Temporal Investigations of Marsh Ecosystems (TIME)


Screen shot 2013-09-10 at 1.48.24 PMWhy this Project?

The Tijuana Estuary is one of the largest intact coastal wetlands in Southern California, and a model case study from which to strengthen our collective understanding of wetland management using information from the past, present, and future.

The TIME project is a collaborative project that brings together the perspectives of scientists and managers to address key needs identified by Southern California Wetlands Recovery Project (SCWRP) and the Tijuana River Valley Recovery Team (TRVRT) by developing a decision-making framework. TIME embodies a collaborative approach that, from the project outset, engages stakeholders to ensure development of locally relevant products.

TIME informational flyer

Curious about Project status?  Check out the stakeholder update webinar that partners hosted in May 2015.  For webinar summary click here.

Using information from the past, present, and future

Numerous studies have been conducted to better understand and restore coastal wetlands in Southern California.  The TIME project seeks to explore several essential elements to support effective wetland recovery at the Tijuana Estuary, with an eye on scaling up to the region:

Image 1  1. Understand stakeholder needs through an issues assessment and communicate lessons learned from synthesizing information from the past, present, and future at the Tijuana Estuary that can inform wetland restoration under changing and uncertain conditions;

Screen shot 2013-09-10 at 1.23.12 PM  2. Characterize ecosystem services provided by coastal wetlands in southern California and how they may change over time;

Screen shot 2013-09-10 at 1.23.21 PM  3. Incorporate information gained from historical ecology studies; and

Screen shot 2013-09-10 at 1.35.08 PM  4. Create visualizations to assess historical and future potential characteristics of the Tijuana River Estuary.


The Team

The TIME project is designed and carried out by a diverse team of collaborators that include applied science and collaboration professionals, and the specified end-users of TIME’s products. Collaborators work together to iteratively incorporate stakeholder feedback into the development of each project phase.




Sacramento State Center for Collaborative Policy (CCP)

Southern California Coastal Water Research Project (SCCWRP)

California State Coastal Conservancy

San Francisco Estuary Institute (SFEI)


Exploring future scenarios for the Tijuana River Estuary.










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Please contact Kristen Goodrich, Coastal Training Program Coordinator, for more information: kgoodrich[at]trnerrtest.wpengine.com

 This project is funded by a grant from the National Estuarine Research Reserve System (NERRS) Science Collaborative.

Field Experiences

CTP also offers field experiences by providing tours of the Reserve and surrounding areas.  Tours provide a mechanism to feature and discuss issues that affect the Reserve and put relevant CTP programming into context through on-the-ground experience and visual highlighting of the unique setting and challenges, including transboundary coordination.

Tour at Border Monument (June 16, 2011)

Tour with Dr. Robinson (August 28, 2010)

Napolitano Restoration Site

Once part of a natural wetland habitat, this 1.25 acre area of land was bought to become a real estate parcel. Even though it was later abandoned due to the site’s government protection, the ecosystem was severely degraded from its original state. Caltrans acquired this site and began their Supplemental Environmental Project (SEP) designed to restore and protect the Napolitano site.


To establish a functional, long term, self-sustaining habitat that can support the native plants and animals found in local salt-marsh communities, as well as provide needed habitat for the light-footed clapper rail.


Alteration 1:

To create physical conditions similar to those of a local salt marsh habitat, a tidal channel was created to distribute flow throughout the low marsh. Also, debris was removed and storm drain water diverted to prevent sedimentation.

First, a meandering tidal channel was created to distribute tidal flow to the low marsh. To compensate for sedimentation and side slumping, the channel depth was graded to be .75 m, around 0.3-0.5 m below the mean of the low water level in order to support tidal flow during seasonal fluctuations. In the marsh transition zone, the slope ratio was graded to a ration of 1:1. and outcroppings of asphalt, concrete, brick debris at the eastern boundary of the site were removed. To minimize soil compaction, earth-moving equipment followed a systematic north-to-south track with a buffer strip across the lower marsh.
An earthen trench was dug next to the northern grate of the storm drain system for a reduction in sedimentation around the site and prevent future damage to plants.
The over-excavated soil of the marsh was replaced with a 2:1 ration of topsoil and dried kelp for soil nutrient replenishment.

Alteration 2:

Vegetation was replanted in order to re-establish local marsh habitat. All planted seeds and cuttings were taken from the Tijuana Estuary, basing species composition on a reference site south of the restoration area.
In low marsh habitats, the dominant plants of the ecosystem, pickleweed and Pacific cordgrass, were planted clusters around 1 meter wide. The sub-dominants, saltwort, alkali heath, sea lavender, and jaumea, were planted in clusters dispersed around the dominant plant clusters. Around 2,700 of each of the dominants and 205 each of the sub-dominants were planted.
The transition zone of marsh was planted with clusters including 201 of the dominant plant Distichlis spicata, 18 Salicornia subterminalis, and 8 lyium brevipes, some being onsite salvages.


Preliminary soil borings taken during initial site investigation (Oct 16-17, 1997)
Draft Removal and Restoration Plan completed (March 1998)
Excavation begins (December 1998)
Excavation completed (January 1999)
Planting begins (February 1999)

Present Activity:

-Monitoring: Caltrans 3 year monitoring program following planting completion


Brown and Caldwell and Tierra Environmental Services “Tijuana Estuary Wetlands Restoration Project: Draft Removal and Restoration Plan- California Department of Transportation District 11, San Diego” March 1998

“Caltrans Rescues a Hunk of Marshland.” California Transportation Journal November-December 2002: 40-43

Sewage Ponds Restoration

Constructed in the 1930s, these sewage ponds were used up until the 1960s, at which point they were abandoned. Over the next two decades, the ponds gradually filled in.

Native salt marsh vegetation began to recolonize the edges, but it remained sparse and never the filled in ponds themselves. Thus, in the 1980s, access was limited to the site to keep it preserved and in 1979-1980, Spartina foliosa plugs were transplanted to the sewage lagoon. The Spartina colonization was successful and the plants have continued to thrive.


To investigate methods for restoring and enhancing salt marsh vegetation in disturbed habitats.


Alteration 1:

Storm induced river flooding is known to reduce soil salinity and cause extreme sedimentation, which can encourage spartina colonization if it raises the mudflat elevations. From October 2, 1979 to September 17, 1980, the conditions and soil salinity fluctuations encouraged the growth of spartina  and seed germination.


Spartina patches were sorted into three experimental groups for testing. Some patches were given nothing (control), some were fertilized with nitrogen, and some were covered with tiles to test drainage effects. There was no significant difference between the plot groups, which may be attributed to poor seasonal timing, a small measurement period, or already nitrogen saturated soil from nutrient rich sediments and flooding.

Alteration 2:

Spartina seedlings were transplanted to the west side of the ponds, which had previously been lacking in vegetation. Of the 66 cores that contained spartina shoots, 18 survived. Next, 20 clumps raised from seeds were planted at 1 m intervals and covered with aviary wire to minimize grazing, which was a major cause of mortality in the first round of planted shoots.

The next seedling transplant garden tested for transplant shock differences in fresh, brackish, and sea water. 29 clumps were raised for seedlings with 313 shoots total, and were randomly planted at 1m intervals adjacent to the first seedling transplant. These new shoots were also covered with wire cages. No significant difference was seen between the transplants within the different water types.

In the transplant garden from mature S. foliosa, 100 shoots were placed along the tidal creek on the south end of the lagoon. Of these, nearly 100% survived and expanded.

The successful establishment of 840 Spartina plants outside range of existing stands indicates that the species was limited by dispersal over the sewge ponds.
Spartina clones are known to retain sediment, which creates a positive feedback loop. In other words, sedimentation encourages spartina colonization, which in turn encourages more sedimentation. This is a known cause of habitat conversion, creating more areas for salt marsh vegetation and shorebird feeding.

Monitoring studies done in 1979 and 1980 indicated that some patches of the spartina were established from seed, one of the first documented instances of Spartina establishment from seed in San Diego county.


-Sewage evaporation ponds constructed (1930’s)
-Sewage ponds abandoned (1960’s)
-66 cores transplanted (1979)
-Census records 33 patches of Spartina on edge of sewage lagoon (June 29, 1979)
-9 experimental transplant gardens established (June 18, 1980)
– Census shows 103 separate Spartina patches total (July 11, 1980)
-100 Spartina shoots transplanted along tidal creek near south end of sewage lagoon (June 19, 1980)
-20 clumps raised from seeds transplanted (August 5, 1980)
– 2nd seedling transplant garden established (October 13, 1980)
– Census shows 100% survival (October 28, 1980)
-Access limited and Spartina plugs transplanted into the southern pond (1980/81)
-Heavy winter storms and sedimentation (Winter 1993)
-Spartina clones number over 80 (1997)
-Major sediment accretion (1997-1998 ENSO)

-Current Projects: n/a


Nordby, C., Zedler, J., Williams, P., Boland J. “Coastal Wetlands Restoration and Enhancement.” U.S. Department of the Navy- Wildlife and Natural Resource Office. November, 1980

Ward, Kristen M. “Episodic colonization of an intertidal mudflat by cordgrass (Spartina foliosa) at Tijuana Estuary” San Diego State University. 2000

Personal Contact: John Boland

Post-Restoration Developments: Model Marsh

Re-vegetation Results

Overall the re-vegetation plots experienced significant insect and invasive plant infestation. The kelp amendments used to improve the soil quality were successful

in decreasing bulk density and increasing the nitrogen content of the soil and improving the planting conditions.

Over time, cord grass grew at the same rate in both the amended and unamended plots, while  S. foliosa stem length and plant density were significantly greater in the kelp-amended plots. The re-vegetation cells located near creeks did not differ significantly from the cells further from creeks.

Site Experiment 1:

Sudaeda esteroa was planted as an experimental nurse plant. As a nurse plant, S. esteroa would aid the recruitment of seedlings and would be planted as individuals and in clusters. Additional artificial structures were added to aid the nurse plants and other plant recruitment as well.
Result: Nearly all the nurse plants died and there was no seed recruitment.

Site Experiment 2:

Added Limonium californicus, S. esteroa, and Frankenia individuals in three species clusters so that mutualistic intereactions could aid seed recruitment and development.
Result: Seedling survival still low, the burlap bags used to protect plants were covered with sediment and there was low recruitment.


Initially benthic invertebrate samples showed a population spike from 1500 individuals/m² to 5500 individuals (6-10 months after opening). The population then stabilized at ~2700 individuals.
Spionid polychaetes and amphipods were the first colonizers,  followed by capitellid polychaetes.
Unfortunately, the invertebrate assemblage decreased in size after sedimentation event in 2001 and the dominant species shifted from amphipods to dominance by oligochaetes and polychaetes. Amphipods later returned but were displaced by oligochaetes.
Gastropods later became dominant due to large increase in Cerithidae californica and Cerithidea acteocra. These species had the greatest density in the mudflat and the lowest in the marsh plain- possibly because the mudflat is closes to the main channel, which allows post larvae to settle and develop.


Benthic fish are more abundant in the mudflat and spartina zones of the restoration site, with a lower density in the mid-marsh area.
After the initial tidal flushing of the area, arrow goby and longjaw mudsucker  were the first species to establish themselves on the site. Soon after, arrow goby and killifish were the most frequent fish present in samples. Killifish express site fidelity, as they rely for food on the algal-supported food chain of the area.
In December of 2000, striped mullet showed populational dominance, but dissappeared shortly after. Also in 2000, the staghorn sculpin was found in all subsequent winter and spring samples.


The number and diversity of bird species increased over time after the restoration. Observations show that the birds use the marsh’s mudflat and spartina zones once again to forage. After the tidal flushing of the marsh, the regular seasonal patter for bird migratory patterns became apparent in the area, with more birds present in the winter and less in the summer. However, in the years following, the trend reversed, with more birds staying during the summer and less during the winter.

Present Activity:

-Monitoring:  SWMP

On-site Research Projects:

“Interactions between vascular plants and nitrogen-fixing bacteria in southern Californian wetlands: The role of microbial diversity and anthropogenic disturbances” (Serena Moseman)

Abstract: Studies the nature of nitrogen fixation in Spartina foliosa and how sedimentation affects their activity and diversity.


The Model/Friendship Marsh


Before being diked and filled for agricultural and military purposes, the model marsh site had been a fully functional salt marsh.  These human activities in this area along with the natural sedimentation from storm events caused a decrease in the tidal flow and accelerated system degradation to this area.


In order to re-create the variety of habitats usually present across the intertidal marsh plain, expand the area for wetland flora and fauna, and create a coastal habitat that can function similarly to a natural system, artificial tidal creek networks were excavated and native plants were re-vegetated on the restoration site. The Model Marsh as well as a surrounding 500 acre area was later dedicated under the name of Friendship Marsh.


Environmental Alterations

Goal 1:

Excavate former salt marsh filled in by natural and anthropogenic events to create a marsh plain with a variety of habitat types and to simulate a natural network of tidal channels.

Initiially, the mouth of creek networks experienced large sediment depositions (0.4-0.5 m worth), but this gradually decreased. At first, small channels began forming at creek mouths, implying that the mouths would deepen and revert to the original, natural morphology. However, the upper portion of creeks changed little over time and sediment accumulation became greater in the mudflats than in cordgrass or marsh plain areas. The monitored cells without creeks gained more sediment while the cells with creeks retained and facilitated water flow longer than those without because of sediment transportation abilities.
After five years, volunteer creeks unfortunately did not achieve restoration dimension and drainage targets.

Goal 2:

Create a variety of habitats to simulate a natural creek network system.
Pacific cordgrass (Spartina foliosa) was planted with different spacing and kelp soil amendments to find the most effective planting method.  Saltwort was planted as well on the site while pickleweed was naturally recruited. Glasswort, another salt marsh plant, experienced nearly 100% survival when placed in the area. Kelp soil amendments were used to change the physical property of the soil, and thus aid the re-vegetation of the site.

Click here for Post-Restoration Developments


-Excavated approximately 2m of accumulated sediment (winter 1999)
-Model Marsh excavated (January 2000)
-Model Marsh opened to tidal flushing (February 2000)
-500 acre restoration area and Model Marsh dedicated as Friendship Marsh (April 29, 2000)


Morzaria-Luna, Hem N. “Determinants of Plant Species Assemblages in the Californian Marsh Plain: Implications for Restoration of Ecosystem Function.” University of Wisconsin-Madison, 2004

Zedler, Joy. Handbook for Restorting Tidal Wetlands. CRC Press LLC. New York, 2001

Personal Contact- Serena Moseman

Technical Assistance

What is technical assistance?

In the context of CTP, technical assistance is a service provided to local and regional coastal decision-makers that supports and contributes to better informed decision-making to improve coastal stewardship.  This service generally involves repeated interaction over some period of time.


CTP can help address the complexities of decision-making through technical assistance

Other examples of CTP technical assistance include:

  • Aiding land trusts or watershed councils with strategic/action planning
  • Assisting partners with grant writing
  • Creating a publication or website for use by coastal decision-makers
  • Planning GIS products (e.g. map of town’s environmental resources, local land acquisition priorities, etc.)
  • Facilitating meetings
  • Helping state agencies with plan revisions
  • Providing survey and evaluation assistance
  • Serving in an advisory or leadership role on a committee/watershed group
  • Supporting natural resource managers with implementation of best management practices


Are you are a coastal decision-maker interested in receiving technical assistance?

Please contact Kristen Goodrich, Coastal Training Program Coordinator, for more information:  kgoodrich(at)trnerrtest.wpengine.com.




Goat Canyon/ Spooner’s Mesa Restoration


Local Native Americans called the Kumeyaay occupied this area for centuries as part of their fishing grounds. As a result, there are many valuable archaeological sites in proximity to this site. This is also the last site the Serra/Portola expedition stopped at before reaching the location where the first Southern Californian mission (San Diego de Alcalá) was to be established.
In the recent past Goat Canyon became a gravel quarry and was later abandoned. Soon after, it was acquired by public agencies to become part of the Tijuana Estuarine Reserve.
Currently there are chronic and extreme problems with sedimentation, erosion, and trash resulting from squatter encampments further upstream in Tijuana. During regular flooding events poorly constructed buildings and their associated debris are washed downstream to the estuary. The encampments also increase erosion in the canyon and are a large source of sewage.


The restoration project was meant to enhance natural habitat and manage the intense sedimentation coming out of the creek into the estuary. To beneficially use debris left over from the Model Marsh project, the slopes of Goat Canyon were stabilized with the sediment and reinforced with geotextiles and jute netting.
Soon after, to further the recovery of the site, seeds from maritime succulents were
dispersed across the Canyon and an irrigation was installed.


-Goat Canyon Enhancement plan completed (2000)
-Sediment from Model Marsh placed on the slopes of the quarry (Fall 2000)
-Slopes planted with maritime succulent shrub (Fall 2000)
-Irrigation system installed for the plants and germinated seed (Spring 2001)

Tijuana Estuary Tidal Restoration Program

The Tijuana Estuary Tidal Restoration Program (TETRP) is a large multi-phased wetland restoration program located within the Tijuana River National Estuarine Research Reserve. The primary objective of TETRP is to restore valuable habitat processes that have been lost and to increase the exchange of water in a tidal cycle. This will enhance tidal flushing, improve water quality and control sedimentation to ensure the estuary is a sustained natural habitat.


The California Department of Parks and Recreation and the U.S. Fish and Wildlife Service have initiated the scoping process for the preparation of the draft TETRP II Phase I environmental impact report/environmental impact statement. TETRP II Phase I would restore approximately 80 to 85 acres of salt marsh, mudflat, tidal channel, transitional/upland habitats on portions of both Border Field State Park and the Tijuana Slough National Wildlife Refuge.

For more information, click here for the first of several Restoration Updates for this project. 

To view a scanned version of the 1991 TETRP EIR/EIS, click here (26MB).

Important Dates, see https://trnerr.org/about/public-notices/ for details:

May 27, 2021 –  Notice of Intent and Notice of Preparation issued,
comment period begins

June 16, 2021 – Virtual Public Scoping Meetings (2pm and 6pm)
For meeting materials, see https://trnerr.org/about/public-notices/.

July 12, 2021 – Comment period ends

Funding for TETRP II Phase I comes from:
State Coastal Conservancy (http://www.scc.ca.gov)
State of California Wildlife Conservation Board (https://wcb.ca.gov/) 

Aerial photograph showing the general project area, which is located east of the Pacific Ocean and south of the Tijuana River inlet to the ocean. The Model Marsh is visible on the left side of the photo.

General location of the TETRP II Phase I project site. The wetland on the left is the 20-acre Model Marsh restoration project, completed in 2000.

TETRP I Projects

Oneonta Tidal Linkage

The Oneonta Tidal Linkage project, completed in 1997, was designed to improve tidal circulation in areas of mudflat and salt marsh habitat. To accomplish this, a long abandoned sewage treatment basin area known as the “tidal ponds” was connected to Oneonta Slough. Through channel connections, Oneonta Slough meets up with the ocean and thus changes along with the daily oceanic tides.
This project quickly achieved its goals of providing 2 acres of habitat for wetland species and water quality benefits to some 200 acres of salt marsh vulnerable to sedimentation.

The Model/Friendship Marsh

This Model Marsh, created in 1999-2000, was the first phase of the larger Friendship Marsh project. It is a unique and innovative project that focuses on the restoration of diverse ecosystems such as tidal mud flats, cordgrass habitat and marsh plain that were lost due to the deposition of sediment throughout the Tijuana Estuary over time. In the midst of an urban environment many cooperating organizations designed and implemented a program that included excavation, re-vegetation and natural species colonization. Various researchers will monitor the restored tidal marsh for at least ten years to examine the biological success, as well as efficiency of restoration techniques. The 20-acre marsh was dedicated as Friendship Marsh on April 29, 2000 and plans for further expansion in 2001-2002 were made.  More details on the project can be found here.

Goat Canyon Enhancement Project

Goat Canyon, or Cañon de los Laureles, and its creeks are located within the Tijuana River watershed just inland of the ocean. This 4.6 square-mile sub-watershed contains steep slopes, sandy soil and rare coastal sage scrub and riparian habitats. Human activities and land use have disturbed and altered this area, increasing sedimentation and erosion, resulting in habitat losses, public access problems, and safety hazards.

The Goat Canyon Enhancement Plan, completed in 2000, outlines a program for Goat Canyon. This program includes construction of sediment management basins and creek restoration. To find out more of this project read more here.

Other Restoration Projects

Napolitano Restoration

Sewage Ponds Restoration

Los Penasquitos Lagoon Monitoring

What is Los Penasquitos Lagoon?

Los Penasquitos Lagoon (LPL) is a relatively small estuary located in northern San Diego county where the Los Penasquitos watershed meets the ocean. Three sub-watersheds located within the overarching Los Penasquitos watershed are drained by the Los Penasquitos, Carrol Canyon, and Carmel Valley creeks. Recently, due to the urbanization of the watershed, Carrol Canyon and Carmel Valley creeks, which used to only flow during the winter months are now flowing year round causing a shift in vegetation species (from salt marsh to brackish).

Historically, the lagoon was known to be open to the sea year-round. However, increased sedimentation from agricultural and grazing practices as well as railroad construction during the 1920s and 30s brought about a pattern of seasonal mouth closure. In the 1960s, the dumping of treated waste from upstream sewage plants led to high levels of nitrate and phosphate content in the water. Algal growth and decomposition levels skyrocketed, resulting in depleted dissolved oxygen levels in the water. During this time, mosquitoes and midges thrived, while most of the other wildlife died off and decomposing matter accumulated at the lagoon mouth.

How are the problems being dealt with?

In 1985, California Coastal Conservancy developed an LPL Enhancement Plan to deal with the degradation of the lagoon. The Los Penasquitos Lagoon Foundation was put in charge of management and formulated a plan to monitor the water quality and open the mouth mechanically before water quality became too poor to sustain living organisms in the channel. The Pacific Estuarine Research Laboratory (PERL) was contracted to monitor the lagoon and its organisms from 1987-2004. The studies performed by PERL helped the timely opening of the mouth and the understanding of the lagoon’s ecosystem. In 2004, the Southwest Wetlands Interpretive Association and Tijuana National Estuarine Research Reserve took up the responsibility of monitoring LPL.

What kind of monitoring is done at LPL?

Water quality is measured by a datalogger placed near the lagoon mouth, which takes readings of turbidity, pH, chlorophyll, salinity, temperature, and water depth. Spatial water quality, taken every two weeks, measures water temperature, salinity and dissolved oxygen at different depths of the mouth at three different stations in the lagoon. Flow rates at the different tributaries of LPL are measured monthly.  Additionally, vegetation surveys are taken twice a year  in the lagoon area to document the transition of vegetation species and habitat due watershed urbanization. When mouth closure occurs, this monitoring data is used for the justification and timing of the mechanical mouth opening so that the lagoon remains a thriving natural habitat.

Previous Reports:

2009-2010 LPL report