San Pedro Creek Capistrano Fish Passage Restoration Project

Longitudinal Study

Brian Crowley Adam Edgell GEOG 642 Fall 2006

12/18/2006

Introduction In the fall of 2005, the City of Pacifica restored approximately 1300 linear feet of

San Pedro Creek downstream of the Capistrano Bridge. The main objective of the

project was the removal of a significant obstacle to fish passage while improving habitat

conditions for migrating steelhead trout. Over the years, severe downcutting by the

creek, due to the rapid urbanization of the area, had left the bottom entrance to the bridge

perched approximately nine feet above the downstream channel invert, rendering the

1960’s Denil fish ladder underneath the bridge completely ineffective. This resulted in a

severe migration barrier to spawning steelhead trout trying to work their way upstream.

For this project, the City of Pacifica removed the failing fish ladder from beneath

the bridge, and brought in 12,000 cubic yards of fill to raise and stabilize the streambed at

its 1950s level and gradient, thus improving fish passage underneath the bridge. A series

of nineteen rock and log weirs were then placed along the channel, creating a riffle-pool

and step-pool system that gradually rises in elevation from the downstream gradient up to

the Capistrano Bridge. This restoration will allow juvenile salmonids to move up the

channel in a variety of stream flow conditions, while minimizing the height of the jumps

that they will have to negotiate in order to make it upstream. In addition to enhanced fish

passage, significant bank reconstruction was done as well. Newly regraded slopes, along

with the removal of exotic plant species and replacement with natives found throughout

the watershed, will help to reduce the sediment contribution from bank erosion, to

increase canopy cover, and to maintain or lower water temperatures. It will also help to

create a stable, slightly laid-back bank, with the added benefit of reducing stream

velocities through the reach (Temple 2006, SPCWC website).

Our group was given the task of performing a longitudinal and cross-sectional

study of the reach of San Pedro Creek that was restored in the Capistrano Fish Passage

Restoration Project. We collected streambed elevation data along the thalweg of the

creek, beginning at the Capistrano Bridge and working downstream. From this data, we

were able to construct a longitudinal profile of the stream, from which we could derive

gradient changes resulting from deposition and/or erosion. We also collected cross-

sectional elevation data at a number of points along the stream corridor. This data

allowed us to note any major changes in bank shape and stability, as well as the

opportunity to document erosional movement along the stream of the originally-placed

weirs. The main purpose of this study is to compare our data and profile with data

collected and documented in the as-built plans for the project in November 2005. In this

way, we hope to provide some initial insight into the ongoing effectiveness of the project

in preserving and protecting salmonid fish habitat.

Background on San Pedro Creek Watershed

San Pedro Creek is a perennial stream that flows northwesterly through San Pedro

Valley in the city of Pacifica in San Mateo County, California, and empties into the

Pacific Ocean. It drains a 5,257 acre (8.2 square mile) basin containing the mainstem of

the creek and five major tributaries (North Fork, Middle Fork, South Fork, Sanchez Fork,

and one unnamed tributary), and composed of seven major subwatersheds (North Fork,

Middle Fork, South Fork, Sanchez Fork, Shamrock, Pedro Point, and Hinton) and a

number of minor subwatersheds. The North, Middle, and South Forks all converge near

the eastern end of the San Pedro Valley, and are met downstream to the northwest by the

Sanchez Fork before reaching the Pacific Ocean. The upper reaches of the creek have

healthy riparian areas and substantial winter flows that support migrating steelhead trout,

making it the only creek within 30 miles of San Francisco that offers this type of habitat

(Collins 2001, McDonald 2004, SPCWC website).

The area of our study is a roughly 1150-foot reach along the mainstem of the

creek, extending from the Capistrano Bridge downstream to a bend in the creek near

where it runs behind the Sanchez Art Center.

San Pedro Creek Watershed Geology and Geomorphology

The San Pedro Creek Watershed (SPCW) is located at the northern extent of the

Santa Cruz Mountains. Montara Mountain, at the southern extent of the watershed, is the

highest point at 1,989 feet, and, along with San Pedro Mountain and Whiting Ridge,

forms the southern boundary of the watershed. Sweeney Ridge, peaking at 1,220 feet,

forms the eastern boundary, and connects to Cattle Hill, which marks the northern extent

of the watershed. The creek flows towards the northwest where it meets the Pacific

Ocean.

The SPCW lies on the western edge of the North American tectonic plate, at its

junction with the subducting Pacific plate. This leads to significant uplift and faulting in

the region. The largest fault in the area is the Pilarcitos fault, a strike-slip fault that runs

through the center of the watershed. The northern side of the fault is called the Pilarcitos

block, while the southern side is the La Honda block. South of the Pilarcitos fault is the

smaller San Pedro Mountain fault, which separates the La Honda block from the geologic

structures to its north and south. This fault moves granitic rocks upward relative to the

downward movement of the sedimentary rocks to the north. There are also a number of

smaller, unnamed faults in the northern half of the valley that run nearly parallel to these

two faults. The SPCW is characterized by alternating, sheared, northwest-trending beds

of the Jurassic/Cretaceous Franciscan formation that are faulted against Tertiary

sedimentary rocks, that are, in turn, faulted against Cretaceous granitic rocks at the

southernmost ridge top. The bottom of the San Pedro Valley is composed primarily of

alluvium deposited from runoff from the surrounding highlands. These factors combine

to make many areas within the SPCW prone to slope failure. (Collins 2001, Sims 2004,

McDonald 2004).

SPCW and San Pedro Creek as Steelhead Habitat

As mentioned earlier, San Pedro Creek is notable in that it is the nearest creek to

San Francisco that provides habitat to support migrating steelhead trout. In fact, the creek

even supported a population of Coho salmon up until the 1950s. Although decent habitat

for spawning is located throughout the mainstem and into the Middle Fork tributary, the

best spawning habitat appears to be in the upper reaches of the Middle Fork.

However, the mainstem provides the best conditions for rearing steelhead to smolt size

(at about two years old) and for stages of development beyond spawning (Davis 2004,

Hagar Environmental Science 2002, SPCWC website).

Sediments from upland hillslope sources are a major contributing factor to the

condition of steelhead habitat. Upland sediments contribute gravels that are important for

spawning, but also contribute fine sediments that can bury those gravels, thus increasing

the stream’s turbidity and disrupting the natural pool and riffle systems that are crucial to

steelhead spawning and rearing. A growing concern is that, although the San Pedro Creek

mainstem is currently supporting steelhead, it is always at risk for elevated

mobilization of sediment and an increase in fine sediment loads, given the amount of

development and human activity in the area. Some research suggests that the substrate of

the mainstem is lower in gravels than what is ideal for supporting steelhead, and that,

therefore, steelhead using the mainstem are more vulnerable to water quality degradation

from siltation compared to the Middle Fork tributary. (Hagar Environmental Science,

2002)

There are a number of other factors that adversely affect the steelhead

environment, among them the bridges along the mainstem of San Pedro Creek, which

serve as obstacles to adult steelhead trying to get to spawning areas, as well as to the free

movement of the younger steelhead. Also of concern is the destruction of riparian

corridors due to the region’s rapid suburban development, which adversely affects fish

habitat. This riparian vegetation is vitally important because it provides shade to

moderate water temperature for the fish, while also providing overhead cover (Hagar

Environmental Science, 2002).

Development and Land Use in San Pedro Creek Watershed

Up until the mid-1800s, what are now the lower reaches of San Pedro Creek were

comprised of a large seasonal wetland and lagoon. Early maps of the area show a large

willow thicket in the area east of what is now Linda Mar Shopping Center. West of this

willow thicket lay a seasonal lagoon. The original stream channel was probably quite

indistinct through this area, and during the dry season may have dwindled to nothing

more than a few isolated pools. In all likelihood, the lagoon probably formed during the

dry season behind a sandbar at the mouth of the stream. The stream would then drain into

the lagoon during the wet season when streamflow became high enough to breach the

sandbar.

The first known human modifications to the area were by the Ohlone Indians who

set frequent fires as part of a regular burning regimen, converting much of the coastal

shrub and forested areas into grassland. As a result, mollisols, which are primarily

grassland soils, are the dominant soil order in the region. (Collins 2001, Davis 2004,

Hagar Environmental Science 2002).

Beginning in the 1850s, intensive agriculture came to the San Pedro Valley.

Sometime prior to 1928, the willow thicket was entirely removed, and San Pedro Creek

was confined to an aligned channel that ran through the area, while the original channel

and lagoon were plowed over and planted with crops. The agriculture practiced in the

area had a profound effect on the creek by increasing the area of exposed soil, which led

to increased erosion rates, accelerated channel incision, and heavier sediment loads.

Suburban development began in the area during the 1950s, leading to a number of

dramatic changes in the watershed. The most far-reaching of these were the placement of

most of the North Fork watershed into underground culverts, the development of a series

of new bridges on the mainstem of the creek, and increasingly dense residential

development of much of the valley floor and northern hillslopes. This development led,

in turn, to a drastic increase in the impermeable surface area of the watershed, resulting in

a decrease in runoff lag time and an increase in the peak amount of runoff. In addition,

off-road motorcycle use, primarily during the second half of the 20th century, increased

the impermeable surface area further, especially in the Pedro Point and South Fork

watersheds. The effects of these changes are evident today in active slopewash, gullies,

and landslides throughout the watershed (Collins 2001; Georgeades, et. al. 2005; Hagar

Environmental Science 2002, McDonald, 2004).

Today, the San Pedro Creek Watershed exists in a wide variety of land use

conditions, ranging from dense residential and commercial development along the

mainstem at the valley floor, extensive culvertization of the North Fork subwatersheds,

and relatively undisturbed parklands on the Middle and South Fork subwatersheds.

Estimates of the amount of developed land within the watershed range anywhere from 13

to 33%, and those numbers continue to increase. Although much of the watershed’s

uplands are designated as county, state, and federal recreation and parklands, and are

therefore protected from development, residential development continues to increase in

density both along the valley floor and on the northern and eastern hillslopes. (Collins

2001, Davis 2006, Hagar Environmental Science 2002). This is especially true in our

study area, where housing developments run right up to, and sometimes within, the

riparian corridor.

Overview of Materials and Methodology

Our study site was on the San Pedro Creek mainstem channel, starting at the

Capistrano Bridge and extending 1147 feet downstream. Following basic reference reach

procedures, we proceeded to perform a longitudinal survey and four cross-sectional

surveys along this reach. The materials used to perform the surveys included: an optical

level and tripod, a hand level, a stadia rod (marked in tenths of feet), and a 300-foot field

tape measure (marked in tenths of feet). In addition, we used rebar and flagging tape to

monument benchmarks, turning points, and other points of interest; two-way radios to

enhance communication between team members; and field notebooks to record data and

observations.

We began our survey by setting up the optical level on the tripod on an upslope

area just downstream of the bridge. By performing a backsight (BS) to a benchmark with

a known elevation (in this case a drainage grate on the paved surface of the bridge), we

were able to establish the height of the instrument (HI). By next performing a foresight

(FS) to an arbitrary turning point, then setting up the instrument at a new location within

sight of the area under the bridge and performing another backsight to that turning point,

we were able to establish the height of instrument for the first part of our longitudinal

survey. Starting at a point in the stream at the northeast corner of the bridge culvert that

had previously been staked with rebar, we proceeded to pull the field tape measure to its

full extent along the thalweg of the stream. The stadia rod was then placed at various

numbered and referenced stations along the thalweg. These points were chosen for their

significance in portraying the overall shape of the pools and riffles in the stream, and

include the beginning and ending points of pools and riffles, the deepest point of each

individual pool, and any notable points of inflection in the streambed. Using the optical

level, we collected foresight readings from the stadia rod for each station and recorded

this data in our field notebooks. This data was later used to calculate thalweg bed

elevations. As we reached the end of the 300-foot tape measure, we placed a monument

and laid out the tape over the next 300-foot length of thalweg. We performed the

foresight-backsight operation at various turning points along the way so that the level

could stay within sightline of the stadia rod as we moved downstream. These turning

points were recorded in our notebooks, and most were monumented with rebar and/or

flagging tape as well.

On the second day of data collection, we performed cross-sectional surveys of

four points along the reach. After following the procedure to establish the height of

instrument, we proceeded to take stadia rod readings along a line running perpendicular

to the stream, being sure to include readings at regular intervals (every 2 feet, except for

Cross-Section D which was measured at every 1 foot), as well as at any other points of

interest we might observe (such as in the thalweg, at the bank’s edge, on weirs and

revetments, etc.

All of this field data was later imported into Excel spreadsheets for analysis and

visualization. By plotting channel length on the horizontal axis and channel elevation on

the vertical axis, we constructed a longitudinal profile of the studied reach. A similar

procedure was used to construct graphs of the four cross sections, with horizontal

distance across the stream on the horizontal axis and elevation readings along the vertical

axis.

Results and Data Analysis

Without any further supporting data, the profile we have created is little more than

a “geomorphic snapshot” of the reach we surveyed (Georgeades, et. al. 2005). It also

must be noted that several factors contributed to our inability to collect the quantity, and

possibly quality, of data which we had hoped to obtain. For one thing, due to time

constraints, we did not measure water surface elevation as had originally been planned.

Also, due to damage to one of the two-way radios that occurred during the longitudinal

survey, long-distance communication between team members was restricted to a series of

hand signals, as proximity to residential housing limited the acceptable volume level of

communications. This obviously had a negative effect on the efficiency and accuracy of

communications, which could have been reflected in an increased chance for human

error. Most of all, we were restricted by the logistics of performing the survey with a

group of only two people. The increased responsibilities and stresses placed upon each

team member contributed to higher levels of physical and mental fatigue, which

increased the probability of introducing human error into the data collection process.

Despite these issues, however, certain conclusions can be obtained by comparing this

data that was obtained with that collected at the creation of the restoration project and

documented within the as-built plans.

When comparing the longitudinal data, some interesting questions arise. One is

why, in our measurements, much of the thalweg is actually above the weir elevations

documented in 2005 and those recorded in the survey (Figure 1). One possibility has to

do with how the log weirs were constructed and how their elevation was originally

documented. The log weirs are typically constructed of timber that is approximately

three feet in diameter. The as-built drawings do not show the cuts that were made near

the center of many of the logs to facilitate flow near the center of the channel. The

elevation of each weir is called out to its lowest top surface point; however, there seems

to be some ambiguity with respect to where exactly this lowest point is – on an un-cut

surface, or at the top of a cut, or perhaps halfway down the cut (if it’s sloping

significantly). Although this could explain the discrepancy, we must also consider the

possibility that this is simply the result of human error, either in the collection or the

processing of the data itself.

It seems that this is the most likely answer to the seemingly erroneous thalweg

elevations. When we first started our longitudinal survey, we noticed that we were

having a hard time seeing the crosshair sights through the optical level’s lens. After

consulting with a professional, we realized that we did not have the lens focused

correctly. After adjusting the lens, we could see the crosshairs perfectly and were

satisfied with our readings; however, due to time constraints, we decided not to perform a

new setup on the instrument and to trust our readings up to that point. It now seems

likely, therefore, that during those initial readings, we were quite possibly looking at the

upper crosshairs instead of the middle ones, resulting in our higher than expected

elevation totals along the entire stream. We did an additional sighting to the bridge

benchmark on the second day, and, after adjusting for the elevation difference compared

to the readings the first time, the graph looks much more as would be expected (Figure

2). Of note is the striking elevation drop from the weirs into subsequent pools, which we

noticed in our visual observations, a striking feature which is not evident in the original

graph, but reappears in the adjusted one.

Longitudinal Profile - San Pedro Creek (Capristrano Restoration Reach)

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Thalweg Length (ft)

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Longitudinal Profile - San Pedro Creek (Capristrano Restoration Reach)

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Figure 1

Figure 2

Another question is how to explain the decrease in slope between that portrayed

in the as-built plans and that recorded in our observations. Over the roughly 1150 feet

surveyed, there was a difference of approximately 0.1% of slope – 1.5% in our survey

versus 1.6% in 2005. This appears to have been caused by an increase in the meander of

the thalweg compared to that constructed as part of the restoration project. This does not,

however, signify a change in the overall form of the channel. Rather it is more likely a

result of the disbursement of boulders and large cobbles by the initial year of runoff flows

that created localized scouring and high spots, resulting in a somewhat more circuitous

channel. This reach appears to still be moving toward equilibrium; the slope may

increase or decrease more over time.

We also collected interesting data at our four cross section sites. For Cross-

Section A, Figures 3 and 4 show the as-built diagram and our cross-sectional graph for

the same location – Weir #1. It should be noted that a majority of the stations that we

sampled in this cross-section were not on the tops of boulders on this boulder-only weir,

but were on the sand and gravels that had collected between them since their installation.

Placement of the stadia rod in this way may have resulted in a slightly lower elevation for

the cross-section than might have resulted otherwise.

A detailed comparison of these two figures is difficult because of a lack of a

horizontal control that is common to both. However, some coarse conclusions can be

drawn. First, the 2006 channel elevation at 83.7 feet is still well above the pre-restoration

elevation of approximately 74 feet. Correspondingly, the overall shape of the 2006

channel is less entrenched than its pre-restoration form. Finally, while it is difficult to

determine the location of the “corners” that make up the start of the terraces at the 96-98

foot elevation in the as-built drawing, it is clear that nowhere within the 62-foot width of

the our cross-section was there an elevation measuring over 92 feet. This indicates a fair

degree of bank erosion from the upper portions of the channel cross-section over the past

year.

Figure 3: As-built plan of Weir #1 (Cross-Section A)

Cross-Section A

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Figure 4: Graph of Cross-Section A

The location for Cross-Section B was chosen because of its proximity to both the

gabion bank reinforcement and the approximately 24-inch diameter storm drain outlet

that empties into the creek at that location. The distribution pattern of boulders and large

cobbles directly across the channel from the storm drain outlet indicates that outflows

from this pipe might at times be quite substantial. This section in particular might be

instructive to observe over time.

Cross-section B

Figure 5: Area of Cross-Section B on as-built plan

Cross-section C has no real unique feature of interest that stands out. It was

chosen to represent a “typical” cross-section for the reach. It should be noted that data to

determine the absolute elevation was not available – either the sighting to a vertical

benchmark was overlooked, the data was not recorded, or the data was lost. Regardless,

we did capture the relative elevation of the top of the rebar monument, so future

surveyors will be able to determine the absolute elevation by reconciling this to a vertical

benchmark of their choosing.

Cross-Section # B

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Figure 6: Graph of Cross-Section B

Cross-Section C

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Figure 7: Area of Cross-Section C on as-built plan

Figure 8: Graph of Cross-Section C

Cross-Section D shows a slightly deepened section in the outer half of the

channel, as would be expected in the latter part of a relatively sharp bend in the stream.

This cross-section was chosen largely because of the convenience of using the nearby

utility poles as visible landmarks for locating it in the future. Rebar monuments with

marking tape were put in place, one at the base of the utility pole on the north side of the

creek and one approximately thirty feet downslope from the utility pole on the south side,

along the line of the cross-section.

Cross-section D

Figure 9: Area of Cross-Section D on as-built plan

Conclusion

While the data gathered from this survey is quite informative, it still leaves many

questions unanswered. As a snapshot in time, it does show that small but recordable

changes are occurring in the meander pattern of the stream as well as in the structure of

its artificially created step-pool system. However, our data gives little insight into the

future dynamics of the stream system in this reach and how it will continue to respond to

the changes brought about by the restoration project. It also gives data that only

indirectly informs about the stream’s suitability as habitat.

To answer these questions, more data needs to be collected. Longitudinal and

cross-sectional surveys of similar methodology should continue to be performed along

this reach, so that small-scale changes such as those we observed can be measured over a

longer time period in a search for broader patterns. Also, specific research should be

done to measure what, if any, impact the restoration project has had on sediment levels

Cross-Section - D

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Figure 10: Graph of Cross-Section D

downstream, while also checking upstream for evidence of successful steelhead trout

migration past the site of the old fish ladder. Hopefully our observations will serve as a

valuable resource for these and any other future assessments of the San Pedro Creek

Watershed.

BIBLIOGRAPHY

Collins, L., P. Amato, and D. Morton, 2001. San Pedro Creek Geomorphic Analysis (accessed at http://pedrocreek.org/research.html).

Davis, J., 2004. San Pedro Creek Watershed Sediment Source Analysis, Volume I:

Background and Synthesis. Prepared for the City of Pacific and the California State Water Resources Control Board. Funded by the U.S. Environmental Protection Agency Clean Water Act. (accessed at http://bss.sfsu.edu/jdavis/ pedrocreek/research/default.htm).

Davis, J., Fall 2006. Lecture. GEOG/GEOL 642. Watershed Assessment and Restoration.

San Francisco State University. Georgeades, A., A. Jurek, M. Snow, 2005. San Pedro Creek Longitudinal Study. Course

project for GEOG/GEOL 642. (accessed at http://bss.sfsu.edu/jdavis/geo_642/ WshedProjects.htm).

Hagar Environmental Science, 2002. Steelhead Habitat Assessment for the San Pedro

Creek Watershed. (accessed at http://pedrocreek.org/research.html). Harrelson, C., C.L. Rawlins, and J.P. Potyondy, 1994. Stream Channel Reference Sites:

An Illustrated Guide to Field Technique. United States Department of Agriculture.

McDonald, K., 2004. San Pedro Creek Flood Control Project: Integrative Analysis of

Natural Hazard Response. San Francisco State University: MA Thesis (accessed at http://pedrocreek.org/research.html).

San Pedro Creek Watershed Coalition website: www.pedrocreek.org. Sims, S., 2004. San Pedro Creek Watershed Sediment Source Analysis, Volume II:

Hillslope Sediment Source Assessment of San Pedro Creek Watershed. Prepared for the City of Pacifica and the California State Water Resources Control Board. Funded by the U.S. Environmental Protection Agency Clean Water Act. (accessed at http://bss.sfsu.edu/jdavis/pedrocreek/research/default.htm).

Temple, Syd, 2006. Salmonid Habitat Restoration and Fish Passage Improvement in an

Urban Creek: A Case Study of a Recently Completed Project on San Pedro Creek, Pacifica, California.