Spatial perspective for delta smelt: A summary of contemporary survey data

Abstract

We utilized recently available data from the 20-mm Tow-Net and Spring Kodiak Trawl, together with other Interagency Ecological Program and regional monitoring programs, to provide a comprehensive description of the range and temporal and geographic distribution of delta smelt (Hypomesus transpacificus) by life stage within the San Francisco Estuary, California. Within 21 sampled regions we identified 289,401 survey events at 624 monitoring stations. Delta smelt were observed at 430 stations (69%) in an area from northern San Francisco Bay in the west, to the confluence of the Sacramento and Feather rivers in the north, and to the disjunction of Old and San Joaquin rivers in the south, an area of approximately 51,800 ha. Delta smelt were observed more frequently and at higher densities (at all life stages) near the center of their range, from Suisun Marsh down through Grizzly Bay and east Suisun Bay through the Confluence to the Lower Sacramento region, and into the Cache Slough region. Delta smelt larvae were observed in the San Francisco Estuary from March through July, sub-juveniles in April through August, juveniles in May through December, sub-adults in September through December, and pre-spawning and spawning adults in January through May. This comprehensive review provides managers and scientists an improved depiction of the spatial and temporal extent of the delta smelt throughout its range and lends itself to future analysis of delta smelt population assessment and restoration planning.

Full text

CALIFORNIA FISH AND GAME Vol. 97, No. 4
164
Spatial perspective for delta smelt: a summary of contemporary
survey data
Joseph e. Merz*, scott haMilton, paul s. BergMan, and Bradley cavallo
Cramer Fish Sciences, 13300 New Airport Road, Auburn, CA 95602, USA (JM, PB, BC)
Center for California Water Resources Policy and Management, 1017 L Street #474,
Sacramento, CA 95814, USA (SH)
*Correspondent: jmerz@shsciences.net
We utilized recently available data from the 20-mm Tow-Net and Spring
Kodiak Trawl, together with other Interagency Ecological Program and
regional monitoring programs, to provide a comprehensive description
of the range and temporal and geographic distribution of delta smelt
(Hypomesus transpacicus) by life stage within the San Francisco Estuary,
California. Within 21 sampled regions we identied 289,401 survey
events at 624 monitoring stations. Delta smelt were observed at 430
stations (69%) in an area from northern San Francisco Bay in the west,
to the conuence of the Sacramento and Feather rivers in the north, and
to the disjunction of Old and San Joaquin rivers in the south, an area of
approximately 51,800 ha. Delta smelt were observed more frequently and
at higher densities (at all life stages) near the center of their range, from
Suisun Marsh down through Grizzly Bay and east Suisun Bay through
the Conuence to the Lower Sacramento region, and into the Cache
Slough region. Delta smelt larvae were observed in the San Francisco
Estuary from March through July, sub-juveniles in April through August,
juveniles in May through December, sub-adults in September through
December, and pre-spawning and spawning adults in January through
May. This comprehensive review provides managers and scientists an
improved depiction of the spatial and temporal extent of the delta smelt
throughout its range and lends itself to future analysis of delta smelt
population assessment and restoration planning.
Key words: Delta smelt, distribution, Hypomesus transpacicus, spatial
analysis, life stage, observed presence, Sacramento River delta, San
Francisco estuary, San Joaquin River delta
California Fish and Game 97(4):164-189; 2011

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The delta smelt (Hypomesus transpacicus) is a small, euryhaline sh endemic to the
San Francisco Estuary of California (Estuary). Once the most abundant sh captured in trawl
surveys conducted in the Sacramento-San Joaquin Delta (Stevens and Miller 1983, Moyle and
Herbold 1989, Stevens et al. 1990) the species suffered a reduction in numbers sufcient to
justify threatened listing in 1993 under both the federal and California Endangered Species
Acts (ESA). Similar to other Estuary sh species, delta smelt experienced a further decline
beginning in 2000 (Sommer et al. 2007) and was listed as endangered under the California
ESA in 2009. As a result, the delta smelt has received considerable attention as one of four
pelagic sh species experiencing declines in abundance (see Armor et al. 2005, Baxter et
al. 2008, Feyrer et al. 2010, Mac Nally et al. 2010, Thompson et al 2010).
Despite the critical condition of the delta smelt population, a geographical summary
of its distribution by life stage has not been clearly dened. Conservation planning under
federal and state statutes requires spatial resolution (Tracy et al. 2004, Carroll et al. 2006).
Distributional summaries of delta smelt were provided in the formal notice conferring its
federal protection (USFWS 1993), subsequent designation of critical habitat (USFWS 1994),
and completion of conservation planning documents (see USFWS 1996, 2003; California
Resources Agency 2005, 2007). However, these sources lack a spatial depiction of where
and when delta smelt have been observed. In a California Department of Fish and Game
(CDFG) status review (Sweetnam and Stevens 1993), the historical range for the species
was described using life history descriptions from existing literature. The United States
Fish and Wildlife Service (USFWS 1996) has also provided delta smelt distribution maps
using data from the Fall Midwater Trawl, and the CDFG has created interactive maps using
individual surveys for some of its monitoring programs (see http://www.dfg.ca.gov/delta).
However, to our knowledge, no effort has been made to map the range of delta smelt using
all available sampling data or to summarize distribution of delta smelt by life stage.
The distribution of at-risk species is important information for conservation planning.
Nearly all ecological data necessary to develop effective resource management agendas
have attributes that can be portrayed spatially. Distributional data in the forms of species
range maps, breeding surveys, and biodiversity atlases have become tools used commonly
in analyses of species-environment relationships (Brundage and Meadows 1982, Flather
et al. 1997, Ferrier 2002, Ceballos and Ehrlich 2006, Hulbert and Jetz 2007, Cabeza et al.
2010) and for conservation and management plans for endangered or threatened species,
environmental risk assessment, and for calculating responses of at-risk species under future
management scenarios (Dormann et al. 2007). Conservation and monitoring programs
designed to assess the effectiveness of those actions frequently are site-specic, and are
more likely to be successful when spatial elements of planning are well understood (Tracy
et al. 2004, Carroll et al. 2006).
Delta smelt are vulnerable to many environmental stressors (USFWS 1993, Moyle
2002, Baxter et al. 2008, Healey et al. 2008), and the signicance of a particular stressor
may change in relation to its manifestation or proximity to the species (Tong 2001, Armor
et al. 2005). Furthermore, delta smelt are migratory (Bennett et al. 2002, Dege and Brown
2004, Hobbs et al. 2007, Sommer et al. 2011), and habitat requirements differ by life stage.
An understanding of where delta smelt are distributed throughout their range at each life
stage may provide insight about habitat attributes important for each life stage and, therefore,
help inform strategies as managers undertake habitat restoration actions.

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The purpose of this paper is to present a geographic summary of publicly available
data on the distribution of delta smelt by life stage. With initiation of the 20-mm Tow-Net
in 1995 and the inception of the Spring Kodiak Trawl in 2002, the CDFG and other agencies
that comprise the Interagency Ecological Program (IEP) provide data on the distribution of
delta smelt at various life stages. Using data from these surveys and a variety of publicly
available sources, we rened knowledge of the spatial extent and distribution of delta smelt
in the Estuary. Specically, we reviewed all available data on observed presence and density
of delta smelt from a spatial perspective in an effort to document (1) the observed geographic
extent of delta smelt, and (2) the spatial and temporal distributions for identied life stages.
MethodS
Study area.—The Estuary is the largest of its kind along the U.S. Pacic Coast
(approximately 1,235 km2, Roseneld and Baxter 2007; Figure 1). Formed by the conuence
of the Sacramento and San Joaquin watersheds with San Francisco Bay, the Estuary drains
an area of approximately 163,000 km2 (40% of California’s surface area; van Geen and
Luoma 1999, Sommer et al. 2007) that stretches from the upstream limits of the Sacramento
River in the north to the mountain tributary streams of the San Joaquin River in the south
(Moyle 2002, Sommer et al. 2007). The Estuary is brackish and tidally inuenced through
its connection to San Francisco Bay, and is an example of an inverted river delta (whereby
the narrow end of the delta emerges on the seafront and the wide end is located further
inland), one of only a few existing worldwide. The water bodies east of the Sacramento
River conuence with the San Joaquin River are commonly referred to as the Sacramento-
San Joaquin Delta (Delta). The Delta is the upstream portion of the Estuary where riverine
freshwater tidally washes back and forth within leveed channels, roughly between the cities
of Sacramento, Stockton, Tracy, and Antioch. The Delta extends about 37 km east to west
and 77 km north to south and includes parts of Sacramento, San Joaquin, Contra Costa,
Solano, and Yolo counties (Moyle 2002, Lund et al. 2007).
To facilitate the spatial depiction of delta smelt, we grouped monitoring locations
into Estuary regions (Table 1; Figure 1) based on preliminary work by Kimmerer (2009) and
physical landmarks (e.g., bays, sloughs) (Figure 1). To distinguish areas with large-scale
habitat differences (e.g., watershed drainages, conuences), we subdivided (1) the upper
Sacramento River into two regions, differentiating the Ship Channel, Yolo Bypass, and
Cache Slough from the rest of the upper Sacramento River; (2) San Pablo Bay into western
and eastern regions; and, (3) the South Delta into the South Delta and upper San Joaquin
River. We also added a Sacramento Valley region (covering upstream from the conuence
of the Sacramento and American rivers), two Napa River regions (split between the lower
and upper), and a San Francisco Bay region.
IEP monitoring programs.—The CDFG and USFWS, as members of the IEP, have
surveyed sh at a number of stations throughout the Estuary for several decades (Table 2,
Figure 1). These monitoring programs include the 20-mm Tow-Net (20-mm), Summer
Tow-Net (STN), Fall Midwater Trawl (FMWT), Bay Study Midwater Trawl (BMWT),
Spring Kodiak Trawl (Kodiak), and Beach Seine (herein collectively referred to as the IEP
monitoring programs). Each IEP monitoring program is conducted during a different season
and sampling frequency (monthly or bi-weekly), and at a varying number of stations (30-
113; Table 2). By employing different gears during different time periods, each monitoring

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FIgure 1.—Monitoring stations of Interagency Ecological Program surveys conducted in the San Francisco
Estuary by the California Department of Fish and Game (Summer Tow-Net, Fall Mid-Water Trawl, Bay Mid-
Water Trawl, Spring Kodiak Trawl, and 20-mm Tow Net) and the United States Fish and Wildlife Service (Beach
Seine). Dashed lines indicate regional boundaries. The white area represents the legal Delta as set forth in the
Delta Protection Act of 1959.

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taBLe 1.—San Francisco Estuary sampling regions and associated stations by sample method. IEP monitoring
programs are described in Table 2 and regional monitoring programs are described in Table 3. NS = not sampled
and NI = no regional sampling identied.
taBLe 2.—Interagency Ecological Program monitoring programs that sample delta smelt: years and months
surveyed, number of survey stations, and size of delta smelt captured for each monitoring program.

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Fall 2011 DELTA SMELT SURVEY DATA
program is selective for different sizes of delta smelt, and therefore different life stages
(Table 2). The methods for the IEP monitoring programs have been described previously
(Moyle et al. 1992, USFWS 2003, Bennett 2005), as have the merits of several resulting
abundance indices (Bennett 2005).
Regional monitoring programs.—In addition to the IEP monitoring programs,
numerous other monitoring programs are carried out by various governmental and non-
governmental entities, and for a variety of purposes (Table 3). These programs utilize an
assortment of gears including seining, electroshing, and tow-nets. Some of these programs
have been carried out for a decade or more. Collectively, they are referred to as regional
monitoring programs throughout the remainder of this paper.
taBLe 3.—Regional monitoring programs sampling delta smelt: survey location, survey gear, project, study pe-
riod, and data source.

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Observed geographic extent.—To identify the geographic extent of delta smelt, we
utilized records taken from IEP and regional monitoring programs. We present all years of
available data for each monitoring program (Tables 2 and 3). If delta smelt were detected
at least once at any given monitoring location, they were designated as present at that site;
otherwise they were designated as not observed. Because the detection probability for each
type of survey gear is not available and each monitoring program is conducted at different
sampling frequencies and levels of effort, we did not consider delta smelt to be absent from
locations where the species was not observed (Pearce and Boyce 2006). Since our objective
was to identify the range of delta smelt presence, and not to examine where delta smelt are
absent, we did not further assess the likelihood of falsely identifying delta smelt as being
absent at a given location.
We developed a boundary for the observed geographic extent of delta smelt by
using a 1-km buffer around sites where delta smelt were observed, including all open water
between points within the boundary (Graham and Hijmans 2006 for discussion of buffer
size). We then calculated the surface area of all waters within the boundary.
We also examined the geographic distribution of sampling stations and sampling effort
among the IEP and regional monitoring programs. We enumerated how many stations were
sampled by each of the IEP monitoring programs and all the regional monitoring programs
combined within each of the 21 identied regions, and calculated the percentage of regions
sampled by each monitoring program.
Distribution by life stage.—Extending from the life history discussions of Moyle
(2002) and Bennett (2005), we differentiated ve separate delta smelt life stages: larvae,
taBLe 4.—Delineation of delta smelt life stages by the Interagency Ecological Program, sh size or reproduc-
tive stage, time periods, and years of available samples. 20-mm = 20-mm Tow-Net, STN = Summer Tow-Net,

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Fall 2011 DELTA SMELT SURVEY DATA
sub-juveniles, juveniles, sub-adults, and mature adults (Table 4). We chose a 15-mm total
length as the cut-off between larvae and sub-juveniles because when delta smelt reach 16-18
mm their ns are more developed and their swim bladder is lled with gas, making them more
mobile within the water column (Moyle 2002). We used 30 mm as the cut-off between sub-
juveniles and juveniles because this size is associated with a change in feeding regime (Moyle
2002). We chose 55 mm as the cut-off between juveniles and sub-adult and mature adults
because growth slows between 55 and 70 mm (with most of the available energy diverted
to gonadal development [Radtke 1966, Erkkila et al. 1950]). Because maturation rate of
captured delta smelt was reported for the Spring Kodiak Trawl, we used reproductive stage
to further subdivide mature adults into pre-spawners and spawners. Reproductive stages 1
to 3 for females, and 1 to 4 for males, were classied as pre-spawning. Reproductive stages
4 in females, and 5 in males, were classied as spawning (J. Adib-Samii, CDFG, personal
communication; additional information is available at: http://www.dfg.ca.gov/delta/data/
skt/eggstages.asp).
We used data from the IEP monitoring programs to elicit information on the temporal and
spatial distribution of life stages. For each life stage, we delineated a period of several months
when delta smelt of that life stage often were observed. We excluded months when delta
smelt were caught in very low numbers (<3% of the total for that life stage) because those
data would have biased frequency of observation and observed density results downward.
Where possible, we used data from multiple monitoring programs that sampled the same
life stage at different months during the year (Table 4).
Although data are available for juveniles and adults back to 1967 (FMWT), we
present only results from 1995 onward to compare life stage distributions during similar
time periods; 20-mm Tow-Net surveys were rst conducted in 1995, and provided data
for larvae, sub-juveniles, and juveniles. Data from two monitoring programs were not
available for the full period from 1995 to 2009: the Kodiak (2002-2009), and the BMWT
(1995-2006), which after 2006 was adjusted to avoid high levels of delta smelt take (R.
Baxter, CDFG, personal communication). We excluded supplemental samplings because
such surveys were conducted for special purposes and were not always consistent with the
protocol for the program (R. Baxter, CDFG, personal communication). To avoid introducing
anomalies caused by the addition of new stations, we included only sampling stations that
were sampled consistently (i.e., stations that were sampled ≥ 90% of the years).
We calculated the average annual frequency of delta smelt observation at consistently
surveyed stations for each life stage in each region for all years as
Plrpy = (Slrpy / Nrpy) (100) (1)
where: Plrpy is the percent of sampling events (i.e., a sample at a station) when delta smelt
of life stage l were caught in region r during time period p and year y, Slrpy is the number of
sampling events in region r when delta smelt of life stage l were caught during time period
p and year y, and Nrpy is the total number of sampling events in region r during time period
p and year y. Next, the average annual frequency of delta smelt observation for each life
stage and region was calculated as a simple average over all years.
We calculated the yearly observed density (Density; i.e. relative measure of abundance)
of delta smelt for each life stage and region for all years by dividing the summed catches
C of delta smelt for each life stage l, region r, time period p, and year y by the volume of
water in cubic meters V that was sampled for each region and year, then multiplying by

CALIFORNIA FISH AND GAME Vol. 97, No. 4
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10,000 to determine the catch per 10,000 m3 of water for each life stage, region, and year as
Densitylry = (ΣClry /ΣVry) (10000) (2)
Next, the average annual observed density for each life stage and region was
calculated as a simple average over all years. To standardize these data, the average
observed density for each life stage and r egion was then divided by the highest average
annual observed density for that life stage and multiplied by 100.
While recognizing that the gear employed to sample Estuary shes varies in catch
efciency, and that catch efciency varies both between monitoring programs and within
samples of each monitoring program depending on a variety of factors including the size of
individual sh, we did not attempt to adjust the results reported here for catch efciency. As
a result, we did not attempt to draw conclusions regarding differences in densities between
monitoring programs, or between life stages within a given monitoring program.
Our treatment of catch data was limited to frequency of observation and average
observed density, rather than population estimates. The latter would have required
estimates of the volume of the body of water and reliance on the assumption that samples
are representative of the density of smelt in the targeted water body. The validity of such
an assumption may be questionable in a variety of circumstances, particularly when using
Beach Seine data since the demarcation between “beach habitat” and “open-water habitat”
is difcult to specify.
To describe the temporal extent of the presence of each life stage across all years,
we calculated the frequency of observation and observed density by month for each life
stage. In so doing, we built upon the conceptual and analytical work of Bennett (2005), who
provided a model of delta smelt life history that included the approximate months during
which each life stage exists. The percentage of delta smelt caught in any individual month
was calculated as the total number of smelt of that life stage caught in that month since
1995, divided by the total number of smelt of that life stage caught since 1995. Because
we did not attempt to compare catch between monitoring programs, we reported this result
separately for each monitoring program. We also reported the frequency with which each
life stage was observed in each month in each monitoring program.
reSuLtS
Within the 21 identied regions of the San Francisco Estuary, we identied 289,401
survey events (a sampling event at a given location and time) at 624 monitoring stations. Of
these, 444 (71%) were from IEP and 180 (29%) were from regional monitoring programs.
The program with the single greatest number of monitoring stations was FMWT (136),
followed by the Beach Seine (97), 20-mm (67), Kodiak (53), BMWT (52), and STN (39)
(Table 1). Delta smelt were observed at 347 of the 444 (78%) IEP monitoring stations and
at 83 of the 180 (46%) regional monitoring stations identied in this study.
Observed geographic extent.—Delta smelt were observed in all of the 21 regions
covering an area of about 51,800 ha (Figure 2). Observations occurred as far west as
Berkeley in San Francisco Bay, north on the Sacramento River to its conuence with the
Feather River, and the San Joaquin River south of Stockton. Tributary observations included
the Napa River, Cache Slough, the American River to the north, and the Mokelumne and

173
Fall 2011 DELTA SMELT SURVEY DATA
Calaveras rivers to the east. Delta smelt were also observed in seasonally-inundated habitat
of the Yolo Bypass and the Cosumnes River at its conuence with the Mokelumne River.
No single IEP monitoring program sampled all of the 21 regions (Table 1) that make
up the observed extent of range (Figures 3 to 5). The 20-mm and the FMWT had the highest
coverage (80% of regions each). The STN covered 71% of the regions, while coverage
among the other IEP surveys ranged from 57 to 76%.
Distribution by life stage.—Delta smelt larvae were observed in the Estuary from
March through July, sub-juveniles during April through August, juveniles during May
FIgure 2.—Observations of delta smelt at monitoring stations of Interagency Ecological Program and Regional
surveys. Circles indicate Interagency Ecological Program stations where delta smelt were observed (closed) or
not observed (open). Triangles indicate Regional survey stations where delta smelt were observed (closed) or
not observed (open). The outlined area represents the observed delta smelt range.

CALIFORNIA FISH AND GAME Vol. 97, No. 4
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FIgure 3.—Location of 20-mm Tow-Net survey stations in relation to the observed delta smelt range (outlined
area). Circles represent stations consistently surveyed across all years (1995-2009). Triangles represent stations
not consistently surveyed.

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Fall 2011 DELTA SMELT SURVEY DATA
FIgure 4.—Location of Summer Tow Net survey stations in relation to the observed delta smelt range (outlined
area). Circles represent stations consistently surveyed across all years (1995-2009). Triangles represent stations
not consistently surveyed.

CALIFORNIA FISH AND GAME Vol. 97, No. 4
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FIgure 5.—Location of Fall Mid-Water Trawl survey stations in relation to the observed delta smelt range (out-
lined area). Circles represent stations consistently surveyed across all years (1995-2009). Triangles represent
stations not consistently surveyed.

177
Fall 2011
through December, sub-adults during September through December, and pre-spawning
and spawning adults during January through May (Tables 5 and 6). For most life stages,
delta smelt were observed most frequently near the center of their range — from Suisun
Marsh down through Grizzly Bay and east Suisun Bay through the Conuence to the Lower
DELTA SMELT SURVEY DATA
taBLe 5.—Percent of years delta smelt were observed in each month in at least one location in the Estuary by life
stage and monitoring program (1995-2009). 20-mm = 20-mm Tow-Net, STN = Summer Tow-Net, FMWT = Fall
Midwater Trawl, BS = Beach Seine, BMWT = Bay Midwater Trawl, and SKT = Spring Kodiak Trawl.
taBLe 6.—Percent of total delta smelt catch occurring in each month by lifestage and monitoring program (1995-
2009). 20-mm = 20-mm Tow-Net, STN = Summer Tow-Net, FMWT = Fall Midwater Trawl, BS = Beach Seine,
BMWT = Bay Midwater Trawl, and SKT = Spring Kodiak Trawl.

CALIFORNIA FISH AND GAME Vol. 97, No. 4
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Sacramento River region, but also in the region of Cache Slough (Figure 6). Regions where
delta smelt were observed most frequently (regions in the upper quartile of each column in
Table 7) for any life stage were northeast Suisun Bay, Grizzly Bay, Suisun Marsh, Conuence,
Lower Sacramento River, Upper Sacramento River, Cache Slough and Ship Channel, and
FIgure 6.—Average annual frequency of delta smelt observation (percentage of sampling events where delta
smelt were observed) by life stage and Region for Interagency Ecological Program surveys. Regions where the
average frequency of detection for a given life stage was zero are indicated by no data column being present.
Regions that were not sampled for a given life stage are indicated by a data column suspended slightly below the
x-axis. Y-axis ticks indicate frequencies of 0, 25, 50, 75, and 100 percent.

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Fall 2011
taBLe 7.—Average annual frequency of delta smelt occurrence by life stage, IEP monitoring program, and region. 20-mm = 20-mm Tow-Net, STN = Summer Tow-Net,
FMWT = Fall Midwater Trawl, BS = Beach Seine, BMWT = Bay Midwater Trawl, and SKT = Spring Kodiak Trawl. NS indicates no survey conducted in the given life-
stage and region.
DELTA SMELT SURVEY DATA

CALIFORNIA FISH AND GAME Vol. 97, No. 4
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Lower San Joaquin River. Westward of Suisun Bay, the frequency of observation tended to
decrease as the distance from Suisun Bay increased. San Pablo Bay typically had the lowest
observed frequencies west of Suisun Bay. The East and South Delta regions generally had
low observed frequencies relative to other regions for the same life stage. The exception
was for larval delta smelt where these regions (with observed frequencies of 15% and 18%,
respectively) were close to the median observed frequency of 16%.
Delta smelt were observed at higher densities near the center of their range — the
same area where they were observed most frequently: from Suisun Marsh down through
Grizzly Bay and east Suisun Bay through the Conuence to the Lower Sacramento River
region, but also in the Cache Slough region (Figure 7). The regions where delta smelt were
FIgure 7.—Relative observed densities (average density for each life stage and region divided by highest
average annual density observed for that life stage multiplied by 100) of delta smelt by life stage and region
for Estuary-wide surveys. Regions where the relative observed density for a given life stage was zero are
indicated by no data column being present. Regions that were not sampled for a given life stage are indicated
by a data column suspended slightly below the x-axis. Y-axis ticks indicate 0, 25, 50, 75, and 100 percent of
highest observed density.

181
Fall 2011
observed in the greatest densities were the Conuence for larvae in the 20-mm; Lower
Sacramento River for sub-juveniles in both the 20-mm and STN; Grizzly Bay for juveniles
in the 20-mm and STN, but Lower Sacramento River for juveniles later in the year in the
FMWT; Lower Sacramento River for sub-adults in the FMWT; Upper Sacramento River for
mature adults in the Beach Seine; Grizzly Bay for mature adults in the BMWT; and Suisun
Marsh for both pre-spawning and spawning adults in the Kodiak (Table 8). Regions with
the highest average observed densities (regions in the upper quartile of each column in Table
8) for any life stage were northeast Suisun Bay, Grizzly Bay, Suisun Marsh, Conuence,
Lower Sacramento River, and Upper Sacramento River. Delta smelt observed densities
(for all but the earliest life stages) were low in the western Suisun Bay and regions further
to the west, and in the east and south Delta, relative to other areas.
dIScuSSIon
Observed geographic extent.—Extent of habitat is a critical piece of information for
assessing the conservation status of a species (e.g., Millsap et al. 1990, IUCN 1994, Lunney
et al. 1996, Burgman and Fox 2003). The historical range of delta smelt was provided by
Sweetnam and Stevens (1993) who described the species as existing as far upstream in the
Sacramento River as the Feather River mouth (citing Wang 1991) and Mossdale on the San
Joaquin River (citing Moyle et al. 1992), and downstream to western Suisun Bay.
We utilized recently available data from the 20-mm (since 1995) and Kodiak (since
2002), together with other IEP and regional monitoring programs (since 1995) to provide
information on areas of the Estuary where identied delta smelt life stages have been
observed. Though our study included additional portions of San Pablo Bay not detailed by
Sweetnam and Stevens (1993), we identied essentially the same distribution of delta smelt
on the Napa River, Cache Slough, Suisun Marsh tributaries, and San Joaquin River inferred
by the earlier study.
Observations at the most upstream sampling stations in the Napa River, Cache Slough,
and Sacramento and Calaveras rivers indicate that the extent of delta smelt distribution in
these locations remains unknown. Recently, Cache Slough and its tributaries have been
identied as key habitat for delta smelt across all life stages (DSC 2010). However, available
survey data suggest the full distributional range of delta smelt in the Cache Slough drainage
has not been identied by current sampling efforts. These observations suggest sampling
locations beyond those covered by current IEP monitoring could yield further insights into
distribution and habitat requirements of this endangered sh.
Distribution by life stage.—While numerous factors affect the distribution of delta
smelt (EET 1997, Meng and Matern 2001, Bennett et al. 2002, Kimmerer 2002, Baskerville-
Bridges et al. 2004, Dege and Brown 2004, Feyrer 2004, Grimaldo et al. 2004, Sommer et
al. 2004, Bennett 2005, Feyrer et al. 2007, Baxter et al. 2008, Nobriga 2008), it was beyond
the scope of this paper to relate distribution to causal factors. Nevertheless, important
information can be gleaned from this review, which may inform conservation planning and
lead to research into factors driving delta smelt distribution. For example, high frequency
of observation and observed density of mature adults and early life stages are indicators of
areas that could be spawning regions (Sommer et al. 2011). Spawning occurring upstream
in freshwater has been supported elsewhere through high catches of larval delta smelt along
the edges of rivers and in adjoining sloughs in the western Delta (Moyle et al. 1992). The
DELTA SMELT SURVEY DATA

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newer IEP monitoring programs provide potentially important information regarding general
spawning locations. The relatively higher presence of spawning adults in Suisun Marsh,
Cache Slough, and the Lower Sacramento River indicate possible proximity to spawning
areas, a suggestion also supported by high relative observed densities of larval smelt in
downstream areas. The Upper Napa River has relatively high observed densities of larvae,
suggesting that this may also be an important area for spawning; considering their poor
swimming ability, it is unlikely that larvae would have migrated up the Napa River from
other locations. The Napa River, which at one time was considered to be a population sink
for delta smelt, is now considered a contributor to the adult population (Hobbs et al. 2007).
An important rearing area appears to be the stretch of water between the Lower
Sacramento River and Grizzly Bay, with Grizzly Bay supporting an increasing proportion
of young delta smelt as they mature. The highest relative observed densities of juveniles in
STN (with surveys from June to August) were found in Grizzly Bay. This is corroborated by
data from the 20-mm, which also showed Grizzly Bay to have the highest relative observed
densities of juveniles (May to July). By fall, the FMWT data indicate the highest relative
observed juvenile densities usually are found further to the east in the Conuence and Lower
Sacramento River regions — an area where sub-adults were also found in relatively high
observed densities.
Spawning in the upstream regions of Napa River, Suisun Marsh, the Upper
Sacramento River and Cache Slough, and maturing downstream in waters from Grizzly
Bay upstream to the Lower Sacramento River is consistent with the well-noted migration of
delta smelt (Grimaldo et al. 2009, Sommer et al. 2011). The data also suggest year-round
populations in the central regions (Lower Sacramento River downstream to Suisun Marsh)
and in the Cache Slough and Ship Channel region. Collectively, these observations, along
with the report of Hobbs et al. (2007), are an indication of variability in the migratory
patterns observed by Sommer et al. (2011).
Outside of the central regions, the Cache Slough and Ship Channel was the only
region that yielded high catches of delta smelt relative to other regions across multiple life
stages for years 1995-2009. Recent monitoring efforts have shown that delta smelt are
utilizing the near-shore habitats of the Cache Slough and Ship Channel region (a restored
tidal marsh) not only during the spawning season, but also on a year-round basis (DSC
2010). Many IEP studies are underway to understand the environmental mechanisms in
Cache Slough that help create critical habitat for delta smelt.
A number of observations can be taken from these distributional data that could
contribute to more effective conservation planning for delta smelt. First, some of the
highest observed densities of delta smelt are found close to shore (Table 8), suggesting that
some necessary or desired habitat conditions exist along the shoreline, possibly related to
migration (Sommer et al. 2011) or spawning. Second, it could be inferred from subregional
delta smelt observed densities that, under contemporary conditions, the sh seem to be
exhibiting higher densities in areas that are most similar to historic habitat — deep channels
that occur proximate to more extensive areas of shallow water (Whipple 2010), which may
to some degree be insulated from the inuences of anthropogenic environmental stressors.
Third, it appears that the monitoring programs may be missing useful information at some
life stages in areas potentially important for delta smelt (e.g., areas upstream of existing
consistently monitored stations in the Napa River, around Cache Slough and the adjacent
ship channel, and several other tributaries to the Sacramento River).

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taBLe 8.—Average observed densities (number of sh per 10,000 m3) of delta smelt by life stage, Interagency Ecological Program monitoring program, and region.
20-mm = 20-mm Tow-Net, STN = Summer Tow-Net, FMWT = Fall Midwater Trawl, BS = Beach Seine, BMWT = Bay Midwater Trawl, and SKT = Spring Kodiak
Trawl. NS indicates no survey conducted in the given life-stage and region.
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According to Feyrer et al. (2007), one factor limiting the utility of delta smelt
empirical data is that those data frequently pertain to a particular life stage or time period
when sampling was conducted. Thompson et al. (2010) suggested a life history model
linking the abundances of each life stage would provide a more continuous picture of the
population and would capitalize more fully on available data. Martin et al. (2007) suggested
that conservation of migratory species depends largely on understanding links between
different periods of life cycles. These suggestions highlight the importance of, and the need
for, a clearer understanding of the distribution of the various life stages of delta smelt.
Concepts regarding restoration of native sh habitat and buffering from potential
environmental disaster within the San Francisco Estuary have evolved considerably in recent
years, particularly the restoration of tidal wetlands and oodplain habitats (Moyle 2008).
While signicant issues include the management of ow, invasive species responses, and
future climatic effects (Brown and May 2006), our review provides important information
on the life stage-specic distribution of delta smelt that was made possible by monitoring
programs implemented by the IEP and other agencies since 1995.
According to Holl et al. (2003), a common conclusion of many restoration efforts is
that success varies substantially among sites. At least in part, varying success results from
differences in hydrology, microclimate, and movement of plants, animals, and disturbance
regimes. Our review of the spatial distribution of delta smelt highlights general regions that
appear important for specic life stages. Such information will be useful when addressing
management issues such as anthropogenic stressors, habitat restoration efforts, and testing
the success of experimental approaches to achieving habitat objectives for desirable species
(Moyle et al. 2010). This comprehensive review of delta smelt distribution within the San
Francisco Estuary provides managers and scientists an improved depiction of the spatial and
temporal extent of the delta smelt throughout its range, and lends itself to future analysis of
population assessment and restoration planning.
acknowLedgMentS
We gratefully acknowledge the CDFG, USFWS, and IEP, especially R. Baxter, K. Hieb,
R. Titus, V. Afentoulis, D. Contreras, B. Fujimara, S. Slater, J. Adib-Samii and J. Speegle
for many years of data collection and dissemination. We also thank The Fishery Foundation
of California, East Bay Municipal Utility District Fisheries and Wildlife staff, The Moyle
Lab (University of California, Davis) and the California Department of Water Resources
for sharing data. P. Rueger and J. Melgo provided valuable data and spatial analyses. D.
Murphy provided signicant input to, and three anonymous reviewers provided valuable
insight and guidance on, an earlier draft of this manuscript. Funding for this project was
provided by the Center for California Water Resources Policy and Management and the
State and Federal Contractors Water Agency.
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Submitted 20 September 2011
Accepted 27 October 2011
Associate Editor was K. Shaffer
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