SAN FRANCISCO ESTUARYESTUARYESTUARY&WAT & WATERSHED&WATERSHEDERSHED Published for the San Francisco Bay-Delta SCIENCEScience Consortium by the John Muir Institute of the Environment SAN FRANCISO ESTUARY & WATERSHED SCIENCE VOLUME 2, ISSUE 1 FEBRUARY 2004 ARTICLE 1 Open Water Processes of the San Francisco Estuary: From Physical Forcing to Biological Responses WIM KIMMERER ROMBERG TIBURON CENTER SAN FRANCISCO STATE UNIVERSITY Copyright © 2003 by the authors, unless otherwise noted. This article is part of the collected publications of San Francisco Estuary and Watershed Science. San Francisco Estuary and Watershed Science is produced by the eScholarship Repository and bepress. FEBRUARY 2004 SAN FRANCISCO ESTUARYESTUARYESTUARY&WAT & WATERSHED&WATERSHEDERSHED Published for the San Francisco Bay-Delta SCIENCEScience Consortium by the John Muir Institute of the Environment Open Water Processes annual variation in freshwater flow; in particular, abundance of several estuarine-dependent species of of the San Francisco Estuary: fish and shrimp varies positively with flow, although From Physical Forcing the mechanisms behind these relationships are largely to Biological Responses unknown. The second theme is the importance of time scales in determining the degree of interaction WIM KIMMERER between dynamic processes. Physical effects tend to ROMBERG TIBURON CENTER dominate when they operate at shorter time scales SAN FRANCISCO STATE UNIVERSITY than biological processes; when the two time scales are similar, important interactions can arise between physical and biological variability. These interactions DEDICATION can be seen, for example, in the response of phyto- plankton blooms, with characteristic time scales of I dedicate this work to the memory days, to stratification events occurring during neap of Don Kelley. tides. The third theme is the key role of introduced KEYWORDS species in all estuarine habitats; particularly notewor- thy are introduced waterweeds and fishes in the tidal Ocean, hydrology, geochemistry, tidal processes, phys- freshwater reaches of the estuary, and introduced ical forcing, fisheries, water management, water diver- clams there and in brackish water. The final theme is sions, conceptual model, San Francisco Estuary, the rather heterogeneous set of results from monitor- California ing and research in the estuary. For example, some ABSTRACT topics have been subjects of intense activity both in research and monitoring (e.g., physical dynamics of This paper reviews the current state of knowledge of the upper estuary, phytoplankton blooms), while oth- the open waters of the San Francisco Estuary. This ers have received little attention (e.g., microzooplank- estuary is well known for the extent to which it has ton). In addition, both research and monitoring have been altered through loss of wetlands, changes in emphasized some regions of the estuary (e.g., the hydrography, and the introduction of chemical and Sacramento-San Joaquin Delta) over others (e.g., San biological contaminants. It is also one of the most- Pablo Bay). In addition, ecological modeling and syn- studied estuaries in the world, with much of the thesis has emphasized lower trophic levels over high- recent research effort aimed at supporting restoration er. Opportunities for restoration in the open waters of efforts. In this review I emphasize the conceptual the estuary are somewhat limited by the lack of scien- foundations for our current understanding of estuar- tific basis for restoration, and the difficulty in detect- ine dynamics, particularly those aspects relevant to ing ecosystem responses in the context of high natu- restoration. Several themes run throughout this paper. ral variability. First is the critical role physical dynamics play in set- ting the stage for chemical and biological responses. SUGGESTED CITATION Physical forcing by the tides and by variation in freshwater input combine to control the movement of Kimmerer WJ. 2004. Open water processes of the San Francisco Estuary: from physical forcing to biological responses. the salinity field, and to establish stratification, mix- San Francisco Estuary and Watershed Science [online serial]. ing, and dilution patterns throughout the estuary. Vol. 2, Issue 1 (February 2004), Article 1. Many aspects of estuarine dynamics respond to inter- http://repositories.cdlib.org/jmie/sfews/vol2/iss1/art1 FEBRUARY 2004 SUMMARY been conducted over the last three decades on physi- cal dynamics and their implications. Patterns of Estuarine ecosystems are extraordinarily complex, freshwater flow, interacting with strong tidal currents with interactions that can be observed only indirect- and wind, produce variability on time scales from ly, and often with great difficulty. The San Francisco days to decades. Long-term changes in flow patterns Estuary is one of the most-studied estuaries in the are therefore relevant to understanding estuarine world, but it reveals its secrets slowly. Yet, we have dynamics. These patterns include direct anthro- learned a great deal about this ecosystem. In particu- pogenic controls, particularly a shift in the seasonal lar, recent years have seen revisions and refinements pattern of freshwater inflow to the Delta, and an to several key conceptual models about the estuarine increase in freshwater exports and concomitant ecosystem. These revisions have come about through decrease in net outflow from the Delta into Suisun two key elements of the regional scientific enterprise: Bay, over the last five decades. An additional tempo- an institutional commitment to long-term monitor- ral change is a continuing trend toward an earlier ing; and an active, vibrant community of scientists runoff peak apparently due to warming of the pursuing their research interests, with substantial regional climate. At the same time, sediment input to funding for research relevant to management of the the estuary has been damped, presumably by trap- estuary and its watershed. ping behind dams, with potential consequences for This paper describes my view of the current state of water clarity and for restoration of wetlands. knowledge of the open waters of the San Francisco Many aspects of estuarine dynamics respond to Estuary, which includes waters from the mouth at the freshwater flow, and distinguishing cause and effect Golden Gate to the landward limit of the tides, has proven difficult. High river flow inundates flood- encompassing San Francisco Bay, San Pablo Bay, plains, increases inputs of nutrients and other materi- Suisun Bay, and the Sacramento-San Joaquin Delta. als to the estuary, moves the salinity gradient sea- The export of large quantities of freshwater from the ward and compresses it, and reduces residence time tidal freshwater Delta is a major concern for manage- of water in most of the estuary. Freshwater flow into ment, particularly for the fish species listed under the San Francisco Estuary is indexed by "X2", the endangered species legislation. In this review I distance from the Golden Gate up the axis of the emphasize issues that seem important to management estuary to where the tidally-averaged near-bottom and restoration, in particular the conceptual founda- salinity is 2. This index has proven useful not only tions for our current understanding of estuarine as an index of flow, but also as a means of under- dynamics, and results of recent research. I also standing some of the physical dynamics of the estu- examine opportunities and constraints for restoration ary. The relationship of annual abundance or survival of the open-water subset of the estuarine ecosystem. of several estuarine-dependent species of fish and The principal themes running through this paper are: shrimp to springtime X2 values has led to a salinity (1) the central role of physical dynamics including standard for the estuary, as well as to an interest in freshwater flow in setting the stage for chemical and the mechanisms underlying these relationships. biological responses; (2) the importance of time Our understanding of how these freshwater flow pat- scales in determining the degree of interaction terns play out in the estuary has changed markedly between dynamic processes; (3) the key role of intro- in the last decade with the development of revised duced species in the estuarine foodweb; and (4) the conceptual models emphasizing dynamic over static heterogeneity of scientific information developed by conditions. For example, a previous model of the the regional research community. estuary depicted the Delta as a river-like system of The importance of physical dynamics in structuring unidirectional flows, with a flow pattern generally oceanic and estuarine systems has been known for westward toward the ocean, and southward toward over a century, but we are still learning the details. the export pumping facilities. Through field studies In the San Francisco Estuary, extensive research has and simulation modeling this view has been sup- SAN FRANCISCO ESTUARY & WATERSHED SCIENCE planted by a dynamic model recognizing the key role tidal energy, influenced by lowered salinity in Central of tides in moving water; even in the western Delta Bay due to high Delta outflow, local stream inputs in under most conditions tidal flows exceed net, river- South Bay, and wind. Field and modeling studies have derived flows. These tidal flows are not merely oscil- explored the consequences of stratification in promot- lations but result in intense mixing and transport of ing phytoplankton blooms that occur predictably