U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Map 3350

Sheet 2 of 7

Prepared in cooperation with the

U.S. Army Corps of Engineers, Albuquerque District, and the U.S. Fish and Wildlife Service

Fish Collection

Fish assemblage surveys 

were done at each sampling site 

(except at the Peña Blanca and 

Bernalillo sites during summer 

2012) at moderate and low 

streamflows. Mesohabitat types 

were subsampled (with targeted 

minimums of 20 mesohabitats per 

sampling site in winter 2011–12 

and 30 mesohabitats per sampling 

site in summer 2012) in proportion 

to their relative abundance at each 

reach. If three or fewer of a given 

mesohabitat type occurred in a 

sampling site, then all mesohabitats 

of that type were typically sampled. 

Fish were collected by using a 

seine while wading during both 

winter and summer sampling. 

The sampling approach was the 

same as the sampling approach 

described in Moring and others 

(2014) and was deliberately 

biased toward collecting fish from 

shallow, low-velocity, nearshore 

habitats preferred by Rio Grande 

silvery minnow and similar fish; 

for example, 3.0-millimeter mesh 

seines were used, as opposed to 

a larger mesh size, to increase 

the likelihood of collecting Rio 

Grande silvery minnow and other 

minnow species. Additional 

details on the fish assemblage 

surveys are provided in Braun 

and others (2015).

Physical Characteristics Over a Range of Streamflows

Physical characteristics 

including stream velocity, depth, 

and substrate type associated 

with different mesohabitats 

were measured over a range 

of streamflows. Instantaneous 

discharge measurements were 

made at most sites in accordance 

with standard USGS discharge 

measurement methods (Rantz 

and others, 1982; Turnipseed and 

Sauer, 2010). At the Barelas site on 

November 10, 2011, and August 11, 

2012, and the Los Lunas II site on 

November 15, 2011, the daily mean 

discharge was obtained from the 

USGS National Water Information 

System (NWIS) for the nearest 

upstream USGS streamflow-gaging 

station (table 1). Instantaneous 

discharge measurements were 

stored in NWIS (U.S. Geological 

Survey, 2014). 

During summer 2012, stream 

velocity and depth were recorded at 

the centroid of each seine haul by 

the crew of technicians collecting 

fish, whereas stream velocity, 

depth, dominant substrate type and 

size, and percent embeddedness 

were recorded during winter 

2011–12 and summer 2012 by 

a second crew of technicians 

who were collecting mesohabitat 

data along randomly selected 

transects within each sampled 

mesohabitat. Additional details 

on the mesohabitat data collection 

methods are provided in Braun 

and others (2015). Velocity and 

depth measurements were made 

by wading the stream with a 

FlowTracker hand-held acoustic 

Doppler velocimeter attached to 

a wading rod (SonTek, 2013). 

Standard USGS protocols 

for measuring velocity were 

followed (Rantz and others, 1982; 

Turnipseed and Sauer, 2010). 

Additional details on the velocity 

measurements are provided in 

Braun and others (2015).

Fish Assemblage Composition

Fish Assemblage Composition 

and Mapped Mesohabitat 

Features

By evaluating fish assemblage 

composition (that is, the number of 

individuals of each species collected either 

at a given sampling site or reach containing 

one or more sampling sites) over a range of 

streamflows during different times of the 

year, insights can be gained into the types 

of mesohabitats used by different species, 

including the Rio Grande silvery minnow, 

and how differences in the number of 

mapped mesohabitats and number of types 

of mesohabitats (depending on the amount 

of streamflow) correspond to changes in fish 

assemblages. 

The average number of fish collected per site during the winter and summer 

sampling periods in each of the four reaches (Cochiti, Angostura, Isleta, and San 

Acacia) was determined by dividing the total number of fish collected per reach by the 

number of sites sampled per reach. The average number of fish collected decreased 

in the downstream direction during winter 2011–12, when the average number of 

fish collected was 1,394 in the Cochiti reach (based on a single sampling at the only 

site in the Cochiti reach, the Peña Blanca site), 154 in the Angostura reach, 97 in the 

Isleta reach, and 39 in the San Acacia reach (table 3). During summer 2012, the site 

in the Cochiti reach was not sampled, and only 3 of the 4 sites in the Angostura reach 

were sampled (the Bernalillo site was not sampled). In the three reaches sampled 

during summer 2012, substantially more fish were collected on average in each reach 

compared to winter 2011–12, with summer averages of 593 fish in the Angostura reach, 

946 fish in the Isleta reach, and 697 fish in the San Acacia reach. 

 In the three reaches sampled in both the winter and summer, the average number 

of species collected per sampling site was higher in summer 2012 compared to winter 

2011–12. The average number of species collected per sampling site within each reach 

generally decreased between the upstream and downstream reaches in both winter 

2011–12 (6.5, 4.4, and 2.2, respectively, in the Angostura, Isleta, and San Acacia 

reaches) and summer 2012 (8.0, 8.0, and 7.2, respectively, in the Angostura, Isleta, and 

San Acacia reaches). The Angostura reach likely maintains greater fish diversity in part 

because it maintains a more consistent discharge relative to the reaches downstream and 

does not go dry from year to year.

The relative abundance of Rio Grande silvery minnows, calculated as the number 

of Rio Grande silvery minnows collected at a sampling site during a sampling period 

(winter 2011–12 or summer 2012) divided by the total number of Rio Grande silvery 

minnows collected at all sampling sites during the same sampling period, was highest in 

the San Acacia reach during 

both winter 2011–12 (about 

62 percent) and summer 

2012 (about 54 percent). 

The relative abundance of 

Rio Grande silvery minnows 

was higher in the Angostura 

reach (about 26 percent) 

in winter 2011–12 than in 

the Isleta reach (about 12 

percent), but the reverse 

was true in summer 2012, 

when the relative abundance 

was about 41 percent in 

the Isleta reach and about 

5 percent in the Angostura 

reach. No Rio Grande silvery 

minnows were collected at 

the Peña Blanca site in the 

Cochiti reach during the one 

time it was sampled (winter 

2011–12). 

The catch per unit 

effort of Rio Grande silvery 

minnows (RCPUE) was 

calculated by dividing the 

number of Rio Grande 

silvery minnows collected 

at a sampling site during 

a sampling period (winter 

2011–12 or summer 2012) 

by the sum of the total area 

seined (in square meters 

[m2]); the resulting quotient 

was multiplied by 100 m2 to 

obtain the RCPUE. The use 

of RCPUE to standardize 

fish data allows for direct 

comparisons between stream 

reaches or mesohabitats of 

different sizes (Nielsen and 

Johnson, 1983). The RCPUE

was highest on average per 

sampling site in the San 

Acacia reach during both 

winter 2011–12 (2.91) and 

summer 2012 (0.20). Like 

the relative abundance, the 

average RCPUE per site 

was higher in the Angostura 

reach (1.33) in winter 

2011–12 compared to the 

Isleta reach (0.47), but the 

reverse was true in summer 

2012, when the RCPUE was 

0.14 in the Isleta reach and 

0.03 in the Angostura reach. The RCPUE was substantially higher in winter 2011–12 

relative to summer 2012 because not only were there far more Rio Grande silvery 

minnows caught in winter 2011–12 (163) than in summer 2012 (22), but the seined area 

tended to be higher in summer 2012 because of a change in methodology between the 

two sampling events (as many as 20 mesohabitats were selected for seining in winter 

2011–12 as compared to 30 mesohabitats in summer 2012). The RCPUE in the Cochiti 

reach was 0 percent in winter 2011–12 because no Rio Grande silvery minnows were 

collected at the Peña Blanca site.

Among all sampling sites, the highest fish-species richness for the winter sampling 

period was measured at the Abeytas site (9 species); the highest fish-species richness 

for the summer sampling period was measured at the Los Lunas I site (10 species). 

The lowest fish-species richness for the winter sampling period was measured at 

the Los Lunas II and Bosque del Apache II sites (one species each); the lowest fishspecies richness for the summer sampling period was measured at the Rio Salado site 

(five species) (table 3). In all cases, the number of species collected at each sampling 

site in winter 2011–12 was less than (or equal to, in the case of the Los Padillas and 

Abeytas sites) the number of species collected at the same sampling site in summer 

2012. In all cases, the total number of fish collected at each sampling site in winter 

2011–12 was less than the number of fish collected 

at the same sampling site in summer 2012. In winter 

2011–12, the most fish were collected at Peña Blanca 

(1,394), and the least were collected at Los Lunas 

II (1); whereas in summer 2012, the most fish were 

collected at Lemitar (1,729), and the least were 

collected at San Pedro (269). It stands to reason 

that there would be greater species richness and 

a larger number of fish collected in summer 2012 

relative to winter 2011–12 because lower flows (and 

subsequently shallower mesohabitats) in summer 

2012 increased the likelihood of seining success. 

Not only is seining easier at shallow depths (because 

of the potential for increased speed and mobility 

from the crew of technicians collecting fish), but the 

overall fish density for each sampling site is also 

higher in the summer (assuming the number of fish 

remains relatively consistent) because the volume 

of water in which the fish are confined is smaller. 

However, it should be noted that the fishing effort 

was commensurate with the number of mesohabitats 

sampled for fish. In most cases, the number of 

mesohabitats sampled for fish increased from about 

20 in winter 2011–12 to about 30 in summer 2012. 

Fewer than 20 mesohabitats were mapped in winter 

2011–12 at Bernalillo (17), La Joya (18), and Lemitar 

(16) (fig. 7), so the number of mesohabitats where 

fish were collected was less than 20 at these three 

sites. 

To account 

for differences 

in sampling 

effort between 

winter 2011–12 

and summer 

2012 associated 

with differences 

in the number 

of mesohabitats 

seined, relative 

abundances 

of Rio Grande 

silvery minnows 

were calculated 

for each of the 

sampling sites 

during both 

winter 2011–12 

and summer 

2012 (table 3). 

The highest 

relative abundance of Rio Grande silvery minnows during winter 2011–12 occurred at 

Arroyo del Tajo (46.0 percent) followed by La Orilla (12.9 percent). Conversely, no 

Rio Grande silvery minnows were collected at 3 of the 15 sites sampled (Peña Blanca, 

Los Lunas II, and Abeytas) during winter 2011–12. The highest relative abundance of 

Rio Grande silvery minnows during summer 2012 occurred at Lemitar (45.5 percent) 

followed in succession by Los Lunas I (22.7 percent) and Los Lunas II (18.2 percent). 

Conversely, no Rio Grande silvery minnows were collected at 7 of the 13 sites sampled 

(La Orilla, Los Padillas, Abeytas, La Joya, Rio Salado, Bosque del Apache I, and 

Bosque del Apache II) during summer 2012. 

At the mesohabitat scale, Rio Grande silvery minnows were collected in 6 of the 

8 mesohabitat types mapped in this study (table 4). Rio Grande silvery minnows were 

collected most often in runs (101 individuals from 35 mesohabitats), followed by flats 

(32 individuals from 9 mesohabitats) and pools (28 individuals from 9 mesohabitats). 

The RCPUE by mesohabitat type was highest in pool mesohabitat types (1.44), 

followed by riffles (1.06) and runs (0.77).

Table 4. Rio Grande silvery minnow collection information based on mesohabitat type in the Middle Rio Grande, 

New Mexico, 2011–12.

[RGSM, Rio Grande silvery minnows; m2, square meters; RCPUE, catch per unit effort; —, not applicable because no RGSM were 

collected in these mesohabitat types]

Mesohabitat 

type

Number of

mesohabitats 

where RGSM 

were collected

Number of RGSM

collected in each

mesohabitat type

Number of seine 

hauls made in each

mesohabitat type

Total area 

seined (m2) RCPUE1

riffle 6 13 47 1,227 1.06

run 35 101 458 13,161 0.77

pool 9 28 97 1,941 1.44

isolated pool 2 5 52 930 0.54

forewater 0 0 10 324 —

backwater 1 6 66 1,521 0.39

embayment 0 0 21 654 —

flat 9 32 237 6,185 0.52

1

Calculated as the number of RGSMs collected within a given mesohabitat type divided by the total area (in square meters) seined 

within that mesohabitat type × 100. 

Mapped Mesohabitat Features

The total number and number of types of mesohabitats were generally 

larger at sampling sites during summer 2012, when streamflows were low, 

compared to winter 2011–12, when streamflows were moderate. During 

summer, streamflow also tended to decrease in the downstream direction in 

the study area. Decreases in streamflow in the summer compared to the winter 

typically led to increases in channel complexity in terms of the number 

of different wetted mesohabitat types present (fig. 7A), total number of 

mesohabitats present (fig. 7B), and the number of channel bars mapped (fig. 

7C). Decreases in streamflow also led to reductions in wetted area at all of the 

sampling sites that were mapped in both winter 2011–12 and summer 2012 

(fig. 7D). Summary statistics associated with winter 2011–12 are based on 

maps generated in November and December 2011 as well as February 2012. 

For sampling sites that were mapped more than once during winter 2011–12 

(San Pedro and Bosque del Apache II), the data associated with sampling in 

February 2012 was used in the calculation of summary statistics because the 

data were accompanied by the collection of physical habitat and fish data, 

whereas no such data were collected in association for San Pedro and Bosque 

del Apache II from December 2011 because of inclement weather. 

Decreases in streamflow between winter 2011–12 and summer 2012 

also led to decreased wetted areas of mesohabitats that were mapped at each 

sampling site. Sampling sites in the lower part of the Angostura reach and 

the upper part of the Isleta reach that pass through or near the city limits 

of Albuquerque, N. Mex., remain perennially wet throughout the year. Six 

sampling sites within these reaches (La Orilla, Barelas, Los Padillas, Los 

Lunas I, Los Lunas II, and Abeytas) had the largest wetted area for the winter 

2011–12 period, and 5 of these 6 sites had the largest wetted area for the 

summer 2012 period (fig. 7D). The wide channel conditions and sustained 

flow at the Barelas site produced the largest wetted areas (113,199 m2 during 

winter 2011–12 and 103,094 m2 during summer 2012) of all sampling 

sites. The greatest difference between wetted areas at a single sampling site 

between winter 2011–12 and summer 2012 was measured at the Abeytas site, 

where a difference in wetted area of 60,314 m2 was measured. The smallest 

wetted area in winter 2011–12 was measured at the Bernalillo site (37,144 

m2), whereas the smallest wetted area in summer 2012 was measured at the 

Lemitar site (13,547m2).

Table 2. Description of mesohabitat types used to describe the study sites as defined by observations and 

physical parameters measured over the course of the study.

[Mesohabitat types and descriptions are modified from Platania (1993)]

Mesohabitat type Description

Riffle Relatively shallow and low to moderate velocity feature characterized by moderately 

turbulent water

Run Relatively high velocity feature with laminar flow and a non-turbulent surface

Pool Feature with little or no velocity that may be deep in places

 Channel Type of pool where current moves in the same flow direction as the channel

 Eddy Type of pool where current moves in the opposite direction relative to flow

Isolated Pool Type of pool that is separate from the main channel; frequently a portion of a former 

backwater or forewater that has become disconnected from a secondary channel

Forewater Slackwater feature oriented into the principal direction of flow

Backwater Slackwater feature oriented in an opposing direction to the principal flow direction

Embayment Slackwater feature located adjacent to the channel and oriented perpendicular to flow

Flat Very shallow, low velocity feature typically located on the periphery of an existing point or 

channel bar; caused by a slight rise in stage

Point Bar Crescent-shaped depositional feature located on the inside of a stream bend; typically either 

devoid of or containing annual vegetation

Channel Bar Transitory parcel of land surrounded by water; typically either devoid of or containing 

annual vegetation

Table 3. Relative abundance of Rio Grande silvery minnows collected during sampling events in winter 2011-12 and summer 2012 on

the Middle Rio Grande, New Mexico.

[MRGBI, Middle Rio Grande Bosque Initiative; RGSM, Rio Grande silvery minnow; CPUE, catch per unit effort; m2, square meters; —, no data were collected 

during this time period] MRGBI Reach Name

Short Name

Winter 2011–12 Summer 2012

Relative

abundance

of 

RGSM1,

in percent

CPUE 

for 

RGSM2

Fish 

species 

richness3

Number of 

RGSM 

collected

Total 

number 

of fish 

collected

Total

area

seined

(m2)

Relative

abundance

of 

RGSM1,

in percent

CPUE 

for 

RGSM2

Fish 

species 

richness3

Number of 

RGSM 

collected

Total 

number 

of fish 

collected

Total

area

seined

(m2)

Cochiti Peña 

Blanca 0 0 4 0 1,394 661 — — — — — —

Aggostura

Bernalillo 1.23 0.38 8 2 450 531 — — — — — —

La Orilla 12.9 2.82 6 21 107 744 0 0 8 0 479 1,089

Barelas 7.98 1.03 5 13 23 1,259 4.55 0.08 9 1 530 1,254

Los Padillas 4.29 1.10 7 7 34 634 0 0 7 0 770 1,185

 Isleta

Los Lunas I 2.45 0.58 3 4 29 693 22.7 0.35 10 5 1,490 1,442

Los Lunas 

II 0 0 1 0 1 651 18.2 0.35 9 4 817 1,155

Abeytas 0 0 9 0 165 717 0 0 9 0 1,216 1,176

La Joya 0.61 0.18 5 1 218 564 0 0 7 0 791 924

Rio Salado 8.59 1.58 4 14 74 885 0 0 5 0 417 780

 San Acacia

Lemitar 7.98 2.46 3 13 57 529 45.5 0.88 8 10 1,729 1,142

Arroyo del 

Tajo 46.0 10.3 3 75 125 729 4.55 0.07 8 1 290 1,416

San Pedro 3.07 0.68 2 5 6 738 4.55 0.08 7 1 269 1,314

Bosque del 

Apache I 1.23 0.27 2 2 3 735 0 0 6 0 528 1,002

Bosque del 

Apache II 3.68 0.82 1 6 6 735 0 0 7 0 670 1,260

1

Calculated as the number of RGSMs collected at a site during a sampling period divided by total number of RGSMs collected at all sites during the same sampling period multiplied by 

100. Percentages may not sum to 100 because of rounding differences.

2

Calculated as the number of RGSMs collected at a site during a sampling period divided by the total area (in square meters) seined multiplied by 100. 

3

Total number of species collected.

Fish Assemblage Composition and Mapped Mesohabitat Features Over a Range of Streamflows

in the Middle Rio Grande, New Mexico, Winter 2011–12, Summer 2012

By

Daniel K. Pearson, Christopher L. Braun, and J. Bruce Moring

2015 Printed on recycled paper

ISBN 978-1-4113-4010-7

9 7 8141 1 3401 0 7

ISSN 2329-1311 (print)

ISSN 2329-132X (online)

http://dx.doi.org/10.3133/sim3350

Any use of trade, product, or firm names in this publication is for descriptive purposes only and 

does not imply endorsement by the U.S. Government

For sale by U.S. Geological Survey, Information Services, Box 25286, Federal Center, 

Denver, CO 80225, 1–888–ASK–USGS

Digital files available at http://dx.doi.org/10.3133/sim3350

Suggested citation: Pearson, D.K., Braun, C.L., and Moring, J.B., 2015, Fish assemblage 

composition and mapped mesohabitat features over a range of streamflows in the Middle 

Rio Grande, New Mexico, winter 2011–12, summer 2012: U.S. Geological Survey Scientific 

Investigations Map 3350, 7 sheets, http://dx.doi.org/10.3133/sim3350.

Mesohabitat Assessments Sampling Assessments and 

Streamflow 

During this study, 13 of the 15 sites were 

assessed under two different seasonal streamflow 

regimes during winter 2011–12 and summer 2012 

(table 1, fig. 4); the two remaining sites (Peña 

Blanca and Bernalillo) were only assessed in 

winter 2011–12. Mesohabitats were mapped and 

sampled during a period of moderate streamflow 

between November 2011 and February 2012 and 

during a period of low streamflow between June 

and August 2012 (table 1; fig. 4). In winter 2011–

12, sites were sampled generally from upstream 

to downstream, whereas in summer 2012, sites 

were sampled in an order that would ensure the 

Middle Rio Grande was flowing at all sites at 

the time of sampling. The reordered sampling 

during low streamflow conditions facilitated the 

assessment of as many sites as possible, as well 

as the measurement of physical properties and 

sampling of fish. Those sites that were at the 

greatest risk of drying were visited in early June 

2012, and those sites that were expected to have 

streamflow throughout the summer were visited 

in August 2012. The period of comparatively 

low streamflows in the summer of 2012 was an 

opportunity to determine available habitat during 

a time of the year when water temperatures in the 

Middle Rio Grande are seasonally high and the 

stream channel is more accessible for sampling, 

thus providing more ideal conditions for the 

evaluation of habitat use by and distribution of 

fishes at low flow.

The approach used to assess mesohabitats in the 

Middle Rio Grande was modified from Parasiewicz 

and Dunbar (2001) (fig. 5). Mesohabitat assessments 

generally consist of (1) geospatial measurements to 

document the sampling site, (2) physical measurements 

of the stream properties, and (3) biological sampling at 

the site. Geospatial measurements (data 

associated with a particular location) 

are made as a first step to generate maps 

over a range of streamflows (that is, how 

the various mesohabitat types change 

under different streamflow conditions) 

(Bovee and others, 1998, 2008). 

Geospatial and physical measurements 

provide a description of the ecohydraulic habitat conditions for the 

streamflow at the time the measurements 

are made. Physical measurements and 

biological measurements are used to 

determine habitat use by selected fish 

species.

For this study, the following 

mesohabitats were mapped at each study 

site when present: riffles, runs, pools 

(channel and eddy), isolated pools, 

forewaters, backwaters, embayments, 

and flats (table 2, fig. 6). Point bars 

and channel bars were also mapped to 

provide a more complete assessment of 

the active channel at each site. Data from 

two types of pools—channel and eddy—

were combined into a “pools” category 

for analysis. 

Digital mapping techniques were 

used for all geospatial measurements. 

The hardware, software, and field 

methods that were used to accomplish 

the study mapping goals were selected 

specifically to overcome the challenges 

of working in a remote, arid riverine 

environment. A geographic information 

system (GIS) (Esri, 2013) and Global 

Positioning System (GPS) were used to 

create the map in the field. Location data 

were collected by using a Trimble DSM 

232 modular receiving unit (Trimble, 

2015a) with an OmniSTAR subscription 

(Trimble, 2015b) for real-time, subfoot 

accuracy observations needed for 

mapping. The GPS observations were 

directly read into a field laptop computer 

for onsite visualization within the GIS, 

and polygons were created by using 

location information, aerial photography, 

and editing tools.

Field mapping was accomplished by using a variety 

of approaches based on streamflow, stream depth, and 

streambank accessibility. Each study reach was visited 

twice (except for Peña Blanca and Bernalillo, which were 

only sampled in winter 2011–12) (table 1), corresponding 

to the periods of moderate and low streamflows identified 

for this study. For the majority of the field mapping, the 

edge of the water throughout a site reach was extracted 

from high-resolution, remotely sensed imagery, which 

was used as a framework for all subsequently mapped 

mesohabitats within a given reach at a site. The field data 

collection process required two individuals working in 

tandem, communicating by 

using a wireless connection 

between the GPS receiver and 

laptop computer. After the edge 

of water was delineated, the 

study reach was subdivided 

into smaller polygons, each 

representing individual 

mesohabitats. Individual 

mesohabitats were created 

by walking boundaries of 

each mesohabitat or through 

photointerpretation in the field. 

Polygons created through 

this process were stored and 

attributed in an ArcGIS 10.0 

personal geodatabase (Esri, 

2013) and stored as Microsoft 

Access (1997–2003) files. 

Collectively, the database 

information and remotely sensed 

imagery made it possible to 

generate a detailed map for each 

study site at each targeted flow. 

Mesohabitat

assessment

Run

Point bar

Channel bar

Channel bar

Example river system

Physical measurement Biological sampling

Geospatial measurement

Mapping

Figure 5. Overview of the approach used to map mesohabitats in the Middle Rio Grande, New Mexico 

(modified from Parasiewicz and Dunbar, 2001). 

Riffle

Backwater

Isolated pool

Forewater

Eddy pool

Channel pool

Run

Embayment

Point bar

Channel

bar

Flat

Run

Run

Run

Riffle

Flat

Run

Margin

Pool

Secondary channel trace

Plan view Profile review

Figure 6. Mapped mesohabitat types identified in the Middle Rio Grande, New Mexico (modified 

from Platania, 1993).