Novato Creek Baylands Historical Ecology Study

San Francisco Estuary Institute (SFEI) | July 31st, 2015

Over the past century and a half, lower Novato Creek and the surrounding tidal wetlands have been heavily modified for flood control and land reclamation purposes. Levees

Over the past century and a half, lower Novato Creek and the surrounding tidal wetlands have been heavily modified for flood control and land reclamation purposes. Levees were built in the tidal portion of the mainstem channel beginning in the late 1800s to convey flood flows out to San Pablo Bay more rapidly and to remove surrounding areas from inundation. Following levee construction, the wetlands surrounding the channel were drained and converted to agricultural, residential, and industrial areas. These changes have resulted in a considerable loss of wetland habitat, reduced sediment transport to marshes and the Bay, and an overall decreased resilience of the system to sea level rise. In addition to tidal wetland modification, land use changes upstream in the Novato Creek watershed have resulted in several challenges for flood control management. Dam construction and increased runoff in the upper watershed have resulted in elevated rates of channel incision, which have increased transport of fine sediment from the upper watershed to lower Novato Creek. Channelization of tributaries and construction of irrigation ditches have likely increased drainage density in the upper watershed, also potentially contributing to increased rates of channel incision and fine sediment production (Collins 1998). Downstream, sediment transport capacity has been reduced by construction of a railroad crossing and loss of tidal prism and channel capacity associated with the diking of the surrounding marsh. As a result of the increased fine sediment supply from the watershed and the loss of sediment transport capacity in lower Novato Creek, sediment aggradation occurs within the channel, which in turn reduces the flood capacity of the channel, necessitating periodic dredging (fig. 1; Collins 1998, PWA 2002).

Nutrient Dynamics of the Delta: Effects on Primary Producers

University of California, Davis (UC Davis) | December 1st, 2016

Increasing clarity of Delta waters, the emergence of harmful algal blooms, the growth of aquatic water weeds, and the altered food web of the Delta have recently brought

Increasing clarity of Delta waters, the emergence of harmful algal blooms, the growth of aquatic water weeds, and the altered food web of the Delta have recently brought nutrient dynamics to the forefront. This paper focuses on the sources of nutrients, the transformation and uptake of nutrients, and the links of nutrients to primary producers. The largest loads of nutrients to the Delta come from the Sacramento River with the San Joaquin River seasonally important, especially in the summer. Light regime, grazing pressure, and nutrient availability influence rates of primary production at different times and locations within the Delta. Modern sensor technology and networks are now deployed that make high frequency measurements of nitrate, ammonium, and phosphate. Data from such instruments allow a much more detailed assessment of the spatial and temporal dynamics of nutrients. Four fruitful directions for future research include utilizing continuous sensor data to estimate rates of primary production and ecosystem respiration, linking models of the Delta with the transport and fate of dissolved nutrients, studying nutrient dynamics in various habitat types, and exploring the use of stable isotopes to trace the movement and fate of effluent-derived nutrients.

Nutrient Fluxes from Sediments in the San Francisco Bay Delta

Estuaries and Coasts (Springer) | January 1st, 2014

In September 2011 and March 2012, benthic nutrient fluxes were measured in the San Francisco Bay Delta, across a gradient from above the confluence of the Sacramento and

In September 2011 and March 2012, benthic nutrient fluxes were measured in the San Francisco Bay Delta, across a gradient from above the confluence of the Sacramento and San Joaquin Rivers to Suisun Bay. Dark and illuminated core incubation techniques were used to mea- sure rates of denitrification, nutrient fluxes (phosphate, ammonium, nitrate), and oxygen fluxes. While benthic nutrient fluxes have been assessed at several sites in northern San Francisco Bay, such data across a Delta–Bay transect have not previously been determined. Average September rates of DIN (nitrate, nitrite, ammonium) flux were net positive across all sites, while March DIN flux indicated net uptake of DIN at some sites. Denitrification rates based on the N2/Ar ratio approach were between 0.6 and 1.0 mmol m−2 day−1, similar to other mesotrophic estuarine sediments. Coupled nitrifica- tion–denitrification was the dominant denitrification pathway in September, with higher overlying water nitrate concentra- tions in March resulting in denitrification driven by nitrate flux into the sediments. Estimated benthic microalgal productivity was variable and surprisingly high in Delta sediments and may represent a major source of labile carbon to this ecosystem. Variable N/P stoichiometry was observed in these sediments, with deviations from Redfield driven by processes such as denitrification, variable light/dark uptake of nutrients by microalgae, and adsorption of soluble reactive phosphorus.

Nutrient Management Strategy Science Plan Report

San Francisco Estuary Institute (SFEI) | September 9th, 2016

The San Francisco Bay (SFB) estuary receives large inputs of the nutrients nitrogen and phosphorous from anthropogenic sources, and has the potential to suffer negative

The San Francisco Bay (SFB) estuary receives large inputs of the nutrients nitrogen and phosphorous from anthropogenic sources, and has the potential to suffer negative impacts from nutrient overenrichment. Nutrient concentrations in SFB exceed those in other estuarine ecosystems where degradation is strongly expressed. To date, SFB has shown resistance to some of the classic symptoms of nutrient over-enrichment, such as excessive phytoplankton biomass as chlorophyll-a (chl-a) and low dissolved oxygen (DO). Recent observations, however, suggest that SFB’s resistance to nutrient enrichment is weakening, and have generated concern that SFB may be trending toward, or may already be experiencing, adverse impacts due to its high nutrient loads. In response to these concerns, the San Francisco Bay Regional Water Quality Control Board (SFBRWQCB) worked collaboratively with stakeholders to develop the San Francisco Bay Nutrient Management Strategy (NMS).1 The NMS lays out an overall approach for developing the underlying science to support nutrient management decisions. This report presents a Draft Science Plan for implementing the SFB NMS. The report’s main goals include: Lay out a multi-year Science Plan representing a logical sequence of studies to inform major management decisions, assuming a time-line of 10+ years. Develop an approach and rationale for sequencing and prioritizing among studies, and identify specific high-priority studies, in particular those that should proceed in FY2016- 2018. Provide realistic estimates of the time-frame and funding needed to support a Science Plan that will successfully inform management decisions. The Draft Science Plan was developed in 2014-15 with input from science advisors (Table 1.1), the NMS Steering Committee, and the NMS Nutrient Technical Work Group (Fig. 1.1). Projects are described in more detail in the first 1-3 years, and in increasingly less detail over time, recognizing that the Science Plan will be iteratively refined based on new insights gained as work progresses.

Nutrient Management Strategy Science Program

San Francisco Estuary Institute (SFEI) | September 1st, 2017

San Francisco Bay (SFB) receives large inputs of the nutrients nitrogen (N) and phosphorous (P) from anthropogenic sources. N and P are essential components of a healthy

San Francisco Bay (SFB) receives large inputs of the nutrients nitrogen (N) and phosphorous (P) from anthropogenic sources. N and P are essential components of a healthy estuary, supporting primary production at the base of the food web. However, ambient N and P concentrations in SFB exceed those in many other estuarine ecosystems, including those considered eutrophic1 and that experience nutrient-related impairment, such as excessive phytoplankton blooms and prolonged periods of low dissolved oxygen (DO). Unlike those other nutrient-enriched estuaries, though, SFB has exhibited resistance to classic eutrophication symptoms. Recent observations, however, suggest that SFB’s resistance to nutrient enrichment is weakening (e.g., Cloern et al., 2007; Cloern et al., 2010; SFEI 2014a).  These San Francisco Bay Nutrient Management Strategy (NMS) Science Program was launched in 2014 to develop the scientific foundation to support nutrient management decisions. The NMS Steering Committee, representing 13 stakeholder groups (regulators, dischargers, water purveyors, NGOs, resource agencies) oversees the NMS’ implementation, including financial oversight and alignment of NMS science activities with high priority management questions. The San Francisco Estuary Institute (SFEI) serves as the technical lead on implementing the NMS Science Program. SFEI staff work with regional collaborators to carry out NMS projects, including field investigations, monitoring, and data interpretation. 

Observational Study of Sycamore Regeneration at two sites in Santa Clara County after the 2016-2017 Water Year

San Francisco Estuary Institute (SFEI) | June 1st, 2018

This memo serves as an update to the Sycamore Alluvial Woodland Habitat Mapping and Regeneration Study (Beagle et al. 2017), and describes changes seen at the two study s

This memo serves as an update to the Sycamore Alluvial Woodland Habitat Mapping and Regeneration Study (Beagle et al. 2017), and describes changes seen at the two study sites, Upper Coyote Creek and Pacheco Creek, between fall 2015 and fall 2017. We were tasked with augmenting tree core data as reported in 2017 by adding additional trees to further investigate the relationship between sycamore establishment and geomorphic position, which partially serves as a proxy for the role flood processes play in improving the suitability of conditions for sycamore seedling establishment and growth. Coincidentally, major flooding during water year 2016-2017 provided us with an exciting opportunity to observe sycamore regeneration at these two study sites. This memo reports on tree coring results; documents and maps sycamore seedlings and other observed regeneration strategies of sycamores during 2018 related to geomorphic change at the two study sites; proposes natural and anthropogenic drivers of sycamore regeneration; and outlines next steps for further investigation. 

Old and Middle River Flow Review: USGS Gauge Readings versus Index Calculations for 2011 through 2017

California Department of Water Resources (DWR) | November 17th, 2017

This report will demonstrate the strong flow correlation between the United States Geological Survey gages at the Old and Middle Rivers (USGS OMR), and the OMR Index calc

This report will demonstrate the strong flow correlation between the United States Geological Survey gages at the Old and Middle Rivers (USGS OMR), and the OMR Index calculations, which have been used by the State Water Project and the Central Valley Project (the Projects) to operate to, and comply with, Old and Middle River (OMR) flow requirements. The results of the two different methodologies for determining OMR will be compared with daily, 5-day average, and 14-day average values, and will demonstrate a close correlation and tracking between the two methodologies. The time-span will be from December to June of the Water Years 2011 to 2017 and gives a background view and general effectiveness of using the OMR Index. The difference between the methodologies is that the USGS OMR values are based on tidally filtered hourly flow values of Old and Middle Rivers near Bacon Island, whereas the Index methodology uses an empirical equation based on net flows into and out of the Southern Delta. The USGS OMR flow values have been difficult for the Projects to operate to, in large part because the tidally filtering calculation is lagged by three days. What’s more, atmospheric conditions exert an unpredictable influence on OMR values and missing data introduces errors. By contrast, the OMR Index is much easier to work with because the San Joaquin River at Vernalis (VNS) gage used in the OMR Index equation is located upstream of the Delta and is therefore not affected significantly by tidal effects or atmospheric conditions and has only a one-day delay in the OMR Index equation. Using prior day flows from the VNS gage allows the Projects’ operations to be more predictable since current day exports can be closely controlled. Through regression analysis and empirical graphs, this report will show that the OMR Index method produces results that are closely correlated with values from the USGS OMR. And since the Index method can be used to closely approximate the USGS OMR flow values over an averaging period, the Index method is a satisfactory alternative to using the lagged USGS OMR flow data for real-time operations.

Order Approving Temporary Urgency Changes to Water Right License and Permit Terms Relating to Delta Water Quality Objectives

California State Water Resources Control Board (SWRCB) | February 21st, 2023

Our Vision for the California Delta

Delta Vision Blue Ribbon Task Force (Delta Vision) | March 19th, 2008

Our Vision for the California Delta

Delta Vision Blue Ribbon Task Force (Delta Vision) | March 19th, 2008

Executive Order S-17-06, directed us to “develop a durable vision for sustainable management of the Delta” with the goal of “...managing the Delta over the long te

Executive Order S-17-06, directed us to “develop a durable vision for sustainable management of the Delta” with the goal of “...managing the Delta over the long term to restore and maintain identified functions and values that are determined to be important to the environmental quality of the Delta and the economic and social well being of the people of the state.” The executive order calls for our vision to be completed by January 1, 2008 and a strategic plan by November 2008.