean length was

50+ mm in all reaches. In contrast, mean TL of other common collected fishes remained

the same or increased. In Reach 5, the proportion of large channel catfish (> 500 mmTL)

did not change appreciably, but the abundance of individuals < 300 mm was substantially

greater in 1997 than 1993. There was no apparent shift in proportion of age- or sizeclasses in Reach 4; nonetheless mean TL was less in 1997 than 1993. The increase in

abundance in Reach 3 was largely attributable to increased abundance of individuals <

250 mm. The decline in mean TL of channel catfish may be a consequence of ongoing

efforts to suppress their abundance. If so, the capture techniques (raft electrofishing and

hoop nets) may have been selective for large individuals. Alternatively, removal of large

individuals may have enhanced survival of small individuals. A third explanation may
163

involve increased reproductive success or enhanced recruitment. In Reach 3, where

juvenile abundance was typically high, the highest abundance was found in 1996 and

1997. Mean TL of the smallest cohort in 1996 was about 160 mm (Range = 100 to 224

mm), indicating they were about Age 2 and therefore spawned in 1994, an average spring

runoff year. In 1997, mean TL of the smallest cohort was about 200 mm (Range = 100 to

249 mm) and likely included Age 2 and 3 individuals. The Age 2 fish were spawned in

1995, a high spring runoff year. Data from Reach 3 on the influence of spring runoff on

channel catfish reproduction and survival are therefore ambiguous.

During this study, few sub-adult and adult Colorado squawfish or razorback

sucker were found in secondary channels during spring inventories. Their rarity in these

habitats was more likely a reflection of their overall rarity in the system than an

indication of avoidance. In 1996 and 1997, Age-0 Colorado squawfish were stocked in

the river. As these fish attain sub-adult and adult sizes, it is likely they will seasonally

use habitats provided by secondary channels. Low numbers (< 1000 annually) of subadult razorback suckers have been stocked in the San Juan River since October 1994

(Ryden and Pfeifer, 1996) and a few were collected in secondary channels. As numbers

stocked increase, or stocked individuals spawn, it is likely that its occurrence in

secondary channels will increase.

Data collected on San Juan River fishes during spring inventories indicated shifts

in overall assemblage structure of secondary channels. The most apparent reason for

these shifts was restoration of a more natural annual flow regime. Between closure of

Navajo Dam in 1962 and initiation of the San Juan River Seven Year Research Program

in 1991, the annual flow regime was characterized by depressed or truncated spring flows

and elevated flows for the remainder of the year. For the seven years of this study,

discharge rarely exceeded 2500 cfs during non-spring runoff season, but between 1984

and 1990 discharge frequently exceeded 2500 cfs in all seasons (Table 69). Beginning in

1992, releases from Navajo Reservoir were modified to simulate more natural annual

flow regimes with elevated flows during spring and flows near, albeit higher than,

historic (pre-dam) levels for the remainder of the year. The shift to more natural flow

regimes affected a variety of physical attributes of the river, including habitat availability

and quality (Bliesner and Lamarra, 1996). Changes in physical attributes of the system

were manifested by changes in the fish assemblages of secondary channels. An essential

question is whether these changes were detrimental to the native fish community

(including Colorado squawfish and razorback sucker) or will they contribute to

restoration of a more “natural balance” among native species and diminished abundance

of nonnative fishes. For example, abundance of flannelmouth sucker declined through

the study period (1993 through 1997), but size-structure of the population did not. The

abundance of flannelmouth sucker prior to restoration of natural flow regimes may have

been unnaturally high. Restoration of natural flow regimes may have restored or

enhanced mortality factors that were depressed during the period of comparative flow

stasis. The lack of change in flannelmouth sucker size- and age-structure suggests that

the apparent decline in abundance has not negatively affected the population.
164

Table 68. Number of days San Juan River discharge > 2,500 cfs at Shiprock USGS gage

during spring runoff and non-runoff seasons for the seven years preceding initiation of

Seven-Year Study and seven years of the study. Spring runoff defined as 1 March

through 31 July each year, non-runoff remainder of year. Counts based on water years

(1 October – 30 September).

1984 1985 1986 1987 1988 1989 1990

SPRING RUNOFF 77 140 113 142 17 0 12

NON-RUNOFF 33 31 145 139 11 1 2

1991 1992 1993 1994 1995 1996 1997

SPRING RUNOFF 20 83 128 65 137 32 90

NON-RUNOFF 0 7 4 0 2 0 19

However, it is unclear from the data obtained in this study if the decline in flannelmouth

sucker abundance will continue or has its abundance has reached a new equilibrium.

Data obtained from spring inventories of secondary channels suggest that

common carp was impervious to changes in the flow regime (and associated habitat

changes). The data did not reveal any apparent trends in abundance, size- or agestructure, or mean length. Changes in attributes of channel catfish populations, however,

suggest this species was affected by changes in flow regime. Mean length declined

markedly and in Reach 3 abundance steadily increased over the course of the study.

Efforts to suppress channel catfish may have influenced these apparent trends.

Spring inventories of San Juan River secondary channels demonstrated that these

habitats are seasonally used by all large-bodied fish species present in the San Juan River

within the study area (Reaches 5 through 3). This effort also indicated that changes in the

flow regime of the river affected secondary channel fish assemblages. It is possible,

perhaps likely, that shifts (changes in overall assemblage structure as well as speciesspecific changes) will continue for several more years.

During summer months (July through September), flows were sufficient in most

years of study to inundate at least 50% of the San Juan River secondary channels within

the study area. The particular mix of habitats within secondary channels depended upon

contemporary and previous flows. Habitats in some secondary channels consisted only

of isolated, silt-bottomed pools while others had flowing water with riffle, run, and pool

habitats. Regardless of the type and extent of habitats available, fish were almost always

found. The species found, and the abundance of each, was mediated, in part, by the

habitats present (Gido and Propst, 1999). On a secondary channel scale, considerable

differences in habitats available were found and as a consequence the fish assemblages of

individual secondary channels often differed substantially. On a Geomorphic Reach
165

scale, the influence of channel-specific differences diminished as each Reach had a range

of secondary channels (and habitats). By grouping fish assemblage data by Reach,

channel-specific influences, or aberrations, were reduced and the grouped data thus better

represented the overall fish assemblages.

The summer fish assemblages of San Juan River secondary channels were

numerically dominated by, often by a large margin, nonnative fish species. Red shiner

and fathead minnow were typically the most common fish species. Large numbers of

western mosquitofish were found in 1996 (a low-flow year). Speckled dace was

relatively common in all years, except 1996. Flannelmouth sucker was moderately

common in the 1991 and 1992 collections but was less abundant in subsequent years.

Summer secondary channel abundance of bluehead sucker was greatest in 1995 (a high

spring runoff year) when it was almost 12% of the total collection; in other years its

abundance was low.

In addition to characterizing the fish fauna of secondary channels, this study was

designed to gain insights to seasonal changes in their fish assemblages and to characterize

the response of these assemblages to different flow regimes. A basic hypothesis was that

different flow regimes would be reflected by numeric differences among species. The

mechanisms by which different flow regimes affected individual species populations

were not known. For example, did elevated flows differentially displace native or

nonnative fishes? Did low flows result in habitat loss to the detriment of native or

nonnative species? Did altered flow regimes change thermal regimes to the benefit or

detriment of a particular species? Were certain life stages more susceptible to changes in

flow regime than others? Alternatively, changes in flow and habitat availability may

have had no discernable effect on abundance of species. In such a scenario, there would

be no “controlling” factors, just random variation in abundance.

The summer fish assemblage of San Juan River secondary channels was quite

different from that found during spring runoff. Although the species present did not

change, the abundance and size-structure of each species was different. For example, in

spring large-bodied flannelmouth sucker, bluehead sucker, common carp, and channel

catfish numerically dominated collections, but in summer these species were uncommon

and most individuals of each were small (< 150 mm TL). Summer collections were

numerically dominated by all age-classes of small-bodied species, particularly red shiner,

fathead minnow, and speckled dace.

Some research indicates that elevated flows, particularly floods, diminish the

abundance of nonnative fishes (e.g., Minckley and Meffe, 1986; Gido et al., 1997) and do

not have a detrimental effect on native fish assemblages. Minckley and Meffe (1986)

suggested that the evolution of native western North American fishes in highly varible

systems enables them to survive the rigors imposed by severe flooding, but nonnative

fishes, most from mesic regions with less severe flooding, are not able to withstand

floods typical of the arid west.
166

In the unregulated San Juan River, the most “predictable” flood was annual spring

runoff. Although volume and duration changed substantially from year to year, some

elevation in flow occurred in all years during spring. Other floods were associated with

storm events, particularly summer convectional storms. However, Navajo Dam enabled

regulation of the natural flows of the river and resulted in a reduction (and sometimes

elimination in low runoff years) of elevated spring flows. In addition, reservoir releases

to meet irrigation needs increased base flows during traditional low-flow periods

(summer and early autumn).

During summer, the majority of fishes found in secondary channels were Age-0

individuals. Nonnative red shiner and fathead minnow and native speckled dace were

most common. Native flannelmouth and bluehead suckers were typically present, but

were not normally common. Western mosquitofish was occasionally abundant, but most

other nonnative species collected were uncommon in all years. Channel catfish and

common carp, both common during spring inventories, were rare in most summer

secondary channels during summer. Few roundtail chub and Colorado squawfish were

found in secondary channels during summer. This was largely a function of their overall

rarity in the system.

Although abundance of each species varied considerably among years and among

Geomorphic Reaches, general (all years combined) longitudinal patterns of abundance

were discerned (Figure 100). The abundance pattern of each was related, at least in part,

to their habitat preferences and life history strategies. Bluehead sucker was substantially

more abundant in Reach 5 (1.02/m2

 ) than downstream reaches (0.27 and 0.14/m2).

Speckled dace and fathead minnow had similar, but less dramatic, patterns. Bluehead

sucker feeds on perilithic plants; cobble-bottomed riffles and runs with seasonally

abundant vegetation were more common in Reach 5 than downstream reaches (Bliesner

and Lamarra, 1996). In addition, such areas are also the primary spawning habitat of the

species (McAda and Wydoski, 1983; Maddux and Kepner, 1988). The comparatively

high abundance of Age-0 bluehead sucker (versus flannelmouth sucker) in secondary

channels during summer may be related to bluehead sucker spawning later in

spring than flannelmouth sucker. By the time of summer inventories (mid August), Age0 flannelmouth sucker had moved from secondary channels habitats to the primary

channel, but later-spawned bluehead sucker remained in the low-velocity habitats of

secondary channels. The summer longitudinal abundance pattern of bluehead sucker

reflected its spring abundance pattern. Although speckled dace was most commonly

associated with riffles, it also occurred in other habitats with flowing and standing water

(Minckley, 1973; Gido and Propst, 1999). Variety of habitats used coupled with feeding

habits (insectivorous) explains, in part, the slightly decreasing longitudinal abundance

pattern of speckled dace. The comparatively high abundance of fathead minnow in

Reach 5 and lower abundance in Reach 3 may be related to the reproductive biology of

the species. Males establish territories near submerged debris or vertical and undercut

banks in low-velocity water and the adhesive eggs are deposited on instream structures

(Becker, 1983). Areas with requisite physical features for fathead minnow spawning

were comparatively common in secondary channels in Reach 5 but less so in downstream

reaches. The relative rarity of flannelmouth sucker in secondary channels during summer
167

may be more a function of time of sampling than avoidance or non-use of secondary

channels. Red shiner was the only commonly collected species that was most abundant

in Reach 4. Habitat availability and thermal regime may have contributed to its higher

abundance in Reach 4. The convergence of optimal water temperature for spawning (22

to 26°C) and habitat (gravel- and small cobble-bottomed riffles)(Gale, 1986) likely

occurred in Reach 4.

Comparison of summer abundance of commonly collected species to attributes of

spring runoff indicated that there were positive relationships for several species. The

greatest abundance of fishes in secondary channels was in 1993 and 1995, high spring

runoff years. Regression analysis revealed positive, if not significant, relationships

between spring runoff and summer densities of several species. Red shiner abundance

was most strongly correlated, but not significantly, to spring runoff in Reach 4. Speckled

dace abundance was significantly related to most attributes of spring runoff in Reaches 4

and 3 and bluehead sucker abundance was strongly correlated with spring runoff

attributes in Reach 5. Neither fathead minnow nor channel catfish abundance appeared to

be related to spring runoff.

The lowest summer abundance of all species, native and nonnative, was in 1997, a

year of high spring runoff. The low abundance of fishes in 1997 seemingly contradicts

the presumed positive relationship between spring runoff and summer abundance of

several species. Several factors, however, may have caused this apparent anomaly.

Spring runoff in 1996 was lower than in any other year of the study. While abundance of

all fishes was lower in 1996 than 1995, native fishes declined more than nonnatives

(native fishes were 34.3% of the fishes collected in 1995 but in 1996 native fishes were

only 15.0% of the collections). Between 1995 and 1996, total abundance of red shiner

declined from 5.73 to 2.50/m2

, but speckled dace declined from 2.56 to 0.14/m2 and

bluehead sucker from 1.46 to 0.02/m2. These summary data suggest that short-lived (and

small-bodied) nonnative fishes had greater reproductive success or survival of young than

did speckled dace (also a short-lived species) in 1996. Native fishes spawn primarily

during spring runoff or runoff recession while the two most common nonnatives spawn

after runoff recession. If spring runoff is low, native fish reproductive success, or

survival of young, is presumably lowered. The low abundance of all species, particularly

short-lived, in summer 1997 was in part a consequence of low numbers of 1996 yearclass individuals. The high spring runoff of 1997 likely had a relatively greater positive

effect on the reproductive success of native than nonnative fishes; native fishes were a

larger proportion of the collections in summer 1997 than in 1996, lending some credence

to this scenario.

During summer, San Juan River secondary channels provide habitats used by

native and nonnative fishes, particularly Age-0 individuals (Gido and Propst, 1999). Red

shiner, fathead minnow, and speckled dace spawn in secondary channels and this

contributes to their summer abundance in these habitats. Flannelmouth and bluehead
168

543

0

1

2

3

4

5

6

7

543

01234

ABUNDANCE (FISH/M2

)

0

1

2

3

4

5

6

7

543

Figure 99. Mean summer abundance of commonly collected fish species

 in San Juan River secondary channels, 1993 - 1997. 

REACH

543

0

1

2

3

4

5

6

7

RED SHINER FATHEAD MINNOW

SPECKLED DACE FLANNELMOUTH SUCKER

BLUEHEAD SUCKER
169

may spawn in secondary channels during spring runoff or their young drift into secondary

channels. Regardless of their origin, native suckers were typically a small proportion of

secondary channel summer fish assemblages. With few exceptions, no age-class of either

common carp or channel catfish was common in secondary channels during summer.

Their paucity suggests that during summer secondary channels have limited amounts of

the habitats these species need or use.

By autumn abundance of fishes in secondary channels was substantially less than

in summer, but the species present and their rank did not change noticeably. Although

there were some changes in habitat, these were minor; autumn flows were about the same

or slightly greater than during summer. During 1993 and 1997, summer storms caused

flow spikes but in other years flow was comparatively constant from spring runoff

recession through autumn.

Mean autumn longitudinal abundance trends of red shiner and fathead minnow

were different from that noted for summer. In average, red shiner abundance was

greatest in Reach 4 in summer, but greatest in Reach 3 in autumn (Figure 101). In

summer, fathead minnow abundance decreased in a downstream direction, but was least

in Reach 4 in autumn and almost equal in Reaches 5 and 3. In contrast, native fish

(speckled dace, flannelmouth sucker, and bluehead sucker) abundance trends changed

little between summer and autumn. Speckled dace was most abundant in Reach 5 in both

seasons, but the downstream decrease was more pronounced in autumn than summer.

Generally, low summer flows and absence of flow spikes benefited nonnative

fishes, particularly fathead minnow. Native fishes were negatively affected by low

summer flows (especially number of days discharge < 500 cfs) and elevated summer

flows (including flow spikes) did not have an apparent effect (negative or positive) on

native fish abundance.

The most likely reason for the positive effect of low summer flows on the autumn

abundance of nonnative fishes (red shiner, fathead minnow, and western mosquitofish)

was related to their requirements for spawning and tolerance of elevated temperature and

depressed dissolved oxygen (Matthews and Hill, 1979; Fader et al., 1994; Hubbs, 1996).

Each spawns when water temperatures exceed 20°C. Water temperatures do not

normally attain this level until after recession of spring runoff in mid to late July, and

rarely exceeded 25°. Water temperatures typically drop 5°C or more during summer

flow spikes. In 1993, 1994, and 1996, there were no substantial summer flow spikes; red

shiner autumn abundance was highest in these years. In 1995 and 1997, years having

summer flow spikes, red shiner abundance was comparatively low (although not

considerably lower in 1995). Fathead minnow and western mosquitofish autumn

abundance was highest in 1994 and 1996 and lowest in 1995 and 1997. Autumn

abundance of both was low in 1993, a year with comparatively high spring runoff but no

summer flow spikes. Speckled dace autumn abundance was highest in 1993 and 1995,

years with high spring runoff and summer flow spikes. Although its autumn abundance

in 1997 was low compared to 1993 through 1995 levels, it was substantially higher than
170

that found in 1996, a low spring runoff year with low base summer flows (and no

summer flow spikes). Both flannelmouth and bluehead suckers autumn abundance

patterns were similar to that of speckled dace, but with some differences. Flannelmouth

sucker abundance was comparatively low in 1995 (high spring runoff year). Autumn

abundance of both sucker species was greater in 1997 (high spring runoff and summer

flow spikes common) than in 1996 (low spring runoff and no summer flow spikes).

Although secondary channel summer abundance of nonnative red shiner, fathead

minnow, and western mosquitofish were depressed somewhat by high spring runoff, the

greater negative impact on their autumn abundance appeared to be elevated summer

flows (particularly flow spikes). Low summer flows appeared to have no negative effect

on their abundance and seemed to enhance that of at least western mosquitofish. The low

summer flows of 1996 had a major negative impact on native fishes in secondary

channels. In contrast, elevated summer flows did not have discernible negative effects on

native fish abundance, but low, stable summer flows depressed native fish abundance.

Prior to 1997, paucity of Colorado squawfish and razorback sucker in the San Juan River

precluded evaluation of their use of secondary channel habitats. The capture of

comparatively large numbers of Colorado squawfish in secondary channels in autumn

1997 indicates the species readily uses habitats (particularly low-velocity) of secondary

channels.

The 1991 through 1997 seasonal ichthyofaunal inventories of San Juan River

secondary channels demonstrated extensive use of these habitats by native and nonnative

fishes. Flow levels appeared to have a major influence on the attributes of the fish

assemblages. During spring runoff, large-bodied fishes (native and nonnative) were

common in secondary channels, but during low flow periods assemblages were

numerically dominated by small-bodied fishes, particularly nonnative red shiner and

fathead minnow; native speckled dace was the only common native species in summer

and autumn assemblages. The occurrence of large numbers of juvenile Colorado

squawfish in autumn 1997 suggested secondary channels provide habitat for the species.

Manipulation of flows during summer and early autumn may be a method to control or

suppress abundance of undesirable nonnative fish species, particularly small-bodied

species such as red shiner, fathead minnow, and western mosquitofish. In contrast,

elevated flows during spring have limited negative effects on abundance of several

nonnative species but positive effects on abundance of several native fish species.
171

543

0

1

2

3

543

543

ABUNDANCE (FISH/M2

)

0

1

2

3

543

Figure 100. Autumn abundance of commonly collected fish species 

 in San Juan River secondary channels, 1993 - 1997.

REACH

543

0

1

2

3

RED SHINER FATHEAD MINNOW

SPECKLED DACE FLANNELMOUTH SUCKER

BLUEHEAD SUCKER
172

FISH ASSEMBLAGES OF SAN JUAN RIVER

SECONDARY CHANNELS

1991 – 1997

CONCLUSIONS AND MANAGEMENT IMPLICATIONS
173

CONCLUSIONS AND MANAGEMENT IMPLICATIONS

OVERALL

♦ Study objectives met? Yes.

♦ Flows at time of sampling did not effect Spring and Summer CPUE, but

negatively effected autumn CPUE.

♦ There are substantial seasonal changes in the fish assemblages of secondary

channels.

♦ Secondary channels provide substantial habitat for native and nonnative fishes.

♦ Autumn sampling likely yielded the most representative samples of the smallbodied fish assemblage of secondary channels.

♦ Only spring sampling will provide information on use of secondary channels by

large-bodied fishes.

♦ Spring secondary channel assemblages composed mainly of large-bodied

individuals of flannelmouth sucker, bluehead sucker, common carp and channel

catfish, but sampling technique biased against small-bodied fishes.

♦ Abundance of fishes during spring did not change in Reach 5, declined in Reach

4, and varied but did not change over the course of the study in Reach 3.

♦ Over the course of the study there were distinct changes in the structure of

secondary channel spring fish assemblages.

♦ In each season sampled, there were measurable differences in the fish

assemblages in Geomorphic Reach.

♦ Summer secondary channel assemblages composed mainly of small-bodied

fishes. Red shiner, fathead minnow, and speckled dace most common species

during summer.

♦ Autumn secondary channel assemblages composed mainly of small-bodied fishes.

Red shiner, fathead minnow, and speckled dace most common species during

autumn.

♦ Elevated spring runoff appeared to be positively correlated with summer

secondary channel abundance of fishes in secondary channels.

♦ Elevated spring runoff did not appear to have definite negative impacts on any

small-bodied species, but had positive effects on summer abundance of several.

♦ Elevated summer flows appeared to be detrimental to abundance of some

nonnative species but no, or slightly positive, effect on native fishes.

♦ Low summer flows had a negative impact on abundance of native fishes but had

no effect or positive effect on nonnative species.

FLANNELMOUTH SUCKER

♦ Flannelmouth sucker was typically the most abundant species during in all

Reaches in all years.
174

♦ Spring abundance declined in all reaches (5, 4, and 3), but mean TL remained the

same (Reach 5) and was the same from 1993 through 1996 and increased in 1997

(Reaches 4 and 3).

♦ Spring size- and age-structure remained similar among reaches and years.

♦ Spring total biomass declined in all reaches, but mean biomass was the same

(Reach 5) or increased (Reaches 4 and 3).

♦ Spring abundance was usually greater in Reaches 5 and 4 than Reach 3.

♦ Summer abundance varied from 1991 through 1995 and declined to study low in

1997.

♦ Summer abundance was positively related, but not significantly, to elevated

spring discharge; strongest relationships were with days flows exceeded 3,000

and 5,000 cfs.

♦ Autumn abundance decreased from 1993 through 1996 and increased in 1997.

♦ Autumn abundance was greatest in Reach 5 and least in Reach 4.

♦ Autumn abundance was negatively related, but not significantly, to low summer

flows and in Reach 3 to days discharge > 1000 cfs.

♦ Autumn abundance was significantly, and positively, related to summer

abundance.

♦ Sub-adults and adults were rarely found in secondary channels during summer

and autumn; most specimens were juveniles and larvae.

BLUEHEAD SUCKER

♦ Bluehead sucker varied from the second- to fifth-most abundant species in spring

inventories.

♦ Spring abundance declined from 1993 through 1995 in all reaches, and increased

through 1997.

♦ Spring abundance of bluehead sucker was usually greatest in Reach 5 and least in

Reach 3.

♦ Spring size- and age-structure changed slightly during the study; small individuals

(<150 mm, Age-0 and –1) were more common in 1993 and 1994.

♦ Mean TL varied some in Reaches 5 and 4, and declined slightly in Reach 3.

♦ Total spring biomass was usually greatest in Reach 5 and least in Reach 3.

♦ Summer abundance peaked in 1993 and 1995, high spring runoff years, and was

least in 1991, 1996, and 1997. Spring runoff was low in 1991 and 1996, but high

in 1997.

♦ Summer abundance was positively, and significantly, related to elevated spring

runoff, particularly in Reaches 5 and 3.

♦ Autumn abundance was comparatively high in 1993, but low in all succeeding

years.

♦ Autumn abundance was greatest in Reach 5 and least in Reach 3.

♦ Summer flow attributes generally had little effect on bluehead sucker autumn

abundance; low summer flow had very weak negative effects on autumn

abundance.
175

♦ There was weak correlation between summer and autumn abundance of bluehead

sucker.

COMMON CARP

♦ Common carp was the second- or third-most abundant species in spring

inventories.

♦ Spring abundance was similar from 1993 through 1995 and increased through

1997 in Reaches 5 and 4; abundance varied among years in Reach 3, peaking in

1996.

♦ Abundance was not consistently greater in a single Reach during the study; it was

least in Reach 4 in 1995 and greatest in Reach 3 in 1996.

♦ Spring size- and age-structure was similar in all reaches in all years.

♦ Total spring biomass was usually greater in 1996 and 1997 than preceding years.

♦ Total spring biomass was greatest in Reach 5 from 1993 through 1995, greatest in

Reach 3 in 1996, and greatest in Reach 5 in 1997.

♦ Mean total length did not change in any reach during the study; mean biomass

remained the same in Reach 5 and increased slightly in Reaches 4 and 3.

♦ Common carp was rarely collected in secondary channels during summer and

autumn.

CHANNEL CATFISH

♦ Channel catfish was the second- to sixth-most abundant species in spring

inventories.

♦ Spring abundance was similar from 1993 through 1996, but increased in 1997 in

Reach 5; was similar among years (except 1994) in Reach 4; and increased from

1993 through 1997 in Reach 3.

♦ Adults were the majority of specimens collected in spring from 1993 through

1995, but sub-adult abundance increased in 1996 and 1997. Individuals < 300

mm TL increased, as a proportion of samples, from 1993 through 1997.

♦ Mean spring TL decreased in all reaches.

♦ Total spring biomass decreased from 1993 through 1996 and increased in 1997 in

Reach 5, mean biomass declined; total biomass was similar (except 1994) in

Reach 4, mean declined; total biomass increased from 1993 through 1995 and

remained the same thereafter in Reach 3, mean biomass decreased.

♦ Summer abundance of channel catfish increased from 1991 through 1994 and

then declined through 1997.

♦ In Reaches 5 and 3, there was no relationship between spring runoff attributes and

summer abundance; in Reach 4 summer abundance was weakly, and positively

related to elevated flows.

♦ Autumn abundance declined from 1993 through 1996, and increased slightly in

1997.
176

♦ Autumn abundance was least in Reach 5 and greatest in Reach 3.

♦ Autumn abundance was generally negatively related to elevated summer

discharge, and significantly so in Reach 4.

♦ Summer abundance was not related to autumn abundance.

RED SHINER

♦ Spring sampling methods (raft-mounted electrofishing) was not an efficient

method of red shiner collection.

♦ Insufficient numbers of red shiner were collected to characterize their distribution

and status during spring.

♦ Red shiner was the most abundant species collected in secondary channels during

summer in all years except 1994 and 1996 (low spring runoff years).

♦ Total summer abundance of red shiner peaked in 1993 and 1995 (high spring

runoff years), and was lowest in 1997 (also a high spring runoff year). Summer

and autumn flows were higher in 1997 than 1993 or 1995.

♦ Total summer abundance was greatest in Reach 4 and least in Reach 3.

♦ Summer abundance was positively, but not significantly, related to elevated

spring discharge (except days flow > 5000 cfs in Reaches 4 and 3, which were

significant).

♦ Red shiner was the most abundant species in autumn in all years.

♦ Total autumn abundance was about the same from 1993 through 1995, but

declined to study low in 1997.

♦ Total autumn abundance was greatest in Reach 3 and least in Reach 4.

♦ Autumn abundance was negatively, but not significantly, related to elevated

summer flows.

♦ Autumn abundance was not correlated with summer abundance.

FATHEAD MINNOW

♦ Spring sampling techniques did not yield representative collections of fathead

minnow.

♦ Spring sampling obtained fathead minnow in all years, except 1997.

♦ Total summer fathead minnow abundance peaked in 1993 (high spring runoff),

1994 (low spring runoff), and 1996 (low spring runoff). Total abundance was

least in 1997 (high spring runoff).

♦ Summer abundance was generally not related to spring runoff levels.

♦ Summer abundance was greatest in Reach 5 and least in Reach 3.

♦ Total autumn abundance was greatest in 1995 and least in 1997.

♦ Autumn total abundance was greatest in Reach 3 and least in Reach 4.

♦ Autumn abundance was negatively, but not significantly, related to elevated

summer flows; abundance was positively related to days flow < 500 cfs

(significantly in Reach 4).
177

♦ Autumn abundance was significantly related to summer abundance.

SPECKLED DACE

♦ Boat electrofishing was not an effective method for sampling speckled dace

during spring inventories.

♦ Speckled dace was collected during each spring inventory and was the most

abundant small-bodied species in all years except 1994 and 1996 (low spring

runoff years).

♦ During summer, speckled dace was the second- or third-most abundant species in

all years except 1996 (low spring runoff and low summer base flows).

♦ Total summer abundance peaked in 1993 (high spring runoff) and was least in

1996 (low spring runoff and low summer base flows).

♦ Total summer abundance was greatest in Reach 5 and least in Reach 4 (only

slightly less than Reach 3).

♦ Summer abundance of speckled dace was positively related to all attributes of

elevated spring discharge. In reaches 4 and 3, most relationships were significant.

♦ Autumn total abundance decreased from 1993 through 1996 and then increased in

1997.

♦ Autumn total abundance was greatest in Reach 5 and least in Reach 3.

♦ There was no relationship between any summer flow attribute and autumn

abundance, except days flow < 500 cfs. That relationship was negative, but not

significant, in all reaches.

♦ Autumn abundance was positively, and significantly, related to summer

abundance.

WESTERN MOSQUITOFISH

♦ Raft-mounted electrofishing gear failed to capture western mosquitofish during

spring inventories.

♦ Total summer abundance was usually low, except in 1996.

♦ Total summer abundance was greatest in Reach 5 and least in Reach 4.

♦ Total autumn abundance peaked in 1994 and 1996 and was least in 1997 (elevated

summer flows).

♦ Autumn abundance was greatest in Reach 5 and least in Reach 3.

♦ Autumn abundance was greatest in Reach 5 and least in Reach 3.

♦ Autumn abundance was negatively related to elevated summer flows and

positively (significantly in Reaches 5 and 4) related to days flow < 500 cfs.

♦ Autumn abundance was significantly related to summer abundance.
178

COLORADO PIKEMINNOW

♦ No adult Colorado pikeminnow was captured in secondary channels during spring

inventories.

♦ One juvenile Colorado pikeminnow was captured in a secondary channel in 1997.

♦ Colorado pikeminnow was the third most abundant species in secondary channels

in autumn 1997. It was not found in secondary channels in preceding years.

♦ Colorado pikeminnow autumn abundance was greatest in Reach 5 and least in

Reach 4 in 1997.

RAZORBACK SUCKER

♦ Razorback sucker was found in secondary channels during spring inventories in

1996 and 1997.

♦ No razorback sucker was found in secondary channels during summer or autumn

inventories.

ROUNDTAIL CHUB

♦ Roundtail chubs (juveniles) were found in secondary channels during summer and

autumn inventories in 1997. None was collected during spring.

♦ Roundtail chub was found in Reaches 4 and 3 during summer but not Reach 5.

♦ During autumn, roundtail chub was found in Reaches 5, 4, and 3.

OTHER NONNATIVE FISHES

♦ During spring inventories, eight nonnative species (in addition to those listed

above) were collected. All were rare and none was collected in all years.

♦ Summer inventories yielded four nonnative species (in addition to those listed

above). None was collected in all years. Plains killifish was the most common of

these but was never abundant.

♦ Autumn inventories yielded the same rare nonnative fishes as found during

summer (black bullhead, plains killifish, green sunfish, and largemouth bass).

♦ Plains killifish was the most common rare nonnative fish in autumn collections,

but was never abundant.

♦ Centrarchids were rare in San Juan River secondary channels in all seasons.

♦ Ictalurids, except channel catfish, were rare in San Juan River secondary channels

in all seasons.
179

FISH ASSEMBLAGES OF SAN JUAN RIVER

SECONDARY CHANNELS

1991 – 1997

LITERATURE CITED
180

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