An Introduction to the San Francisco Estuary

Bay Institute | April 8th, 2012

San Francisco Bay enters most of our lives as an obstacle to pass over as quickly as traffic-choked bridges allow. Although this beats earlier attitudes—when we saw the

San Francisco Bay enters most of our lives as an obstacle to pass over as quickly as traffic-choked bridges allow. Although this beats earlier attitudes—when we saw the Bay mainly as a dumping ground, a dam site, or a pit to fill in and pave over—we remain largely oblivious to one of the most remarkable wild resources in urban North America. Beneath our wheels lies a world of interesting and outlandish life, with much that puzzles even the scientists who regularly plumb its depths.

An ongoing shift in Pacific Ocean sea level

American Geophysical Union (AGU) | July 30th, 2016

Based on the satellite altimeter data, sea level off the west coast of the United States has increased over the past 5 years, while sea level in the western tropical Pac

Based on the satellite altimeter data, sea level off the west coast of the United States has increased over the past 5 years, while sea level in the western tropical Pacific has declined. Understanding whether this is a short-term shift or the beginning of a longer-term change in sea level has important implications for coastal planning efforts in the coming decades. Here, we identify and quantify the recent shift in Pacific Ocean sea level, and also seek to describe the variability in a manner consistent with recent descriptions of El Nino-Southern Oscillation (ENSO) and particularly the Pacific Decadal Oscillation (PDO). More specifically, we extract two dominant modes of sea level variability, one related to the biennial oscillation associated with ENSO and the other representative of lower-frequency variability with a strong signal in the northern Pacific. We rely on cyclostationary empirical orthogonal function (CSEOF) analysis along with sea level reconstructions to describe these modes and provide historical context for the recent sea level changes observed in the Pacific. As a result, we find that a shift in sea level has occurred in the Pacific Ocean over the past few years that will likely persist in the coming years, leading to substantially higher sea level off the west coast of the United States and lower sea level in the western tropical Pacific.

An overview of multi-dimensional models of the Sacramento-San Joaquin Delta

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

Over the past fifteen years, the development and application of models in San Francisco Bay and the Sacramento-San Joaquin Delta has transformed our ability to analyze an

Over the past fifteen years, the development and application of models in San Francisco Bay and the Sacramento-San Joaquin Delta has transformed our ability to analyze and understand the underlying physics of the system. Initial applications of three-dimensional models focused primarily on salt intrusion, and provided a valuable resource for investigating how sea level rise and levee failures in the Delta could influence water quality in the Delta in the future. However, multi-dimensional models have also provided significant insights into some of the fundamental biological relationships that have shaped our thinking about the system by exploring the relationship between X2, flow, fish abundance, and the low salinity zone. Through modeling, it has been possible to move beyond salinity to understand how large-scale changes to the system are likely to affect sediment dynamics, and to assess the potential effects on species that rely on turbidity for habitat. Lastly, the coupling of multi-dimensional hydrodynamic models with particle tracking models has led to advances in our thinking about residence time, the retention of food organisms, the effect of south Delta exports on larval entrainment, and the pathways and behaviors of salmonids that travel through the Delta. This chapter provides an overview of these recent advances and how they have increased our understanding of the distribution and movement of fish and food organisms. The applications presented serve as a guide to the current state of the science of Delta modeling and provide examples of how we can use multidimensional models to predict how future Delta conditions will affect both fish and water supply.  

An unprecedented coastwide toxic algal bloom linked to anomalous ocean conditions

American Geophysical Union (AGU) | October 9th, 2016

A coastwide bloom of the toxigenic diatom Pseudo-nitzschiain spring 2015 resulted in the largest recorded outbreak of the neurotoxin, domoic acid, along the North Ameri

A coastwide bloom of the toxigenic diatom Pseudo-nitzschiain spring 2015 resulted in the largest recorded outbreak of the neurotoxin, domoic acid, along the North American west coast. Elevated toxins were measured in numerous stranded marine mammals and resulted in geographically extensive and prolonged closures of razor clam, rock crab, and Dungeness crab fisheries. We demonstrate that this outbreak was initiated by anomalously warm ocean conditions. Pseudo-nitzschia australis thrived north of its typical range in the warm, nutrient-poor water that spanned the northeast Pacific in early 2015. The seasonal transition to upwelling provided the nutrients necessary for a large-scale bloom; a series of spring storms delivered the bloom to the coast. Laboratory and field experiments confirming maximum growth rates with elevated temperatures and enhanced toxin production with nutrient enrichment, together with a retrospective analysis of toxic events, demonstrate the potential for similarly devastating ecological and economic disruptions in the future.

An Update of the Death Valley Regional Groundwater Flow System Transient Model, Nevada and California

U.S. Geological Survey (USGS) | October 31st, 2016

The U.S. Geological Survey (USGS) has revised the regional-scale Death Valley regional groundwater flow system (DVRFS) numerical model with new data and interpretations s

The U.S. Geological Survey (USGS) has revised the regional-scale Death Valley regional groundwater flow system (DVRFS) numerical model with new data and interpretations since the original numerical flow model was published in 2004 (Belcher (2004); re-published as Belcher and Sweetkind [2010]). Since the original publication of the DVRFS flow model, additional data have been collected and interpretations have been made. Cooperators such as the Bureau of Land Management, National Park Service, U.S. Fish and Wildlife Service, the Department of Energy, and Nye County, Nevada, recognized a need to update the existing regional numerical flow model to maintain its viability as a groundwater management tool for regional stakeholders. For the purposes of this report, the version of the DVRFS numerical flow model documented in Belcher and Sweetkind (2010) and Faunt, Blainey, and others (2010) is designated as DVRFS v. 1.0. The updated version, as presented in this report, is referred to as DVRFS v. 2.0. Knowledge of basin water balances and the magnitude of interbasin groundwater flow is the basis for regional groundwater management and water-resource planning in the Great Basin of Nevada (Scott and others, 1971). Rapid population growth, arid conditions, and increased water use have led to development of available groundwater resources. Groundwater use in some alluvial-fill basins has resulted in continued water-level declines and land subsidence. Adjacent bedrock aquifers are increasingly being targeted for additional development. Such groundwater development may potentially impact local and regional water quantity and quality, existing water rights, and wildlife habitats. An understanding of hydrogeologic processes that control the rate and direction of groundwater flow in southern Nevada is necessary to assess the potential effects of any proposed large-scale groundwater development. Potential water-resource conflicts exist because of disparate interests in the region, particularly with respect to the development of groundwater resources to meet agricultural, municipal, and industrial water demand and the need to protect habitat for endangered and threatened species. Water demands in the Amargosa Farms area from agricultural and suburban development, and rapidly urbanizing areas in Las Vegas and Pahrump Valleys place increasing pressure on existing groundwater resources. In addition, several solar-energy facilities have been proposed within the Death Valley region; water demands for these facilities will vary. Natural groundwater discharge at springs and seeps sustains habitat for numerous species, many of which are threatened, endangered, or otherwise considered sensitive. In 2004, the USGS documented a calibrated numerical flow model of the DVRFS (Belcher, 2004). The model, DVRFS v. 1.0, incorporated elements of several precursor numerical models but defined the boundaries of the regional flow system slightly different than in previous versions. The model simulates transient groundwater flow conditions in the DVRFS from 1913 through 1998. The report was subsequently revised and published as a USGS Professional Paper (Belcher and Sweetkind, 2010). Since release of DVRFS v. 1.0 in 2004, continued use of the model by cooperators, stakeholders, and interested parties in the region has demonstrated the need to improve specific aspects (such as the flow into northern Yucca Flat and parts of the Amargosa Desert), to update it with more recently acquired geologic and hydrologic data, and to extend the simulation period.

Anadromous Salmonid Fish Passage Facility Design

National Marine Fisheries Service (NMFS) | July 26th, 2011

The primary effect of barriers (e.g., hydroelectric dams, water storage projects, irrigation diversions, impassable culverts, etc.) on Pacific salmonids is the reduction

The primary effect of barriers (e.g., hydroelectric dams, water storage projects, irrigation diversions, impassable culverts, etc.) on Pacific salmonids is the reduction in population abundance and productivity through excessive mortality and reduction in habitat quantity and quality. Individuals are lost to the population due to death from passing through turbines, disproportionate predation in reservoirs, entrainment at unscreened or improperly screened diversions, etc. Spatial structure and diversity have also been reduced by the loss of nearly 40% of salmon habitat from dams (NRC 1996), either through complete blockage or inundation. This document is intended to assist with improving conditions for salmonids that must migrate past barriers to complete their life cycle. The task involved in successfully passing fish upstream or downstream of an in-river impediment is a dynamic integration of fish behavior, physiology, and bio-mechanics with hydraulic analysis, hydrologic study, and engineering. Installing a fish passage structure does not constitute providing satisfactory fish passage unless all of the above components are adequately factored into the design. The following document provides criteria, rationale, guidelines, and definitions for the purpose of designing proper fish passage facilities for the safe, timely, and efficient upstream and downstream passage of anadromous salmonids at impediments created by artificial structures, natural barriers (where provision of fish passage is consistent with management objectives), or altered instream hydraulic conditions. This document provides fishway facility design standards for the National Marine Fisheries Service, and is to be used for actions pertaining to the various authorities and jurisdictions of NMFS, including Section 18 of the Federal Power Act (FPA), the Endangered Species Act (ESA), and the Magnuson-Stevens Fishery Conservation and Management Act (MSA) in the Northwest Region (NWR). This document intends to provide generic guidance as an alternative to active participation by NMFS engineers in a design process, for the purpose of providing designs that will be acceptable for fishways that fall within NMFS jurisdictions. If passage facilities are designed and constructed in a manner consistent with these criteria, adverse impacts to anadromous fish migration will be minimized. Instances will occur where a fish passage facility may not be a viable solution for correcting a passage impediment, due to biological, sociological, or economic constraints. In these situations, removal of the impediment or altering operations may be a suitable surrogate for a constructed fish passage facility. In other situations, accomplishing fish passage may not be an objective of NMFS because of factors such as limited habitat or lack of naturally occurring runs of anadromous fish upstream of the site. To determine whether NMFS will use its various authorities to promote or to prescribe fish passage, NMFS will rely on a collaborative approach, considering the views of other fisheries resource agencies, Native American Tribes, non-government organizations, and citizen groups, and will strive to accomplish the objectives in watershed plans for fisheries restoration and enhancement. This document does not address aspects of design other than those that provide for safe and timely fish passage, and to some extent, preservation of aquatic habitat. Structural integrity, public safety, and other aspects of facility design are the responsibility of the principal design engineer, who should ensure that the final facility design meets all other requirements in addition to the fish passage criteria and guidelines contained in this document.

Anadromous Salmonids in the Delta: New Science 2006-2016

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

As juvenile salmon enter the Delta, they disperse among its complex channel network where they are subject to channel-specific processes that affect their rate of migrati

As juvenile salmon enter the Delta, they disperse among its complex channel network where they are subject to channel-specific processes that affect their rate of migration, vulnerability to predation, feeding success, growth rates, and ultimately, survival. In the decades before 2006, tools available to quantify growth, dispersal, and survival of juvenile salmon in this channel network were limited. Fortunately, thanks to technological advances, much has been learned over the past decade about the role of the Delta in the life cycle of juvenile salmon. One of the most important advances during the past decade has been the widespread adoption of acoustic telemetry techniques. Use of telemetry has shed light on how survival varies among alternative migration routes and the proportion of fish that use each migration route. Chemical and structural analysis have provided insights about when juveniles left their natal river and provided evidence of extended rearing in the brackish or saltwater regions of the Delta. New advancements in genetics now allow individuals captured by trawls to be assigned to specific runs. Detailed information about movement and survival in the Delta has spurred development of agent-based models of juvenile salmon that are coupled to hydrodynamic models. Although much has been learned, knowledge gaps remain about how very small juvenile salmon (fry and parr) use the Delta. Understanding how all life stages of juvenile salmon grow, rear, and survive in the Delta is critical for devising management strategies that support a diversity of life history strategies.

Analog Model Study of the Ground-Water Basin of the Upper Coachella Valley, California

U.S. Geological Survey (USGS) | July 18th, 1974

An analog model of the ground-water basin of the upper Coachella Valley was constructed to determine the effects of imported water on ground-water levels. The mod

An analog model of the ground-water basin of the upper Coachella Valley was constructed to determine the effects of imported water on ground-water levels. The model was considered verified when the ground-water levels generated by the model approximated the historical change in water levels of the ground-water basin caused by man's activities for the period 1936-67. The ground-water basin was almost unaffected by man's activities until about 1945 when ground-water development caused the water levels to begin to decline. The Palm Springs area has had the largest water-level decline, 75 feet since 1936, because of large pumpage, reduced natural inflow from the San Gorgonio Pass area, and diversions of natural inflows at Snow and Falls Creeks and Chino Canyon starting in 1945. The San Gorgonio Pass inflow had been reduced from about 13,000 acre-feet in 1936 to about 9,000 acre-feet by 1967 because of increased ground-water pumpage in the San Gorgonio Pass area, dewatering of the San Gorgonio Pass area that took place when the tunnel for the Metropolitan Water District of Southern California was drilled, and diversions ofsurface inflow at Snow and Falls Creeks. In addition, 1944-64 was a period of below-normal precipitation which, in part, contributed to the declines in water levels in the Coachella Valley. The Desert Hot Springs, Garnet Hill, and Mission Creek subbasins have had relatively little development; consequently, the water-level declines have been small, ranging from 5 to 15 feet since 1936. In the Point Happy area a decline of about 2 feet per year continued until 1949 when delivery of Colorado River water to the lower valley through the Coachella Canal was initiated. Since 1949 the water levels in the Point Happy area have been rising and by 1967 were above their 1936 levels. The Whitewater River subbasin includes the largest aquifer in the basin, having sustained ground-water pumpage of about 740,000 acre-feet from 1936 to 1967, and will probably continue to provide the most significant supply of ground water for the upper valley. The total ground-water storage depletion for the entire upper valley for 1936-67 was about 600,000 acre-feet, an average stor age decrease of about 25,000 acre-feet per year since 1945. Transmissivity for the Whitewater River subbasin ranges from 360,000 gal- lons per day per foot (near Point Happy) to 50,000 gallons per day per foot, with most of the subbasin about 300,000 gallons per day per foot. In contrast, the transmissivities of the Desert Hot Springs, Mission Creek, and Garnet Hill sub-basins generally range from 2,000 to 100,000, but the highest value, beneath the Mission Creek streambed deposits, is 200,000 gallons per day per foot; the transmissivity for most of the area of the three subbasins is 30,000 gallons per day per foot. The storage coefficients are representative of water-table conditions, ranging from 0.18 beneath the Mission Creek stream deposits to 0.06 in the Palm Springs area. The model indicated that the outflow at Point Happy decreased from 50,000 acre-feet in 1936 to 30,000 acre-feet by 1967 as a result of the rising water levels in the lower valley. The most logical area to recharge the Colorado River water is the Windy Point-Whitewater area, where adequate percolation rates of 2 4 acre-feet per acre per day are probable. The Whitewater River bed may be the best location to spread the water if the largest part of the imported water can be recharged during low-flow periods. The area in sec. 21, T. 2 S., R. 4 E., would be adequate for the smaller quantities of recharge proposed for the Mission Creek area. Projected pumpage for the period 1968-2000 was programed on the model with the proposed recharge of Colorado River water for the same period. The model indicated a maximum water-level increase of 200 feet above the 1967 water level at Windy Point, the proposed recharge site, by the year 2000, a 130-foot increase by 1990, and a 20-foot increase by 1980. The model indicated that the proposed quantities of recharge will beneficially affect the ground-water system to Palm Desert by 1980, to Point Happy by 1990, and possibly to the Coachella Canal by 2000. The model indicated that the upper and lower valleys are within the same hydrologic system, and it has been proposed that the model be extended to the Salton Sea. On the basis of the available analyses, changes in the quality of ground water in the Whitewater River subbasin after recharge apparently will be, as a first approximation, proportional to the ratio in which the quantity of recharge and the quantity of ground water are mixed. Where mixing does not occur, the quality of the recharge water will probably not be greatly changed by ion-exchange phenomenon.

Analyses of Rotary Screw Trap Sampling of Migrating Juvenile Chinook Salmon in the Stanislaus River, 1996-2005

Delta Stewardship Council (Delta Council) | August 1st, 2006

Analysis and simulation of regional subsidence accompanying groundwater abstraction and compaction of susceptible aquifer systems in the USA

Mexican Geological Society (Sociedad Geológica Mexicana) | January 17th, 2013

Regional aquifer-system compaction and land subsidence accompanying groundwater abstraction in susceptible aquifer systems in the USA is a challenge for managing groundwa

Regional aquifer-system compaction and land subsidence accompanying groundwater abstraction in susceptible aquifer systems in the USA is a challenge for managing groundwater resources and mitigating associated hazards. Developments in the assessment of regional subsidence provide more information to constrain analyses and simulation of aquifer-system compaction. Current popular approaches to simulating vertical aquifer-system deformation (compaction), such as those embodied in the aquitard drainage model and the MODFLOW subsidence packages, have proven useful from the perspective of regional groundwater resources assessment. However, these approaches inadequately address related local-scale hazards—ground ruptures and damages to engineered structures on the land surface arising from tensional stresses and strains accompanying groundwater abstraction. This paper presents a brief overview of the general approaches taken by the U.S. Geological Survey toward understanding aquifer-system compaction and subsidence with regard to a) identifying the affected aquifer systems; b) making regional assessments; c) analyzing the governing processes; and d) simulating historical and future groundwater flow and subsidence conditions. Limitations and shortcomings of these approaches, as well as future challenges also are discussed