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. 

Nutrients in the Nation’s Streams and Groundwater, 1992–2004

U.S. Geological Survey (USGS) | June 6th, 2011

This report is one of a series of publications, The Quality of Our Nation’s Waters, which describes major findings of the NAWQA Program on water-quality issues of regio

This report is one of a series of publications, The Quality of Our Nation’s Waters, which describes major findings of the NAWQA Program on water-quality issues of regional and national concern. This report presents an assessment of the occurrence and distribution of nutrients in the Nation’s streams and groundwater based on water-quality data from about 500 streams and over 5,000 wells collected from 1992 through 2001. Other topics addressed include the relation of nutrient conditions to aquatic life in streams, changes in nutrient conditions from 1988 through 2004, and implications for future changes. The information in this series is intended primarily for those interested or involved in resource management and protection, conservation, regulation, and policy-making at regional and national levels. In addition, the information is relevant to those at a local level who wish to know more about the general quality of streams and groundwater in areas near where they live and how that quality compares with other areas across the Nation.

Nutrients in the Nation’s Streams and Groundwater: National Findings and Implications

U.S. Geological Survey (USGS) | September 1st, 2010

A comprehensive national analysis of the distribution and trends of nutrient concentrations in streams and groundwater from 1992 through 2004 is provided by

A comprehensive national analysis of the distribution and trends of nutrient concentrations in streams and groundwater from 1992 through 2004 is provided by the National Water-Quality Assessment (NAWQA) Program of the United States Geological Survey (USGS). Findings describe the distribution and causes of varying nutrient concentrations in streams and groundwater throughout the Nation and examine the primary sources that contribute to elevated concentrations. Results show that excessive nutrient enrichment is a widespread cause of ecological degradation in streams and that nitrate contamination of groundwater used for drinking water, particularly shallow domestic wells in agricultural areas, is a continuing human-health concern. Finally, despite major Federal, State and local non-point-source nutrient control efforts for streams and watersheds across the Nation, USGS trend analyses for 1993–2003 suggest limited national progress to reduce the impacts of non-point sources of nutrients during this period. Instead, concentrations have remained the same or increased in many streams and aquifers across the nation, and continue to pose risks to aquatic life and human health. This Fact Sheet highlights selected national fndings and their implications, and serves as a companion product to the complete analysis reported in the USGS Circular titled “The Quality of Our Nation’s Waters—Nutrients in the Nation’s Streams and Groundwater, 1992–2004.”

Oases of the future? Springs as potential hydrologic refugia in drying climates

Ecological Society of America (Wiley) | June 1st, 2020

Natural springs in water‐limited landscapes are biodiversity hotspots and keystone ecosystems that have a disproportionate influence on surrounding landscapes despite t

Natural springs in water‐limited landscapes are biodiversity hotspots and keystone ecosystems that have a disproportionate influence on surrounding landscapes despite their usually small size. Some springs served as evolutionary refugia during previous climate drying, supporting relict species in isolated habitats. Understanding whether springs will provide hydrologic refugia from future climate change is important to biodiversity conservation but is complicated by hydrologic variability among springs, data limitations, and multiple non‐climate threats to groundwater‐dependent ecosystems. We present a conceptual framework for categorizing springs as potentially stable, relative, or transient hydrologic refugia in a drying climate. Clues about the refugial capacity of springs can be assembled from various approaches, including citizen‐science‐powered ecohydrologic monitoring, remote sensing, landowner interviews, and environmental tracer analysis. Managers can integrate multiple lines of evidence to predict which springs may become future refugia for species of concern, strengthening the long‐term effectiveness of their conservation and restoration, and informing climate adaptation for terrestrial and freshwater species.

Objective definition of rainfall intensity-duration thresholds for the initiation of post-fire debris flows in southern California

Landslides (Springer) | June 27th, 2012

Rainfall intensity–duration (ID) thresholds are commonly used to predict the temporal occurrence of debris flows and shallow landslides. Typically, thresholds are sub

Rainfall intensity–duration (ID) thresholds are commonly used to predict the temporal occurrence of debris flows and shallow landslides. Typically, thresholds are subjectively defined as the upper limit of peak rainstorm intensities that do not produce debris flows and landslides, or as the lower limit of peak rainstorm intensities that initiate debris flows and landslides. In addition, peak rainstorm intensities are often used to define thresholds, as data regarding the precise timing of debris flows and associated rainfall intensities are usually not available, and rainfall characteristics are often estimated from distant gauging locations. Here, we attempt to improve the performance of existing threshold-based predictions of post-fire debris-flow occurrence by utilizing data on the precise timing of debris flows relative to rainfall intensity, and develop an objective method to define the threshold intensities. We objectively defined the thresholds by maximizing the number of correct predictions of debris flow occurrence while minimizing the rate of both Type I (false positive) and Type II (false negative) errors. We identified that (1) there were statistically significant differences between peak storm and triggering intensities, (2) the objectively defined threshold model presents a better balance between predictive success, false alarms and failed alarms than previous subjectively defined thresholds, (3) thresholds based on measurements of rainfall intensity over shorter duration (≤60min) are better predictors of post-fire debris-flow initiation than longer duration thresholds, and (4) the objectively defined thresholds were exceeded prior to the recorded time of debris flow at frequencies similar to or better than subjective thresholds. Our findings highlight the need to better constrain the timing and processes of initiation of landslides and debris flows for future threshold studies. In addition, the methods used to define rainfall thresholds in this study represent a computationally simple means of deriving critical values for other studies of nonlinear phenomena characterized by thresholds.

Observational evidence of increased afternoon rainfall downwind of irrigated areas

Nature Portfolio (Springer Nature) | April 10th, 2025

Irrigation plays a vital role in addressing the growing food demand of an increasing global population. It represents one of the most critical and direct human interventi

Irrigation plays a vital role in addressing the growing food demand of an increasing global population. It represents one of the most critical and direct human interventions on the coupled water and energy cycles. As irrigated farmland continues to expand, understanding the climate impact of extensive irrigation becomes increasingly important. Yet, the effect on rainfall patterns near irrigated areas remains unclear. Here, using two global, high-resolution, sub-daily precipitation datasets, we show that afternoon rain events occur more often 10 km to 50 km downwind and less often upwind of extensively irrigated land. However, we also find that the total amount of heavy afternoon rain downwind of irrigated areas is lower than upwind. Our results establish large-scale observational evidence of the local precipitation dynamics surrounding irrigated areas; these insights will help constrain the representation of these processes in next-generation climate and weather forecasting models and provide valuable insights for regional water management.

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. 

Observations of the spawning ecology of the imperiled Clear Lake Hitch

California Department of Fish and Wildlife (CDFW) | October 13th, 2019

Observed and anticipated impacts of drought on forest insects and diseases in the United States

Forest Ecology and Management (Elsevier) | May 11th, 2016

Future anthropogenic-induced changes to the earth’s climate will likely include increases in temperature and changes in precipitation that will increase the fre

Future anthropogenic-induced changes to the earth’s climate will likely include increases in temperature and changes in precipitation that will increase the frequency and severity of droughts. Insects and fungal diseases are important disturbances in forests, yet understanding of the role of drought in outbreaks of these agents is limited. Current knowledge concerning the effects of drought on herbivorous insect and pathogen outbreaks in U.S. forests is reviewed, and compared between the relatively mesic and structurally diverse forests of the eastern U.S. and the more xeric forests of the western U.S. Theory and limited evidence suggests a non-linear relationship between drought intensity and outbreaks of aggressive bark beetle species (i.e., those capable of causing extensive levels of tree mortality), where moderate droughts reduce bark beetle population performance and subsequent tree mortality, whereas intense droughts, which frequently occur in the western U.S., increase bark beetle performance and tree mortality. There is little evidence for a role of drought in outbreaks of the southern pine beetle (Dendroctonus frontalis), the only bark beetle species that causes large amounts of tree mortality in the eastern U.S. Defoliators do not show consistent responses to drought. The response of sap-feeders to drought appears non-linear, with the greatest performance and impacts at intermediate drought intensity or when drought is alleviated by wetter periods. Interactions between tree pathogens and drought are poorly understood, but available evidence suggests reduced pathogen performance and host impacts in response to drought for primary pathogens and pathogens whose lifecycle depends directly on mois- ture (humidity). In these cases, rates of reproduction, spread, and infection tend to be greater when conditions are moist. In contrast, secondary fungal pathogens (i.e., those that depend on stressed hosts for colonization) are anticipated to respond to drought with greater performance and host impacts. In the western U.S., drought increases stress on trees severely infected by mistletoes thereby predisposing mistletoe-infected trees to attack by insects, particularly bark beetles and wood borers. Research needed to advance understanding of drought impacts on forest insects and diseases, and the role of forest man- agement in mitigation of infestations during drought are discussed.

Observed and projected changes in snow accumulation and snowline in California’s snowy mountains

Climate Dynamics (Springer) | May 25th, 2023

The Sierra Nevada and Southern Cascades—California’s snowy mountains—are primary freshwater sources and natural reservoirs for the states of California and Nevada.

The Sierra Nevada and Southern Cascades—California’s snowy mountains—are primary freshwater sources and natural reservoirs for the states of California and Nevada. These mountains receive precipitation overwhelmingly from wintertime storms including atmospheric rivers (ARs), much of it falling as snow at the higher elevations. Using a seven-decade record of daily observed temperature and precipitation as well as a snow reanalysis and downscaled climate projections, we documented historical and future changes in snow accumulation and snowlines. In four key subregions of California’s snowy mountains, we quantified the progressing contribution of ARs and non-AR storms to the evolving and projected snow accumulation and snowlines (elevation of the snow-to-rain transition), exploring their climatology, variability and trends. Historically, snow makes up roughly a third of the precipitation affecting California’s mountains. While ARs make up only a quarter of all precipitating days and, due to their relative warmth, produce snowlines higher than do other storms, they contribute over 40% of the total seasonal snow. Under projected unabated warming, snow accumulation would decline to less than half of historical by the late twenty-first century, with the greatest snow loss at mid elevations (from 1500 to 3300 m by the mountain sub-regions) during fall and spring. Central and Southern Sierra Nevada peaks above 3400 m might see occasionally extreme snow accumulations in January–February resulting entirely from wetter ARs. AR-related snowlines are projected to increase by more than 700 m, compared to about 500 m for other storms. We discuss likely impacts of the changing climate for water resources as well as for winter recreation.