Primary production in context

Estuaries and freshwater wetlands are some of the most productive ecosystems on Earth. These systems support a diverse array of plants, algae, invertebrates, fish, and other aquatic consumers, in turn providing resources for birds, humans, and other connected ecosystems. At the base of the estuarine food web, algae and plants in wetlands and open water fix carbon from the atmosphere into biomass through photosynthesis. This primary production is a first-order control on the carrying capacity for fish and other aquatic consumers.

The historical Sacramento-San Joaquin Delta was a highly productive freshwater estuary. As the largest tidal marsh on the North American Pacific coast, the extensive wetlands of the historical Delta provided habitat and year-round food for fish and other wildlife. Primary production in the historical Delta supported California’s largest salmon runs, bird migrations on the Pacific Flyway, now-threatened, endemic species such as Delta smelt, hundreds of other wildlife species, and many people in the Native American communities of the region. 

In the modern Delta, primary production has largely been converted to human use

Wetland conversion to agriculture has led to a near-complete loss of tidal and non-tidal marshes, eliminated many small tidal channels and straightened large ones, and reduced hydrological connectivity between land and water. The Delta of today remains highly productive as an agricultural region, but at great cost to the native aquatic ecosystem. While Delta phytoplankton production is known to be low relative to other estuaries, the impacts of wetland loss on primary production across a suite of producers has received little study.  

Although these habitat losses have profoundly altered Delta ecosystems, the modern Delta supports many ecological functions and services. The Delta is home to a range of invertebrates, fish, birds, and other aquatic organisms. However, it is well recognized that changes to the status quo are necessary to maintain and improve ecological health, water supply reliability and the resilience of the Delta’s landforms relative to earthquakes and flooding.  Management actions to improve primary productivity, such as habitat restoration, enable managers to support desired ecological communities, particularly when and where they are limited by food availability. Managing effectively for primary productivity requires empirical information on the relative production value of habitat types and configurations (such as marsh size and channel network structure).

Project goals and scope

The Delta Landscapes Primary Production project addresses the question: How has landscape change in the Delta altered the quantity and character of primary production that is potentially available for the aquatic food web?  To evaluate historical changes in primary production, we estimated primary production in the historical (early 1800s) and modern Delta (early 2000s) for wet and dry years, as a result of changes in the extent of hydrologically connected habitats. We quantified changes in Delta-wide production from major producer groups and habitat types, which translate to changes in the portfolio of production entering the aquatic food web. 

This project was designed with decision makers in mind. Metrics of primary production in the historical Delta—the magnitude and composition of primary production entering the historical food web—provide meaningful context for restoration and management decisions. By comparing production rates in wet vs. dry years, we can identify habitat types in the Delta where primary production is responsive to water-availability variations. Additionally, our framework and areal productivity rates can be used to estimate the effect of restoration targets on Delta-wide primary production. 

Report and Appendix


In Delta Landscapes Primary Production, completed in 2020, SFEI researchers and a panel of expert scientists evaluated how landscape change in the Delta has affected the primary production at the base of the aquatic food web.


Mapping Landscape Change in the Delta

The historical and modern hydrologically connected Delta.

The historical and modern hydrologically connected Delta. Landscape change has deeply altered the primary production engine of the Delta. By appropriating productivity for the human food web (agriculture), we have removed nearly all wetlands and most of the riparian vegetation that historically contributed to the base of the aquatic food web. We have created new types of seasonal floodplains and increased the area of open water, augmenting the importance of these habitat types for supporting aquatic food webs

Humans have modified Delta ecosystems in a multitude of ways over the last 200 years. In this highly altered system that faces multiple stressors, this project isolated the effects of one broad change, wetland habitat loss, on one key metric of ecological function: primary production available to the aquatic food web. Other variables related to human impacts were held constant, including nutrient loads, sediment supply, hydrology (e.g., flow regime and precipitation), and the presence of invasive clams.

Within the Delta, we identified the “hydrologically connected Delta,” which we define as the region of open water, wetlands, and other seasonally flooded habitats that are connected via surface flows. This highly productive region contributes plant and algal biomass to the aquatic ecosystems.

We evaluated changes in the hydrologically connected Delta by mapping its historical (early 1800s) and modern (early 2000s) extent for wet and dry years. Resulting maps of the historical hydrologically connected Delta include four dominant habitat types: open water, tidal marsh, non-tidal marsh, and riparian forest/scrub (Table 1). The modern Delta includes a fifth habitat type, other seasonal floodplain, defined as other periodically inundated areas (like agricultural fields, managed wetlands, and grasslands) that are not located behind a levee. A detailed description of the landscape change analysis method can be found in the online appendix (below).

Habitat Type Definition Historical* (Acres) Modern* (Acres) Change (%)
Open Water Mostly permanently inundated areas devoid of emergent vegetation including tidal and fluvial channels, ponds/lakes, and flooded islands. Can also include some seasonally or temporarily flooded depressions, largely devoid of emergent palustrine vegetation (e.g. large vernal pools). 36,000 62,500 +73%
Tidal marsh Perennially wet areas with a high water table dominated by emergent vegetation and at least periodically wetted/inundated by tidal flows 361,200 7,800 -98%
Non-tidal marsh Temporarily to permanently flooded, permanently saturated, freshwater non-tidal wetlands dominated by emergent vegetation occupying upstream floodplain positions above tidal influence. 109,300 1,500 -99%
Riparian forest/scrub Riparian vegetation dominated by woody trees, scrub, or shrubs generally occupying elevated, periodically flooded areas along channels. 55,000 12,100 -78%
Other seasonal floodplain Other seasonally or temporarily flooded areas that are connected to the aquatic ecosystem via surface flows, including agricultural areas, managed wetlands, grasslands, and other areas dominated by short-statured herbaceous vegetation. Largely located within the Yolo Bypass and other floodplains along the Cosumnes and San Joaquin rivers. 0 46,900
Total (all habitat types)   561,600 130,900 -77%
Table 1: Changes in the hydrologically-connected area of major Delta habitat types between the historical and modern eras (shown for wet years only).

Most of the Delta has been disconnected from the aquatic food web. This change was mainly due to loss of tidal and riverine floodplain wetlands.

Estimating Primary Production

Five categories of primary producers within the hydrologically connected Delta contribute to the aquatic food web.

Producer Group Expert Scientist Description
Phytoplankton James Cloern (USGS) Occurring in all habitat types except riparian forest/scrub, phytoplankton are microalgae suspended in the water column.
Attached microalgae James Pinckney (University of South Carolina) Occurring in all habitat types, attached microalgae are benthic algae growing in or on sediments and epiphytic algae on vegetation.
Marsh plants Judith Drexler (USGS) Occurring in tidal marsh and non-tidal marsh habitat types, marsh plants are emergent freshwater macrophytes (e.g., tules).
Aquatic plants Katharyn Boyer and Melissa Patten (San Francisco State University) Occurring in the open water habitat type, aquatic plants include aquatic macrophytes that are rooted or float on the water surface, as well as associated attached macroalgae.
Woody riparian plants Robert Naiman (University of Washington) Occurring in the riparian forest/scrub habitat type, woody riparian plants include trees, shrubs, and their woody and herbaceous understory. Our analysis is limited to material that could potentially enter the aquatic ecosystem (e.g., trees and their litter that fall into adjacent waterways or plant material captured by meandering channels).
Table 2: Estimation Methods by producer group. These producers were identified by a panel of expert scientists and grouped according to major commonalities (Table 2). These categories are meant to be comprehensive, covering all sources of primary production originating in the hydrologically connected Delta. Many of these groups contain a diverse array of producers, but reflect similar habitat associations.

For each producer group, expert science advisors used relatively simple models and equations to derive estimates of production across the hydrologically connected Delta, measured in kilotonnes of carbon per year (kt C/yr). Estimates are of net primary production (NPP), which measures the amount of carbon fixed through photosynthesis that is actually stored as biomass (the total amount of captured energy minus the portion used by the primary producers for their own metabolism/cellular respiration).

Producer Group Estimation Method
Phytoplankton We used a generalized additive model to estimate productivity as a function of water depth and season. Modeled productivity rates were scaled to annual Delta-wide production according to habitat area, depth class, duration of inundation, and light limitation.
Attached microalgae We used separate calculations for three types of attached microalgae: (1) benthic microalgae, (2) epiphytes on emergent vegetation, and (3) epiphytes on aquatic plants. For each type, median literature-based values of areal productivity were scaled to annual Delta-wide production according to habitat area, duration of inundation, and light limitation.
Marsh plants We estimated annual aboveground productivity from literature values of peak standing biomass. These productivity rates were scaled to annual Delta-wide production according to marsh habitat area and the fraction of organic carbon in standing biomass.
Aquatic plants We used remote sensing data and plant species lists from historical and modern periods to estimate the percent cover of dominant aquatic plant species. For each dominant species, literature-based values of areal productivity were scaled to annual Delta-wide production according to open water habitat area and percent cover by depth class.
Woody riparian plants We identified three processes by which riparian production enters the aquatic ecosystem: (1) litterfall, including leaf litter and small woody debris; (2) channel meandering, which contributes woody and herbaceous standing vegetation, and (3) tree mortality, which contributes large woody debris. For litter inputs, annual litterfall rates from the Central Valley were applied to the Delta’s riparian forest/scrub areas (their full extent in wet years and the subset within 25 m of open water in dry years. For channel meandering, literature-based values of ecosystem carbon storage were used with the length of meandering channels and lateral channel migration rates to estimate carbon inputs to the aquatic ecosystem. Annual Delta-wide inputs from tree mortality were estimated from standing aboveground carbon stocks and mortality rates, scaled to the width of the contributing band along the length of the bank.
Table 3. Estimation Methods by producer group.

Regional Restoration Targets

Would achieving regional habitat restoration targets dramatically increase primary production?

The approach developed here can be used to estimate primary production gains from acheiving restoration targets. The draft amendment to Chapter 4 of the Delta Plan (“Protect, Restore, and Enhance the Delta Ecosystem”), sets areal restoration targets for a suite of Delta natural community types, described in Preliminary Draft Performance Measure 4.16. Translated to the habitat types defined in this project, these targets would result in an approximate 2.6-fold increase in total tidal marsh area (+32,500 acres), a 4.8-fold increase in non-tidal marsh (+19,000 acres), and a 2.2-fold increase in riparian forest/scrub (+16,300 acres).

The historical and modern hydrologically connected Delta.

Changes to areal habitat type extents due to restoration targets.

Report and Appendix


In Delta Landscapes Primary Production, completed in 2020, SFEI researchers and a panel of expert scientists evaluated how landscape change in the Delta has affected the primary production at the base of the aquatic food web.


Estimates of primary production

Landscape change, largely the loss of marshes, has reduced primary production that is potentially available to aquatic consumers by more than 90% . 

The loss of marsh and riparian forest/scrub has led to a dramatic reduction in primary production in the hydrologically connected Delta. Marshes contributed over 95% of the primary production in the historical hydrologically connected area. In stark contrast, around half of all primary production in the modern hydrologically connected Delta comes from open water areas.

Despite their precipitous declines, marshes remain important for primary production in the modern Delta. Although only 2% of their historical area remains, tidal and non-tidal marsh contribute ~30% of total annual primary production to the Delta’s aquatic food web, reflecting the high productivity of marshes on a per-area basis (approximately 4 times as high as other habitat types).  

Restoring marshes that are hydrologically connected to aquatic ecosystems in the Delta is an efficient way to increase year-round food resources for aquatic consumers. During the growing season, marshes support grazing invertebrates and the production of attached microalgae and phytoplankton, important resources for Delta fish. During other times of year, decaying marsh vegetation fuels the detrital food web, which in turn supports a range of higher consumers. 

In the modern Delta, other seasonal floodplain areas are a source of primary production to aquatic ecosystems when inundated. There, the extent, depth, and duration of flooding exert strong controls on phytoplankton and attached microalgae growth. By prioritizing flooding in this habitat type, water managers in the Delta may increase aquatic food web support.  This finding is consistent with empirical data and successes associated with managing the Yolo bypass to benefit fish.

The primary production portfolio

For many decision makers in the Delta, primary production is valued as support for fish and other aquatic consumers. Seen this way, not all sources of primary production have equal value. 

The portfolio of production in the modern hydrologically connected Delta bears little resemblance to its historical counterpart. The shift in primary production from wetland-based to open-water based sources has altered relative production from the five producer groups. Marsh plants and attached microalgae were the major sources of primary production in the historical hydrologically connected Delta, whereas the modern-day Delta is dominated by aquatic plants and their associated macroalgae. Notably, the proportion of NPP from open-water phytoplankton has increased by an order of magnitude since the historical era, now accounting for an estimated 15-20% of total primary production.


As food for aquatic consumers, the various producer groups offer different nutritional profiles. Additionally, the timing, location, and connectivity of primary production sets the environmental stage for consumers, with life stage, energetic demands, foraging efficiency, predation and competition all controlling the efficiency with which primary production is assimilated by consumers. Marshes in particular offer indirect benefits that have been lost in the modern Delta. Although marsh vegetation is a relatively low-quality food source compared to algae, marsh plants provide spawning surfaces, protection from predators, and water clarity improvement via sediment trapping. As a food source, they provide year-round inputs to the aquatic food web, as fresh biomass in the growing season, as slow-decomposing litter fueling the detrital food web continuously through the year, and as a surface for nutritious microalgae to attach.

Restoring a portfolio of habitat types and primary producers in the Delta that better reflects the environment in which fish and other native aquatic wildlife once thrived may help native populations recover.

Restoration targets and primary production

Delta Plan targets for wetland restoration have the potential to nearly triple primary production in the hydrologically connected Delta and rebalance the portfolio of production toward more wetland-based sources. With large increases in production from marsh plants and attached microalgae, restoration at this scale would provide food for fish, grazing invertebrates, and the detrital food web.

Delta Plan targets would cause a nearly 7-fold increase in marsh plant production, a 4-fold increase in attached microalgae, and a near doubling of carbon inputs from woody riparian plants. These gains would recover approximately 12% of the annual primary production lost since the historical era, increasing contemporary primary production from 6% to 17% of its historical magnitude.  

Report and Appendix


In Delta Landscapes Primary Production, completed in 2020, SFEI researchers and a panel of expert scientists evaluated how landscape change in the Delta has affected the primary production at the base of the aquatic food web.


Programs and Focus Areas: 
Resilient Landscapes Program
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