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There are nine monitoring elements associated with this monitoring plan. The nine elements were selected in order to characterize the ecology of the restored habitat as completely as possible. The nine elements are inter-related in that information will be used from combinations of elements in order to assess habitat restoration features, habitat use and biochemical changes taking place as a result of the project. Each element addresses specific questions and has specific objectives. Most of the elements (except bathymetry) include a comparison of the Prospect Island restored habitat with habitat in the adjacent Delta channels, the Sacramento Deep Water Ship Channel and Miner Slough (Figure 1). The Delta channels represent the current condition of most of the Delta before shallow-water habitat restoration. For the fish, zooplankton, and water quality elements, there will also be a comparison of habitat in Prospect Island with habitat in Liberty Island, an agricultural island in the northern Delta that was flooded and has been left to develop naturally.

It is noted here that the funds being requested for monitoring cover only a three-year period. This is the maximum length allowed for funding requests from CALFED's Category III program. While the monitoring time frames for many projects of this type fall within the 3-5 year range, closer to 15-20 years is needed to judge the success or lack thereof. One of the fundamental requirements for achieving success is to give the system time, allowing for the self-designing capacity of nature (Mitsch and Wilson, 1996). Ideally, monitoring should cover this time period. To address this concern, after the second year of monitoring and dependent upon subsequent assessment, additional funds may be requested to extend monitoring over a reasonable time period to document the natural progression of restoration and use of the habitat restored.

There are three purposes for monitoring the Prospect Island project. The first is to assess physical processes taking place on the island as a result of restoration activities. Examples include potential subsidence of habitat islands, build-up or loss of sediment on shallow benches on the islands and adjacent to the levees, and water circulation patterns throughout the island resulting from location of the breaches.

The second purpose is to document the establishment of shallow water, riparian and upland vegetation; document the abundance of aquatic and terrestrial animals (fish, waterfowl, shorebirds, terrestrials) on Prospect Island; and document the use of various habitat types by aquatic and terrestrial animals created by this project.

The third purpose is to measure the flux of organic carbon from the restored habitat to Delta channels. Organic carbon is important as a potential food source for organisms downstream and for its potential effects on drinking water quality.

All the monitoring elements are related to one another and address the physical, biological and chemical factors associated with taking a section of agricultural land, creating habitat features on it, then flooding it for purposes of providing aquatic habitat.

The following sections identify the restoration project objectives and criteria and describe their relationship to monitoring objectives. Specific questions to be answered by monitoring activities are also described.

Restoration Project Habitat Objectives

Prospect Island restoration objectives are:

  • Create habitat suitable for Federally listed threatened delta smelt and proposed threatened Sacramento splittail.
  • Develop feeding, cover, and resting areas for anadromous fish including chinook salmon.
  • Improve waterfowl and shorebird habitat.
  • Provide terrestrial and aquatic habitat for other wildlife species.

Table 1 identifies target animals and their associated habitat along with some criteria associated with the habitat. Monitoring elements are designed to assess in part, whether the habitat objectives have been met, whether criteria for the habitat have been met and whether the habitat is being used by targeted and other species. It is important to note that while restoration objectives target native species (in particular native aquatic species), it is expected that many non-native species may also benefit from the habitat restoration. One question monitoring will address is what species use the restored habitat. In part, success of the project will depend upon the answer to this question. If the habitat restored is being used primarily by non-native species (and not by targeted native species), then the project will not have succeeded as intended.

Table 1 – Target Animals and habitat type
Target Animals Habitat Type
Delta Smelt, Sacramento Splittail, Chinook Salmon and Other Native Species
  • Shallow water (3 to 8 feet deep, no greater than 11 feet deep) encompassing open waters and along the edges of rivers, channels and sloughs.
  • Shoal regions containing submerged substrate such as vegetation rocks and roots for spawning and rearing of delta smelt, splittail and cover for chinook salmon.
  • Dead-end sloughs.
  • Flooded vegetation and vegetated open waters for spawning and rearing of splittail.
  • Deeper pools and channels for juvenile chinook to rest and rear.
  • Shaded riverine vegetation to provide cooling, cover and terrestrial insects.
  • Open water to provide zooplankton and crustaceans for juvenile salmon.
Fresh water (<2.0 parts per thousand salinity), well oxygenated (> 5.0 mg/l dissolved oxygen), and relatively cool (44-72 degrees, Fahrenheit) particularly during the winter-spring spawning season for delta smelt and splittail and the out-migration period for juvenile chinook.

Sources: Sommer et al in prep; Sweetnam and Stevens 1993; Meng 1993; Sato and Moyle 1988; Wang 1986; Daniels and Moyle 1983; Moyle 1976; Caywood 1974

  • Tule marsh to provide nesting habitat for dabbling and diving ducks and other crustacean and fish-eating birds such as grebes, coots and great blue herons.
  • A covering of water 3 feet deep or less and/or emergent vegetation over 40-85% percent of the site.
  • Mudflat and SRA habitat to provide a source of invertebrates, especially during winter.
  • Open water to provide loafing areas safe from predators.
  • Upland habitat to provide escape and nesting cover and food for breeding waterfowl.
  • Nesting island with upland vegetation.

Sources: USFWS A 1986

  • Mudflats flooded to depths of zero to 2 inches to provide (invertebrate) food sources for shorebirds.
  • Optimal shorebird habitat greater than 150 feet from disturbance areas (such as footpaths).
  • Nesting and loafing habitat, including nonvegetated or sparsely vegetated islands.

Sources: USFWS B 1986; Corps of Engineers 1990.

Questions to be Addressed by Monitoring and Monitoring Objectives

The following section describes monitoring objectives and questions expected to be addressed for each monitoring element. Additional information on individual monitoring elements detailing gear to be used, sampling methodology and the like are found in subsequent sections.

1. Fish Monitoring Element

Targeted fish and other native fish use is a criterion for successfor this restoration project. The purpose of this element is to document fish use on Prospect Island habitat features. All fish caught will be identified and recorded. General questions to be addressed by this element are:

  • What species use the various habitat structures provided on Prospect Island?
  • What is the abundance and composition of native and non-native species on Prospect Island and how does this compare to the comparison sites- deep channels and Liberty Island (naturally developing site)?
  • What may limit or enhance native and exotic fish use of Prospect Island? (This question may be answered in part by the water quality, vegetation, benthic, phytoplankton and zooplankton monitoring elements).

Objectives to address the questions are:

  • Estimate general fish species use.
  • Estimate spawner use by delta smelt and splittail. Assess associated habitat conditions.
  • Estimate larval rearing by delta smelt and splittail. Assess associated habitat conditions.
  • Estimate salmon fry/smolt use. Assess associated habitat conditions.

2. Wildlife Monitoring Element

Wildlife use is another criteria of success for this project. The purpose of this element is to document wildlife use of habitat features. Assessment of use or non-use by wildlife will be closely coordinated and tied to assessments from the vegetation monitoring element, which in turn is related to assessments from the waterquality and bathymetry monitoring elements. The general questions to be addressed by this element are:

  • What species of wildlife use the various habitat structures provided on Prospect Island?
  • What project features may limit or enhance wildlife use on Prospect Island?

Objectives associated with these questions are:

  • Quantify wildlife use in each of the following habitat types: open water, mudflats, emergent vegetation and riparian communities.
  • Assess conditions of use and/or non-use to vegetation, water quality conditions and/or physical changes of project design resulting from natural events.

3. Water Quality Monitoring Element

The purpose of this element is to document water quality conditions on Prospect Island at various aquatic habitat sites throughout the year (main channel, breach openings, open water, dead-end slough, and shallow water). Information from this element will help assess fish and wildlife use and aquatic vegetation success by providing data on temperature, specific conductance, pH, dissolved oxygen, and water velocities among other parameters. This element will also be closely tied to the phytoplankton and zooplankton monitoring elements providing information on factors that may influence the abundance and species composition of these plants and animals. In addition, data obtained from this element will be used to help assess circulation patterns throughout the Island resulting from placement of the breaches.

The general questions to be addressed are:

  • Are water quality conditions on the Island sufficient to support phytoplankton, zooplankton, targeted fish, wildlife and aquatic vegetation?
  • Are circulation patterns on the Island resulting from placement of the breaches and tidal exchange sufficient to provide adequate water quality conditions throughout the Island?

Monitoring objectives associated with these questions are:

  • Provide comprehensive water quality data on a real-time basis throughout the year at various stations representing different aquatic habitat sites.
  • Assess water quality conditions resulting from placement of the levee breaches.

4. Vegetation Monitoring Element

Open water aquatic, riparian, marsh and upland vegetation are all planned features of this project. Success of establishing vegetation depends primarily upon the interrelationships between elevation and hydrology, and subsequent plant community development. The purposes of this element are to document that targeted plant communities are or are not being established; to assess reasons for non-establishment; and to provide information on the relationships between physical processes at the project site and the response of plant communities. The water quality and bathymetry monitoring elements will also provide data that are useful for these assessments. In turn the vegetation monitoring element will provide information valuable to assessing wildlife use on Prospect Island.

Questions to be addressed by this monitoring element are:

  • What plant communities are being established on Prospect Island ?
  • How do physical processes at the project site affect the establishment of plant communities?
  • What are plant community values (diversity, percent cover, native vs. non-native plants, community structure) at elevation transect sites?

Monitoring objectives associated with these questions are:

  • Track the quality and quantity of plant communities that develop after changing land use from agricultural to tidally influenced open water and wetland habitat.
  • Document the interrelationship between physical processes at the site and the response of plant communities over the three years study.

5. Phytoplankton Monitoring Element

Phytoplankton are an important element of the food chain, and as such, are one of the criteria of "ecological success" of the Prospect restoration project. Some phytoplankton species serve as food for zooplankton which in turn serve as food for fish and other organisms. Other phytoplankton (particularly the blue-green algae) may also be indicators of poor water quality and some species cause taste and odor problems in drinking water supplies. The issue here is not simply documenting phytoplankton presence, but determining species composition and abundance and comparing those qualities to adjacent channels and the Liberty Island comparison site. This monitoring element is closely tied to water quality monitoring (water quality conditions affect and effect phytoplankton production) will also provide information relevant to assessment of the zooplankton community on Prospect Island.

Questions to be addressed through this element are:

  • What communities and quantities of phytoplankton are produced through a restoration project of this nature and how does this compare to adjacent channels and reference sites?
  • Are "good quality" phytoplankton that may provide nutritional benefits to targeted zooplankton organisms produced in sufficient quantities compared to adjacent channels and reference sites?
  • Are "problem" phytoplankton (blue-green algae) being produced in concentrations that may warrant concern (such as taste and odor problems to drinking water supplies)?
  • How do primary production rates of phytoplankton compare between deep and shallow water stations?

Monitoring objectives associated with these questions are:

  • Evaluate phytoplankton species composition, changes in chlorophyll a concentrations and primary production rates at input channels, main channels, open water, sloughs and shallow water.

6. Zooplankton Monitoring Element

Zooplankton, like phytoplankton are another important element of the aquatic food chain. Zooplankton, particularly species of copepods serve as food for many native and non-native fish. The purpose of this monitoring element is to document the composition and abundance of the zooplankton community, including mysid shrimp and amphipods, on Prospect Island and to compare those results with collections made on adjacent channels and the Liberty Island comparison site. As previously mentioned, water quality conditions and phytoplankton community structure greatly influence zooplankton abundance and composition. Therefore, care has been taken to ensure that these elements are monitored synoptically to be able to relate data developed from each element to each other.

The questions to be addressed through this element are:

  • What species and densities of zooplankton are produced and how do they compare with the Liberty Island comparison site, adjacent channels, other delta channels, and Suisun Bay?
  • Will sufficient quantities of copepods preferred by the targeted fish species be produced? Will they be produced when juvenile fish are present?
  • If the project initially fails to produce sufficient quantities of copepods can modifications be made to enable it to do so?

The objective of this element related to the questions is:

  • Quantify and evaluate zooplankton species composition, mysid shrimp, and amphipods in input channels, main channels, open water, sloughs and shallow water.

7. Benthos Monitoring Element

This sampling element proposes to collect and identify benthic organisms from Prospect Island. Soil samples will also be collected and analyzed to relate benthic communities to specific habitat conditions. Benthic (bottom dwelling) organisms are another important food source for fish and waterfowl and aquatic shorebirds. In addition to clams and other permanent benthic dwellers, many free-swimming and flying insects start their life cycle as larvae in the benthos. This monitoring element will provide descriptive information on developing benthic communities and generally assess by way of comparison with the Miner Slough and Sacramento Deep Water Ship Channel sites, this project's ability to contribute benthic derived food sources for other organisms. One element that will not be sampled is emergent insects. UC Davis was contacted for support but they are currently unable to provide a graduate student for this work.

Questions to be addressed by this monitoring element are:

  • What are the developing benthic communities on Prospect Island?
  • How do these communities relate to the substrate types upon which they are found?
  • How does the community structure (number of organisms per square meter, identification of organisms by phylum to species, life stage of organisms) compare to different habitats within and outside of Prospect Island (main channel on Prospect, vegetated and nonvegetated shallow sites, dead-end sloughs, Miner Slough and the Sacramento Deep Water Ship Channel)?

Objectives associated with these questions are:

  • Quantify and evaluate benthic macrofauna from the main channel, vegetated and nonvegetated shallow water sites on Prospect Island and compare findings to Miner Slough and the Deep Water Ship Channel.
  • Assess benthic community development with substrate composition.

8. Bathymetry Monitoring Element

The bathymetric monitoring element is included to provide above and below water elevation baseline information of important and representative project features immediately after the island is flooded and to provide information on the erosion, accretion or subsidence of these features. These features include berms, islands, levees, shallow water and the excavated channels. For example, it is assumed that project islands will initially subside a total of 1-2 feet after project flooding and will stabilize thereafter. This monitoring element will document actual subsidence.

The basic purposes of this element are:

  • To provide information on the natural succession of project features designed to provide habitat (deep channel, shallow water areas, islands, berms and levees);
  • To provide information regarding the relative success or failure of project features (project islands and berms) designed to protect adjacent levees from wind fetch.
  • To provide information on the general condition of project features (levees, berms and islands).

Questions associated with this element are:

  • What are the settling, siltation or erosion rates (natural succession) of important project features such as islands, channels, shallow water, berms and levees?
  • What is the relative success of using project islands and berms to protect levees from wind fetch?

What are the general conditions of levees and berms within Prospect Island as a result of project operation?

9. Organic Carbon Monitoring Element

This monitoring element addresses the possible contribution of the flooded habitat of organic carbon to adjacent Delta channels. Organic carbon is important both as a element in the food chain and as a potential precursor to disinfection by-products in drinking water

  • Is there a net flux of particulate and organic carbon from Prospect Island to adjacent Delta channels?
  • Which habitats within Prospect Island (dead-end sloughs, open channel, vegetated shallow-water, open shallow-water) have greater concentrations of particulate and dissolved organic carbon?
  • Which habitats have greater concentrations of disinfection by-product precursors?

In addition to the habitat benefits, some think that restoration projects of this nature (shallow water, tidal marsh) are an overall benefit to the estuarine environment by providing significant amounts of organic material that serve as nutrients and food sources for lower trophic organisms such as phytoplankton, bacteria, zooplankton. These organisms in turn serve as food for higher trophic organisms such as fish and birds. The first question addresses the issue of whether an extensive shallow water, tidal marsh habitat contributes organic carbon to Delta channels. The second question addresses the issue of which habitats within Prospect Island have greater organic material that may be correlated with fish, vegetation, phytoplankton or zooplankton concentrations.

The third question addresses the issue of whether the organic carbon found in habitats in Prospect Island is the type of organic carbon that will form carcinogenic drinking water disinfection by-products upon drinking water treatment. There has been concern that flooding peaty islands in the Delta may result in increased concentrations of disinfection by-product precursors in Delta channels. Prospect Island is within the general region of the North Bay Aqueduct which provides drinking water to Solano county. The purpose of this element is to assess water quality with regard to disinfection byproduct precursor concentrations resulting from flooding Prospect Island.

The objectives associated with this element are:

  • Determine the net flux of dissolved and particulate organic carbon to adjacent channels.
  • Determine particulate and dissolved organic carbon and disinfection by-product precursor concentrations in different habitats within Prospect Island and compare to concentrations in adjacent channels.


Caywood, M.L. 1974. Contributions to the life history of the splittail Pogonichthys macrolepidotus (Ayres). M.S. thesis. California State University, Sacramento. 77 pp.

Cramer, F.K. and D.F. Hammack. 1952. Salmon research at Deer Creek, California. U.S. Fish and Wildlife Service Spec. Sci. Rep. Fisheries 67. 16 pp.

Daniels, R.A. and P.B. Moyle. 1983. Life History of splittail (Cyprinidae: Pogonichthys macrolepidotus) in the Sacramento-San Joaquin estuary. Fish. Bull. 84:105-117.

Mitsch, W.J. and R.F. Wilson. 1996. Improving the success of wetland creation and restoration with know-how, time and self-design. Eco. App. 6(1):77-83.

Moyle, P.B. 1976. Inland Fishes of California. University of California Press, Berkeley, California. 405 pp.

Sato, G.M. and P.B. Moyle. 1989. Ecology and conservation of spring-run chinook salmon. Annual Report, Water Resources Center Project W-719, July 30, 1988-June 30, 1989.

Sommer, T.R., R. Baxter and B. Herbold. 1997. The resilience of splittail in the Sacramento-San Joaquin Estuary. Trans. Am. Fish. Soc. 126:961-976.

Sweetnam, D.A. and D.E. Stevens. 1993. A status of the delta smelt (Hypomesus transpacificus) in California. Report to the Fish and Game Commission. Candidate Species Report 93-DS. 98 pp.

U.S. Fish and Wildlife Service (A). 1986. Habitat suitability index model for Greater White-Fronted Goose (Wintering).

U.S. Fish and Wildlife Service (B). 1986. Habitat suitability index model for shorebird guild.

Wang, J.C.S. 1986. Fishes of the Sacramento-San Joaquin estuary and adjacent waters, California: A guide to the early life histories. Interagency Ecological Study Program for the Sacramento-San Joaquin Estuary, Tech. Report. 9.