Drivers of change in estuarine-coastal ecosystems: Discoveries from four decades of study in San Francisco Bay

Reviews of Geophysics

Volumn 50, Issue 4, 2012, Pages

  Cloern, James E ^a   Jassby, Alan D ^b  

^a U S GEOLOGICAL SURVEY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

drivers; environmental change; estuarine coastal; monitoring; policy; San Francisco Bay

Indexed keywords

CLIMATE CHANGE; ECOSYSTEMS; ENVIRONMENTAL PROTECTION; MARINE POLLUTION; MONITORING; NUTRIENTS; PUBLIC POLICY; RIVER POLLUTION; SEWAGE; TRUCK DRIVERS; WATER QUALITY;

ENVIRONMENTAL CHANGE; ENVIRONMENTAL MONITORING; ENVIRONMENTAL POLICY; ESTUARINE COASTAL; MONITORING PROGRAMS; NUTRIENT ENRICHMENTS; PLANKTON COMMUNITIES; SAN FRANCISCO BAY;

ESTUARIES;

EID: 85082809916     PISSN: 87551209     EISSN: 19449208     Source Type: Journal    
DOI: 10.1029/2012RG000397     Document Type: Article

References (212)

1. Alpine, A. E., and J. E. Cloern (1992), Trophic interactions and direct physical effects control phytoplankton biomass and production in an estuary, Limnol. Oceanogr., 37(5), 946–955, doi:10.4319/lo.1992.37.5.0946.
2. Arthur, J. F., M. D. Ball, and S. Y. Baughman (1996), Summary of federal and state water project environmental impacts in the San Francisco Bay-Delta estuary, California, in San Francisco Bay: The Ecosystem, edited by J. T. Hollibaugh, pp. 445–495, Pac. Div. of the Am. Assoc. for the Adv. of Sci., San Francisco, Calif.
3. Attrill, M. J. (Ed.) (1998), A Rehabilitated Estuarine Ecosystem: The Environment and Ecology of the Thames Estuary, Kluwer Acad., Dordrecht, Netherlands.
4. Attrill, M. J., and M. Power (2002), Climatic influence on a marine fish assemblage, Nature, 417(6886), 275–278, doi:10.1038/417275a.
5. Baltensweiler, W. (1964), Zeiraphera griseana Hübner (Lepidoptera: Tortricidae) in the European Alps A contribution to the problem of cycles, Can. Entomol., 96, 792–800, doi:10.4039/Ent96792-5.
6. Barnosky, A. D., et al. (2012), Approaching a state shift in Earth's biosphere, Nature, 486(7401), 52–58, doi:10.1038/nature11018.
7. Baron, J. S., N. L. Poff, P. L. Angermeier, C. N. Dahm, P. H. Gleick, N. G. J. Hairston, R. B. Jackson, C. A. Hohnston, B. D. Richter, and A. D. Steinman (2002), Meeting the ecological and societal needs for freshwater, Ecol. Appl., 12(5), 1247–1260, doi:10.1890/1051-0761(2002)012[1247:MEASNF]2.0.CO;2.
8. Bay Delta Conservation Plan (BDCP) (2010), Highlights of the BDCP, report, San Francisco, Calif. [Available at http://resources.ca.gov/docs/Highlights_of_the_BDCP_FINAL_12-14-10_2361.pdf.]
9. Beck, H. J., and G. F. Birch (2012), Metals, nutrients and total suspended solids discharged during different flow conditions in highly urbanised catchments, Environ. Monit. Assess., 184(2), 637–653, doi:10.1007/s10661-011-1992-z.
10. Bennett, W. A. (2005), Critical assessment of the delta smelt population in the San Francisco Estuary, California, San Francisco Estuary Watershed Sci., 3(2), 1–73. [Available at http://escholarship.org/uc/item/0725n5vk.]
11. Beukema, J. J., and R. Dekker (2005), Decline of recruitment success in cockles and other bivalves in the Wadden Sea: Possible role of climate change, predation on postlarvae and fisheries, Mar. Ecol. Prog. Ser., 287, 149–167, doi:10.3354/meps287149.
12. Blum, M. D., and H. H. Roberts (2009), Drowning of the Mississippi Delta due to insufficient sediment supply and global sea-level rise, Nat. Geosci., 2, 488–491, doi:10.1038/ngeo553.
13. Borja, Á., I. Muxika, and J. Franco (2006), Long-term recovery of soft-bottom benthos following urban and industrial sewage treatment in the Nervión estuary (southern Bay of Biscay), Mar. Ecol. Prog. Ser., 313, 43–55, doi:10.3354/meps313043.
14. Bricker, S., B. Longstaff, W. Dennison, A. Jones, K. Boicourt, C. Wicks, and J. Woerner (2007), Effects of Nutrient Enrichment In the Nation's Estuaries: A Decade of Change, NOAA Coastal Ocean Prog. Decis. Anal. Ser., vol. 26, 328 pp., Natl. Cent. for Coastal Ocean Sci., Silver Spring, Md.
15. Brooks, M. L., et al. (2012), Life histories, salinity zones, and sublethal contributions of contaminants to pelagic fish declines illustrated with a case study of San Francisco Estuary, California, USA, Estuaries Coasts, 35(2), 603–621, doi:10.1007/s12237-011-9459-6.
16. Brosnan, T. M., and M. L. O'Shea (1996), Sewage abatement and coliform bacteria trends in the lower Hudson-Raritan Estuary since passage of the Clean Water Act, Water Environ. Res., 68, 25–35, doi:10.2175/106143096X127181.
17. Brown, L. R., and D. Michniuk (2007), Littoral fish assemblages of the alien-dominated Sacramento–San Joaquin Delta, California, 1980–1983 and 2001–2003, Estuaries Coasts, 30, 186–200.
18. Brown, L. R., and P. B. Moyle (2005), Native fishes of the Sacramento–San Joaquin drainage, California: A history of decline, Am. Fish. Soc. Symp., 45, 75–98.
19. Brown, T. C., and P. Froemke (2012), Nationwide assessment of nonpoint source threats to water quality, BioScience, 62(2), 136–146, doi:10.1525/bio.2012.62.2.7.
20. Burt, T. P., N. J. K. Howden, F. Worrall, and M. J. Whelan (2010), Long-term monitoring of river water nitrate: How much data do we need?, J. Environ. Monit., 12(1), 71–79, doi:10.1039/b913003a.
21. California Department of Water Resources (CADWR) (1993), Dams within jurisdiction of the state of California, Bull. Calif. Dep. Water Resour., 17–93, Sacramento, Calif.
22. California Department of Water Resources (CADWR) (2007), California Central Valley unimpaired flow data, 4th edition, report, Sacramento, Calif.
23. Carlton, J. T., and J. B. Geller (1993), The global transport of nonindigenous marine organisms, Science, 261(5117), 78–82, doi:10.1126/science.261.5117.78.
24. Carlton, J. T., J. K. Thompson, L. E. Schemel, and F. H. Nichols (1990), Remarkable invasion of San Francisco Bay (California, USA) by the Asian clam Potamocorbula amurensis. I. Introduction and dispersal, Mar. Ecol. Prog. Ser., 66, 81–94, doi:10.3354/meps066081.
25. Carnegie, R. B., and E. M. Burreson (2011), Declining impact of an introduced pathogen: Haplosporidium nelsoni in the oyster Crassostrea virginica in Chesapeake Bay, Mar. Ecol. Prog. Ser., 432, 1–15, doi:10.3354/meps09221.
26. Carotenuto, Y., A. Ianora, and A. Miralto (2011), Maternal and neonate diatom diets impair development and sex differentiation in the copepod Temora stylifera, J. Exp. Mar. Biol. Ecol., 396(2), 99–107, doi:10.1016/j.jembe.2010.10.012.
27. Carpenter, S. R., et al. (2011), Early warnings of regime shifts: A whole-ecosystem experiment, Science, 332(6033), 1079–1082, doi:10.1126/science.1203672.
28. Carstensen, J., M. Sanchez-Camacho, C. M. Duarte, D. Krause-Jensen, and N. Marba (2011), Connecting the dots: Responses of coastal ecosystems to changing nutrient concentrations, Environ. Sci. Technol., 45(21), 9122–9132, doi:10.1021/es202351y.
29. Catry, T., et al. (2011), Long-term declines of wader populations at the Tagus estuary, Portugal: A response to global or local factors?, Bird Conserv. Int., 21(04), 438–453, doi:10.1017/S0959270910000626.
30. Chambers, J. M. (1992), Linear models, in Statistical Models in S, edited by J. M. Chambers and T. J. Hastie, pp. 95–144, Wadsworth and Brooks, Pacific Grove, Calif.
31. Chauvaud, L., F. Jean, O. Ragueneau, and G. Thouzeau (2000), Long-term variation of the Bay of Brest ecosystem: Benthic-pelagic coupling revisited, Mar. Ecol. Prog. Ser., 200, 35–48, doi:10.3354/meps200035.
32. 2 generators: The Potamocorbula amurensis example in San Francisco Bay, Limnol. Oceanogr., 48(6), 2086–2092, doi:10.4319/lo.2003.48.6.2086.
33. Chenillat, F., P. Rivière, X. Capet, E. Di Lorenzo, and B. Blanke (2012), North Pacific Gyre Oscillation modulates seasonal timing and ecosystem functioning in the California Current upwelling system, Geophys. Res. Lett., 39, L01606, doi:10.1029/2011GL049966.
34. Clavero, M., and E. García-Berthou (2005), Invasive species are a leading cause of animal extinctions, Trends Ecol. Evol., 20, 110, doi:10.1016/j.tree.2005.01.003.
35. Cloern, J. E. (1982), Does the benthos control phytoplankton biomass in South San Francisco Bay?, Mar. Ecol. Prog. Ser., 9, 191–202, doi:10.3354/meps009191.
36. Cloern, J. E. (1987), Turbidity as a control on phytoplankton biomass and productivity in estuaries, Cont. Shelf Res., 7(11–12), 1367–1381, doi:10.1016/0278-4343(87)90042-2.
37. Cloern, J. E. (1996), Phytoplankton bloom dynamics in coastal ecosystems: A review with some general lessons from sustained investigation of San Francisco Bay, California, Rev. Geophys., 34(2), 127–168, doi:10.1029/96RG00986.
38. Cloern, J. E. (1999), The relative importance of light and nutrient limitation of phytoplankton growth: A simple index of coastal ecosystem sensitivity to nutrient enrichment, Aquat. Ecol., 33, 3–15, doi:10.1023/A:1009952125558.
39. Cloern, J. E. (2001), Our evolving conceptual model of the coastal eutrophication problem, Mar. Ecol. Prog. Ser., 210, 223–253, doi:10.3354/meps210223.
40. Cloern, J. E. (2007), Habitat connectivity and ecosystem productivity: Implications from a simple model, Am. Nat., 169(1), E21–E33, doi:10.1086/510258.
41. Cloern, J. E., and R. Dufford (2005), Phytoplankton community ecology: Principles applied in San Francisco Bay, Mar. Ecol. Prog. Ser., 285, 11–28, doi:10.3354/meps285011.
42. Cloern, J. E., and A. D. Jassby (2008), Complex seasonal patterns of primary producers at the land-sea interface, Ecol. Lett., 11(12), 1294–1303, doi:10.1111/j.1461-0248.2008.01244.x.
43. Cloern, J. E., A. E. Alpine, B. E. Cole, R. L. J. Wong, J. F. Arthur, and M. D. Ball (1983), River discharge controls phytoplankton dynamics in the northern San Francisco Bay estuary, Estuarine Coastal Shelf Sci., 16, 415–429, doi:10.1016/0272-7714(83)90103-8.
44. Cloern, J. E., B. E. Cole, R. L. J. Wong, and A. E. Alpine (1985), Temporal dynamics of estuarine phytoplankton: A case study of San Francisco Bay, Hydrobiologia, 129(1), 153–176, doi:10.1007/BF00048693.
45. Cloern, J. E., T. S. Schraga, C. B. Lopez, N. Knowles, R. G. Labiosa, and R. Dugdale (2005), Climate anomalies generate an exceptional dinoflagellate bloom in San Francisco Bay, Geophys. Res. Lett., 32, L14608, doi:10.1029/2005GL023321.
46. Cloern, J. E., A. D. Jassby, J. K. Thompson, and K. A. Hieb (2007), A cold phase of the East Pacific triggers new phytoplankton blooms in San Francisco Bay, Proc. Natl. Acad. Sci. U. S. A., 104(47), 18,561–18,565, doi:10.1073/pnas.0706151104.
47. Cloern, J. E., et al. (2010), Biological communities in San Francisco Bay track large-scale climate forcing over the North Pacific, Geophys. Res. Lett., 37, L21602, doi:10.1029/2010GL044774.
48. Cloern, J. E., et al. (2011), Projected evolution of California's San Francisco Bay-Delta-River System in a century of climate change, PLoS ONE, 6(9), e24465, doi:10.1371/journal.pone.0024465.
49. Cohen, A. N., and J. T. Carlton (1998), Accelerating invasion rate in a highly invaded estuary, Science, 279, 555–558, doi:10.1126/science.279.5350.555.
50. Cohn, T. A., D. L. Caulder, E. J. Gilroy, L. D. Zynjuk, and R. M. Summers (1992), The validity of a simple statistical model for estimating fluvial constituent loads: An empirical study involving nutrient loads entering Chesapeake Bay, Water Resour. Res., 28(9), 2353–2363, doi:10.1029/92WR01008.
51. Cole, B. E., and J. E. Cloern (1984), Significance of biomass and light availability to phytoplankton productivity in San Francisco Bay, Mar. Ecol. Prog. Ser., 17, 15–24, doi:10.3354/meps017015.
52. Cole, B. E., J. K. Thompson, and J. E. Cloern (1992), Measurement of filtration rates by infaunal bivalves in a recirculating flume, Mar. Biol., 113(2), 219–225.
53. Conley, D. J., S. Markager, J. Andersen, T. Ellermann, and L. M. Svendsen (2002), Coastal eutrophication and the Danish National Aquatic Monitoring and Assessment Program, Estuaries, 25, 848–861, doi:10.1007/BF02804910.
54. Conomos, T. J. (1979), San Francisco Bay: The Urbanized Estuary, Pac. Div. of the Am. Assoc. for the Adv. of Sci., San Francisco, Calif.
55. Cyr, H., and I. Cyr (2003), Temporal scaling of temperature variability from land to oceans, Evol. Ecol. Res., 5(8), 1183–1197.
56. Daskalov, G. M., and E. V. Mamedov (2007), Integrated fisheries assessment and possible causes for the collapse of anchovy kilka in the Caspian Sea, ICES J. Mar. Sci., 64(3), 503–511, doi:10.1093/icesjms/fsl047.
57. Diaz, R. J., and R. Rosenberg (2008), Spreading dead zones and consequences for marine ecosystems, Science, 321(5891), 926–929, doi:10.1126/science.1156401.
58. Di Lorenzo, E., et al. (2008), North Pacific Gyre Oscillation links ocean climate and ecosystem change, Geophys. Res. Lett., 35, L08607, doi:10.1029/2007GL032838.
59. Dobson, J. (2000), Long term trends in trace metals in biota in the Forth Estuary, Scotland, 1981–1999, Mar. Pollut. Bull., 40(12), 1214–1220, doi:10.1016/S0025-326X(00)00189-2.
60. Duffy, T. A., A. E. McElroy, and D. O. Conover (2009), Variable susceptibility and response to estrogenic chemicals in Menidia menidia, Mar. Ecol. Prog. Ser., 380, 245–254, doi:10.3354/meps07928.
61. Dynesius, M., and C. Nilsson (1994), Fragmentation and flow regulation of river systems in the northern third the world, Science, 266(5186), 753–762, doi:10.1126/science.266.5186.753.
62. Elton, C. S. (1927), Animal Ecology, Sidgwick and Jackson, London.
63. Enright, C., and S. D. Culberson (2010), Salinity trends, variability, and control in the northern reach of the San Francisco Estuary, San Francisco Estuary Watershed Sci., 7(2), 1–28. [Available at http://escholarship.org/uc/item/0d52737t.]
64. Fan, H., and H. Huang (2008), Response of coastal marine eco-environment to river fluxes into the sea: A case study of the Huanghe (Yellow) River mouth and adjacent waters, Mar. Environ. Res., 65(5), 378–387, doi:10.1016/j.marenvres.2008.01.003.
65. Feyrer, F., B. Herbold, S. A. Matern, and P. B. Moyle (2003), Dietary shifts in a stressed fish assemblage: Consequences of a bivalve invasion in the San Francisco Estuary, Environ. Biol. Fishes, 67, 277–288, doi:10.1023/A:1025839132274.
66. Feyrer, F., K. Newman, M. Nobriga, and T. Sommer (2011), Modeling the effects of future outflow on the abiotic habitat of an imperiled estuarine fish, Estuaries Coasts, 34(1), 120–128, doi:10.1007/s12237-010-9343-9.
67. Fleming, S. W. (2008), Approximate record length constraints for experimental identification of dynamical fractals, Ann. Phys., 17(12), 955–969, doi:10.1002/andp.200810329.
68. Gallegos, C. L., P. J. Werdell, and C. R. McClain (2011), Long-term changes in light scattering in Chesapeake Bay inferred from Secchi depth, light attenuation, and remote sensing measurements, J. Geophys. Res., 116, C00H08, doi:10.1029/2011JC007160.
69. Gilbert, G. K. (1917), Hydraulic mining debris in the Sierra Nevada, U.S. Geol. Surv. Prof. Pap., 105, 154 pp.
70. Gisiger, T. (2001), Scale invariance in biology: Coincidence or footprint of a universal mechanism?, Biol. Rev. Camb. Philos. Soc., 76, 161–209, doi:10.1017/S1464793101005607.
71. Gleick, P. H., and M. Palaniappan (2010), Peak water limits to freshwater withdrawal and use, Proc. Natl. Acad. Sci. U. S. A., 107(25), 11,155–11,162, doi:10.1073/pnas.1004812107.
72. Gowen, R. J., P. Tett, and K. J. Jones (1992), Predicting marine eutrophication: The yield of chlorophyll from nitrogen in Scottish coastal waters, Mar. Ecol. Prog. Ser., 85, 153–161, doi:10.3354/meps085153.
73. Greene, V. E., L. J. Sullivan, J. K. Thompson, and W. J. Kimmerer (2011), Grazing impact of the invasive clam Corbula amurensis on the microplankton assemblage of the northern San Francisco Estuary, Mar. Ecol. Prog. Ser., 431, 183–193, doi:10.3354/meps09099.
74. Greening, H. S., and A. Janicki (2006), Toward reversal of eutrophic conditions in a subtropical estuary: Water quality and seagrass response to nitrogen loading reductions in Tampa Bay, Florida, USA, Environ. Manage. N. Y., 38(2), 163–178, doi:10.1007/s00267-005-0079-4.
75. Greening, H. S., L. M. Cross, and E. T. Sherwood (2011), A multiscale approach to seagrass recovery in Tampa Bay, Florida, Ecol. Res., 29, 82–93, doi:10.3368/er.29.1-2.82.
76. Grenier, J. L., and J. A. Davis (2010), Water quality in South San Francisco Bay, California: Current condition and potential issues for the South Bay Salt Pond Restoration Project, in Reviews of Environmental Contamination and Toxicology, edited by D. M. Whitacre, pp. 115–147, Springer, New York, doi:10.1007/978-1-4419-6260-7_6.
77. Grimaldo, L., T. Sommer, N. Van Ark, G. Jones, E. Holland, P. Moyle, B. Herbold, and P. Smith (2009), Factors affecting fish entrainment into massive water diversions in a tidal freshwater estuary: Can fish losses be managed?, N. Am. J. Fish. Manage., 29(5), 1253–1270, doi:10.1577/M08-062.1.
78. Grosholz, E. D. (2005), Recent biological invasion may hasten invasional meltdown by accelerating historical introductions, Proc. Natl. Acad. Sci. U. S. A., 102(4), 1088–1091, doi:10.1073/pnas.0308547102.
79. Halley, J. M. (1996), Ecology, evolution and 1/f-noise, Trends Ecol. Evol., 11(1), 33–37, doi:10.1016/0169-5347(96)81067-6.
80. Halley, J., and P. Inchausti (2004), The increasing importance of 1/f-noises as models of ecological variability, Fluctuation Noise Lett., 4(2), R1–R26, doi:10.1142/S0219477504001884.
81. Hamilton, D. P., and J. V. Turner (2001), Integrating research and management for an urban estuarine system: The Swan-Canning Estuary, Western Australia, Hydrol. Processes, 15(13), 2383–2385, doi:10.1002/hyp.299.
82. Hamza, W. (2009), Nile: Origin, Environments, Limnology and Human Use, in Monographiae Biologicae, edited by H. J. Dumont, pp. 75–94, Springer, Berlin.
83. Hare, J. A., and K. W. Able (2007), Mechanistic links between climate and fisheries along the east coast of the United States: Explaining population outbursts of Atlantic croaker (Micropogonias undulatus), Fish. Oceanogr., 16(1), 31–45, doi:10.1111/j.1365-2419.2006.00407.x.
84. Harrell, F. E. (2001), Regression Modeling Strategies: With Applications to Linear Models, Logistic Regression, and Survival Analysis, Springer, Berlin.
85. Hastings, A., C. L. Hom, S. Ellner, P. Turchin, and H. C. J. Godfray (1993), Chaos in ecology: Is mother nature a strange attractor?, Annu. Rev. Ecol. Syst., 24, 1–33.
86. Hawkins, S. J., et al. (2002), Recovery of polluted ecosystems: The case for long-term studies, Mar. Environ. Res., 54(3–5), 215–222, doi:10.1016/S0141-1136(02)00117-4.
87. Helsel, D. R., and R. M. Hirsch (2002), Statistical methods in water resources, in Techniques of Water-Resources Investigations of the United States Geological Survey, vol. 4, Hydrologic Analysis and Interpretation, chap. A3, pp. 1–510, U.S. Geol. Surv., Reston, Va.
88. Herbert, D. A., W. B. Perry, B. J. Cosby, and J. W. Fourqurean (2011), Projected reorganization of Florida Bay seagrass communities in response to the increased freshwater inflow of Everglades restoration, Estuaries Coasts, 34(5), 973–992, doi:10.1007/s12237-011-9388-4.
89. Hering, D., et al. (2010), The European Water Framework Directive at the age of 10: A critical review of the achievements with recommendations for the future, Sci. Total Environ., 408(19), 4007–4019, doi:10.1016/j.scitotenv.2010.05.031.
90. Higgins, S. N., and M. J. Vander Zanden (2010), What a difference a species makes: A meta-analysis of dreissenid mussel impacts on freshwater ecosystems, Ecol. Monogr., 80(2), 179–196, doi:10.1890/09-1249.1.
91. Hornberger, M. I., S. N. Luoma, D. J. Cain, F. Parchaso, C. L. Brown, R. M. Bouse, C. Wellise, and J. K. Thompson (2000), Linkage of bioaccumulation and biological effects to changes in pollutant loads in south San Francisco Bay, Environ. Sci. Technol., 34(12), 2401–2409, doi:10.1021/es991185g.
92. Howarth, R. W., A. Sharpley, and D. Walker (2002), Sources of nutrient pollution to coastal waters in the United States: Implications for achieving coastal water quality goals, Estuaries, 25, 656–676, doi:10.1007/BF02804898.
93. Hughes, R. M., and D. V. Peck (2008), Acquiring data for large aquatic resource surveys: The art of compromise among science, logistics, and reality, J. N. Am. Benthol. Soc., 27, 837–859, doi:10.1899/08-028.1.
94. Jackson, R. B., S. R. Carpenter, C. N. Dahm, D. M. McNight, R. J. Naiman, S. L. Postel, and S. W. Running (2001), Water in a changing world, Ecol. Appl., 11(4), 1027–1045, doi:10.1890/1051-0761(2001)011[1027:WIACW]2.0.CO;2.
95. Jackson, S. T. (2007), Looking forward from the past: History, ecology, and conservation, Front. Ecol. Environ, 5, 455, doi:10.1890/1540-9295(2007)5[455:LFFTPH]2.0.CO;2.
96. Jaffe, B. E., R. E. Smith, and A. C. Foxgrover (2007), Anthropogenic influence on sedimentation and intertidal mudflat change in San Pablo Bay, California: 1856–1983, Estuarine Coastal Shelf Sci., 73, 175–187, doi:10.1016/j.ecss.2007.02.017.
97. Jassby, A. D. (1998), Interannual variability at three inland water sites: Implications for sentinel ecosystems, Ecol. Appl., 8(2), 277–287, doi:10.1890/1051-0761(1998)008[0277:IVATIW]2.0.CO;2.
98. Jassby, A. D. (2008), Phytoplankton in the upper San Francisco Estuary: Recent biomass trends, their causes and their trophic significance, San Francisco Estuary Watershed Sci., 6(1), 1–24. [Available at http://escholarship.org/uc/item/71h077r1.]
99. Jassby, A. D., and J. E. Cloern (2000), Organic matter sources and rehabilitation of the Sacramento-San Joaquin Delta (California, USA), Aquat. Conserv., 10(5), 323–352, doi:10.1002/1099-0755(200009/10)10:5<323::AID-AQC417>3.0.CO;2-J.
100. Jassby, A. D., J. E. Cloern, and T. M. Powell (1993), Organic-carbon sources and sinks in San-Francisco Bay - variability induced by river flow, Mar. Ecol. Prog. Ser., 95(1–2), 39–54, doi:10.3354/meps095039.
101. Jassby, A. D., W. J. Kimmerer, S. G. Monismith, C. Armor, J. E. Cloern, T. M. Powell, J. R. Schubel, and T. J. Vendlinski (1995), Isohaline position as a habitat indicator for estuarine populations, Ecol. Appl., 5(1), 272–289, doi:10.2307/1942069.
102. Jassby, A. D., J. E. Cloern, and B. E. Cole (2002), Annual primary production: Patterns and mechanisms of change in a nutrient-rich tidal ecosystem, Limnol. Oceanogr., 47(3), 698–712, doi:10.4319/lo.2002.47.3.0698.
103. Jassby, A. D., A. B. Müller-Solger, and M. Vayssières (2005), Short-term variability of chlorophyll and implications for sampling frequency in the San Joaquin River, IEP Newsl., 18(1), 28.
104. Jaworski, N. A. (1990), Retrospective study of the water quality issues of the upper Potomac Estuary, Rev. Aquat. Sci., 3(1), 11–40.
105. Jaworski, N. A., B. Romano, and C. Buchanan (2007), The Potomac River Basin and its Estuary: Landscape loadings and water quality trends 1895–2005, edited by C. L. Jaworski, report, Interstate Comm. on the Potomac River Basin, Rockville, Md. [Available at http://www.potomacriver.org/2012/projects/pia-intro/37-wildlife-habitat/assessing/147-pia-treatise-pia-treatise.]
106. Jones, P. D. (2006), Water quality and fisheries in the Mersey estuary, England: A historical perspective, Mar. Pollut. Bull., 53(1–4), 144–154, doi:10.1016/j.marpolbul.2005.11.025.
107. Kemp, W. M., et al. (2005), Eutrophication of Chesapeake Bay: Historical trends and ecological interactions, Mar. Ecol. Prog. Ser., 303, 1–29, doi:10.3354/meps303001.
108. Kimmerer, W. (2004), Open water processes of the San Francisco Estuary: From physical forcing to biological responses, San Francisco Estuary Watershed Sci., 2(1), 1–142.
109. Kimmerer, W. (2005), Long-term changes in apparent uptake of silica in the San Francisco estuary, Limnol. Oceanogr., 50(3), 793–798, doi:10.4319/lo.2005.50.3.0793.
110. Kimmerer, W. J. (2006), Response of anchovies dampens effects of the invasive bivalve Corbula amurensis on the San Francisco Estuary foodweb, Mar. Ecol. Prog. Ser., 324, 207–218, doi:10.3354/meps324207.
111. Kimmerer, W., E. Gartside, and J. J. Orsi (1994), Predation by an introduced clam as the likely cause of substantial declines in zooplankton of San Francisco Bay, Mar. Ecol. Prog. Ser., 113, 81–93, doi:10.3354/meps113081.
112. Kimmerer, W. J., N. Ferm, M. H. Nicolini, and C. Penalva (2005), Chronic food limitation of egg production in populations of copepods of the genus Acartia in the San Francisco Estuary, Estuaries Coasts, 28, 541–550, doi:10.1007/BF02696065.
113. Kjerfve, B., C. H. A. Ribeiro, G. T. M. Dias, A. M. Filippo, and V. D. S. Quaresma (1997), Oceanographic characteristics of an impacted coastal bay: Baia de Guanahara, Rio de Janeiro, Brazil, Cont. Shelf Res., 17(13), 1609–1643, doi:10.1016/S0278-4343(97)00028-9.
114. Knowles, N. (2002), Natural and management influences on freshwater inflows and salinity in the San Francisco Estuary at monthly to interannual scales, Water Resour. Res., 38(12), 1289, doi:10.1029/2001WR000360.
115. Lehodey, P., et al. (2006), Climate variability, fish, and fisheries, J. Clim., 19(20), 5009–5030, doi:10.1175/JCLI3898.1.
116. Li, P., S. L. Yang, J. D. Milliman, K. H. Xu, W. H. Qin, C. S. Wu, Y. P. Chen, and B. W. Shi (2012), Spatial, temporal, and human-induced variations in suspended sediment concentration in the surface waters of the Yangtze Estuary and adjacent coastal areas, Estuaries Coasts, 35, 1316–1327, doi:10.1007/s12237-012-9523-x.
117. Lucas, L. V., and J. E. Cloern (2002), Effects of tidal shallowing and deepening on phytoplankton production dynamics: A modeling study, Estuaries, 25(4), 497–507, doi:10.1007/BF02804885.
118. Lucas, L. V., T. Schraga, C. B. Lopez, J. R. Burau, and A. D. Jassby (2002), Pulsey, patchy water quality in the Delta: Implications for meaningful monitoring, IEP Newsl., 15(3), 27.
119. Luoma, S. N., and J. E. Cloern (1982), The impact of waste-water discharge on biological communities in San Francisco Bay, in San Francisco Bay: Use and Protection, edited by W. J. Kockelman, T. J. Conomos, and A. E. Leviton, pp. 137–160, Pac. Div. of the Am. Assoc. for the Adv. of Sci., San Francisco.
120. Luoma, S. N., and P. S. Rainbow (2008), Metal Contamination in Aquatic Environments: Science and Lateral Management, Cambridge Univ. Press, New York.
121. MacArthur, R. H., and E. O. Wilson (1963), An equilibrium theory of insular zoogeography, Evolution, 17(4), 373–387, doi:10.2307/2407089.
122. Mac Nally, R., et al. (2010), Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autogregressive modeling (MAR), Ecol. Appl., 20(5), 1417–1430, doi:10.1890/09-1724.1.
123. Mantua, N. J., S. R. Hare, Y. Zhang, J. M. Wallace, and R. C. Francis (2002), The Pacific Decadal Oscillation, J. Oceanogr., 58, 35–44, doi:10.1023/A:1015820616384.
124. Martin, M. A., J. P. Fram, and M. T. Stacey (2007), Seasonal chlorophyll a fluxes between the coastal Pacific Ocean and San Francisco Bay, Mar. Ecol. Prog. Ser., 337, 51–61, doi:10.3354/meps337051.
125. Matthiessen, P., and R. J. Law (2002), Contaminants and their effects on estuarine and coastal organisms in the United Kingdom in the late twentieth century, Environ. Pollut., 120(3), 739–757.
126. May, C. L., J. R. Koseff, L. V. Lucas, J. E. Cloern, and D. H. Schoellhamer (2003), Effects of spatial and temporal variability of turbidity on phytoplankton blooms, Mar. Ecol. Prog. Ser., 254, 111–128, doi:10.3354/meps254111.
127. McKee, L. J., and D. C. Gluchowski (2011), Improved nutrient load estimates for wastewater, stormwater and atmospheric deposition to South San Francisco Bay (South of the Bay Bridge), report, Bay Area Clean Water Agencies, San Francisco, Calif. [Available at http://bayareanutrients.aquaticscience.org/sites/default/files/u23/Report_Nutrient_load_to_South_Bay_2011-8-31_revised.pdf.]
128. Milliman, J., and J. Syvitski (1992), Geomorphic/tectonic control of sediment discharge to the ocean: The importance of small mountainous rivers, J. Geol., 100(5), 525–544, doi:10.1086/629606.
129. Milliman, J. D., K. L. Farnsworth, P. D. Jones, K. H. Xu, and L. C. Smith (2008), Climatic and anthropogenic factors affecting river discharge to the global ocean, 1951–2000, Global Planet. Change, 62(3–4), 187–194, doi:10.1016/j.gloplacha.2008.03.001.
130. Milly, P. C. D., J. Betancourt, M. Falkenmark, R. M. Hirsch, Z. W. Kundzewicz, D. P. Lettenmaier, and R. J. Stouffer (2008), Climate change. Stationarity is dead: Whither water management?, Science, 319(5863), 573–574, doi:10.1126/science.1151915.
131. Monismith, S. G., W. Kimmerer, J. R. Burau, and M. T. Stacey (2002), Structure and flow-induced variability of the subtidal salinity field in northern San Francisco Bay, J. Phys. Oceanogr., 32(11), 3003–3019, doi:10.1175/1520-0485(2002)032<3003:SAFIVO>2.0.CO;2.
132. Moore, S. K., N. J. Mantua, B. M. Hickey, and V. L. Trainer (2010), The relative influences of El Niño-Southern Oscillation and Pacific Decadal Oscillation on paralytic shellfish toxin accumulation in northwest Pacific shellfish, Limnol. Oceanogr., 55, 2262–2274, doi:10.4319/lo.2010.55.6.2262.
133. Moyle, P. B., J. R. Lund, W. A. Bennett, and W. E. Fleenor (2010), Habitat variability and complexity in the upper San Francisco Estuary, San Francisco Estuary Watershed Sci., 8(3), 1–24. [Available at http://escholarship.org/uc/item/20kf20d32x.]
134. Müller-Solger, A. B., A. D. Jassby, and D. C. Müller-Navarra (2002), Nutritional quality of food resources for zooplankton (Daphnia) in a tidal freshwater system (Sacramento-San Joaquin River Delta), Limnol. Oceanogr., 47, 1468–1476, doi:10.4319/lo.2002.47.5.1468.
135. National Research Council (NRC) (1993), Managing Wastewater in Coastal Urban Areas, 496 pp., Natl. Acad. Press, Washington, D. C. [Available at http://www.nap.edu/catalog.php?record_id=2049.]
136. National Research Council (NRC) (2010), A Scientific Assessment of Alternatives for Reducing Water Management Effects on Threatened and Endangered Fishes in California's Bay Delta, Natl. Acad. Press, Washington, D. C. [Available at http://www.nap.edu/openbook.php?record_id=12881.]
137. Nichols, F. H. (1985), Increased benthic grazing: An alternative explanation for low phytoplankton biomass in northern San Francisco Bay during the 1976–77 drought, Estuarine Coastal Shelf Sci., 21, 379–388, doi:10.1016/0272-7714(85)90018-6.
138. Nichols, F. H., J. E. Cloern, S. N. Luoma, and D. H. Peterson (1986), The modification of an estuary, Science, 231(4738), 567–573, doi:10.1126/science.231.4738.567.
139. Nichols, F. H., J. K. Thompson, and L. E. Schemel (1990), Remarkable invasion of San Francisco Bay (California, USA) by the Asian clam Potamocorbula amurensis. II. Displacement of a former community, Mar. Ecol. Prog. Ser., 66, 95–101, doi:10.3354/meps066095.
140. Nilsson, C., C. Reidy, M. Dynesius, and C. Revenga (2005), Fragmentation and flow regulation of the world's large river systems, Science, 308(5720), 405–408, doi:10.1126/science.1107887.
141. Nixon, S. W. (1988), Physical energy inputs and the comparative ecology of lake and marine ecosystems, Limnol. Oceanogr., 33, 1005–1025, doi:10.4319/lo.1988.33.4_part_2.1005.
142. Nixon, S. W. (1995), Coastal marine eutrophication: A definition, social causes, and future concerns, Ophelia, 41, 199–219.
143. Nixon, S. W. (2003), Replacing the Nile: Are anthropogenic nutrients providing the fertility once brought to the Mediterranean by the great river?, Ambio, 32(1), 30–39.
144. Nixon, S. W., and M. E. Q. Pilson (1983), Nitrogen in estuarine and coastal marine ecosystems, in Nitrogen in the Marine Environment, edited by E. J. Carpenter and D. G. Capone, pp. 565–648, Academic, New York.
145. Nixon, S. W., R. W. Fulweiler, B. A. Buckley, S. L. Granger, B. L. Nowicki, and K. M. Henry (2009), The impact of changing climate on phenology, productivity, and benthic-pelagic coupling in Narragansett Bay, Estuarine Coastal Shelf Sci., 82(1), 1–18, doi:10.1016/j.ecss.2008.12.016.
146. Nobriga, M. L. (2002), Larval delta smelt diet composition and feeding incidence: Environmental and ontogenetic influences, Calif. Fish Game, 88, 149–164.
147. Nobriga, M. L., T. Sommer, F. Feyrer, and K. Fleming (2008), Long-term trends in summertime habitat suitability for delta smelt, Hypomesus transpacificus, San Francisco Estuary Watershed Sci., 6(1), 1–13. [Available at http://repositories.cdlib.org/jmie/sfews/vol6/iss1/art1.]
148. Odum, E. P. (1969), The strategy of ecosystem development, Science, 164(3877), 262–270, doi:10.1126/science.164.3877.262.
149. Orth, R. J., et al. (2010), Long-term trends in submersed aquatic vegetation (SAV) in Chesapeake Bay, USA, related to water quality, Estuaries Coasts, 33(5), 1144–1163, doi:10.1007/s12237-010-9311-4.
150. Parchaso, F., and J. K. Thompson (2002), Influence of hydrologic processes on reproduction of the introduced bivalve Potamocorbula amurensis in northern San Francisco Bay, California, Pac. Sci., 56, 329–345, doi:10.1353/psc.2002.0027.
151. Perez, T., D. Longet, T. Schembri, P. Rebouillon, and J. Vacelet (2005), Effects of 12 years' operation of a sewage treatment plant on trace metal occurrence within a Mediterranean commercial sponge (Spongia officinalis, Demospongiae), Mar. Pollut. Bull., 50, 301–309, doi:10.1016/j.marpolbul.2004.11.001.
152. Petersen, J. K., J. W. Hansen, M. B. Laursen, P. Clausen, J. Carstensen, and D. J. Conley (2008), Regime shift in a coastal marine ecosystem, Ecol. Appl., 18(2), 497–510, doi:10.1890/07-0752.1.
153. Peterson, H. A., and M. Vayssieres (2010), Benthic assemblage variability in the upper San Francisco Estuary: A 27-year retrospective, San Francisco Estuary Watershed Sci., 8(1), 1–27. [Available at http://www.escholarship.org/uc/item/4d0616c6.]
154. Peterson, W. T., and F. B. Schwing (2003), A new climate regime in northeast Pacific ecosystems, Geophys. Res. Lett., 30(17), 1896, doi:10.1029/2003GL017528.
155. Pimentel, D., R. Zuniga, and D. Morrison (2005), Update on the environmental and economic costs associated with alien-invasive species in the United States, Ecol. Econ., 52, 273–288, doi:10.1016/j.ecolecon.2004.10.002.
156. Pimm, S. L., and A. Redfearn (1988), The variability of population densities, Nature, 334(6183), 613–614, doi:10.1038/334613a0.
157. Pritchard, D. W. (1967), What is an estuary: Physical viewpoint, in Estuaries, edited by G. H. Lauf, Publ. Am. Assoc. Adv. Sci., 83, 3–5.
158. R Development Core Team (2012), R: A Language and Environment for Statistical Computing, R Found. for Stat. Comput., Vienna.
159. Riisgård, H. U. (2012), From fish to jellyfish in the eutrophicated Limfjorden (Denmark), Estuaries Coasts, 35, 701–713, doi:10.1007/s12237-012-9480-4.
160. Roegner, G. C., J. A. Needoba, and A. M. Baptista (2011), Coastal upwelling supplies oxygen-depleted water to the Columbia River Estuary, PLoS ONE, 6(4), e18672, doi:10.1371/journal.pone.0018672.
161. Ruiz, G. M., J. T. Carlton, E. D. Grosholz, and A. H. Hines (1997), Global invasions of marine and estuarine habitats by non-indigenous species: Mechanisms, extent, and consequences, Am. Zool., 37(6), 621–632.
162. Santos, M. J., S. Khanna, E. L. Hestir, M. E. Andrew, S. S. Rajapakse, J. A. Greenberg, L. W. J. Anderson, and S. L. Ustin (2009), Use of hyperspectral remote sensing to evaluate efficacy of aquatic plant management, Invasive Plant Sci. Manage., 2, 216–229, doi:10.1614/IPSM-08-115.1.
163. Sañudo-Wilhelmy, S. A., and G. A. Gill (1999), Impact of the Clean Water Act on the levels of toxic metals in urban estuaries: The Hudson River Estuary revisited, Environ. Sci. Technol., 33(20), 3477–3481, doi:10.1021/es981130z.
164. Sarthou, G., K. R. Timmermans, S. Blain, and P. Tréguer (2005), Growth physiology and fate of diatoms in the ocean: A review, J. Sea Res., 53(1–2), 25–42, doi:10.1016/j.seares.2004.01.007.
165. Scheffer, M., J. Bascompte, W. A. Brock, V. Brovkin, S. R. Carpenter, V. Dakos, H. Held, E. H. vanNes, M. Rietkerk, and G. Sugihara (2009), Early warning signals for critical transitions, Nature, 461(7260), 53–59, doi:10.1038/nature08227.
166. Schoellhamer, D. H. (2011), Sudden clearing of estuarine waters upon crossing the threshold from transport- to supply regulation of sediment transport as an erodible sediment pool is depleted: San Francisco Bay, 1999, Estuaries Coasts, 34, 885–899, doi:10.1007/s12237-011-9382-x.
167. Seitzinger, S. P., et al. (2010), Global river nutrient export: A scenario analysis of past and future trends, Global Biogeochem. Cycles, 24, GB0A08, doi:10.1029/2009GB003587.
168. Smith, R. A., R. B. Alexander, and M. G. Wolman (1987), Water-quality trends in the nation's rivers, Science, 235(4796), 1607–1615, doi:10.1126/science.235.4796.1607.
169. Smith, S. E., and S. Kato (1979), The fisheries of San Francisco Bay: Past, present and future, in San Francisco Bay: The Urbanized Estuary, edited by T. J. Conomos, pp. 445–468, Pac. Div. of the Am. Assoc. for the Adv. of Sci., San Francisco, Calif.
170. Smith, S. V., R. M. Chambers, and J. T. Hollibaugh (1996), Dissolved and particulate nutrient transport through a coastal watershed-estuary system, J. Hydrol., 176(1–4), 181–203, doi:10.1016/0022-1694(95)02781-5.
171. Sobczak, W. V., J. E. Cloern, A. D. Jassby, and A. B. Müller-Solger (2002), Bioavailability of organic matter in a highly disturbed estuary: The role of detrital and algal resources, Proc. Natl. Acad. Sci. U. S. A., 99(12), 8101–8105, doi:10.1073/pnas.122614399.
172. Sommer, T., et al. (2007), The collapse of pelagic fishes in the upper San Francisco Estuary, Fisheries, 32, 270–277, doi:10.1577/1548-8446(2007)32[270:TCOPFI]2.0.CO;2.
173. Southward, A. J. (1995), The importance of long time-series in understanding the variability of natural systems, Helgol. Meersunters., 49, 329–333, doi:10.1007/BF02368360.
174. Southward, A. J., G. T. Boalch, and L. Maddock (1988), Fluctuations in the herring and pilchard fisheries of Devon and Cornwall linked to change in climate since the 16th century, J. Mar. Biol. Assoc. U. K., 68, 423–445, doi:10.1017/S0025315400043320.
175. State Water Resources Control Board (2010), Development of flow criteria for the Sacramento-San Joaquin Delta ecosystem, report, Calif. Environ. Prot. Agency, Sacramento. [Available at http://www.swrcb.ca.gov/waterrights/water_issues/programs/bay_delta/deltaflow/docs/final_rpt080310.pdf.]
176. Steele, J. H. (1985), A comparison of terrestrial and marine ecological systems, Nature, 313(6001), 355–358, doi:10.1038/313355a0.
177. Steinberg, P., M. Brett, J. Bechtold, J. Richey, L. Porensky, and S. Smith (2011), The influence of watershed characteristics on nitrogen export to and marine fate in Hood Canal, Washington, USA, Biogeochemistry, 106, 415–433, doi:10.1007/s10533-010-9521-7.
178. Stewart, A. R., S. N. Luoma, C. E. Schlekat, M. A. Doblin, and K. A. Hieb (2004), Food web pathway determines how selenium affects aquatic ecosystems: A San Francisco Bay case study, Environ. Sci. Technol., 38(17), 4519–4526, doi:10.1021/es0499647.
179. Stige, L. C., G. Ottersen, K. Brander, K. S. Chan, and N. C. Stenseth (2006), Cod and climate: Effect of the North Atlantic Oscillation on recruitment in the North Atlantic, Mar. Ecol. Prog. Ser., 325, 227–241, doi:10.3354/meps325227.
180. Stralberg, D., M. Brennan, J. C. Callaway, J. K. Wood, L. M. Schile, D. Jongsomjit, M. Kelly, V. T. Parker, and S. Crooks (2011), Evaluating tidal marsh sustainability in the face of sea-level rise: A hybrid modeling approach applied to San Francisco Bay, PLoS ONE, 6(11), e27388, doi:10.1371/journal.pone.0027388.
181. Syvitski, J. P. M. (2003), Supply and flux of sediment along hydrological pathways: Research for the 21st century, Global Planet. Change, 39, 1–11, doi:10.1016/S0921-8181(03)00008-0.
182. Takata, L., N. Dobroski, C. Scianni, and M. Falkner (2011), 2011 Biennial Report on the California Marine Invasive Species Program, Mar. Facil. Div., Calif. State Lands Comm., Sacramento. [Available at http://www.slc.ca.gov/spec_pub/mfd/ballast_water/Documents/2011_BiennialRpt_Final.pdf.]
183. Takekawa, J. Y., C. T. Lu, and R. T. Pratt (2001), Avian communities in baylands and artificial salt evaporation ponds of the San Francisco Bay estuary, Hydrobiologia, 466, 317–328, doi:10.1023/A:1014546524957.
184. Taleb, N. N. (2007), Black swans and the domains of statistics, Am. Stat., 61(3), 198–200, doi:10.1198/000313007X219996.
185. Tąs, S., E. Okus, and A. Aslan-Yilmaz (2006), The blooms of a cyanobacterium, Microcystis cf. aeruginosa in a severely polluted estuary, the Golden Horn, Turkey, Estuarine Coastal Shelf Sci., 68(3–4), 593–599, doi:10.1016/j.ecss.2006.02.025.
186. Thébault, J., T. S. Schraga, J. E. Cloern, and E. G. Dunlavey (2008), Primary production and carrying capacity of former salt ponds after reconnection to San Francisco Bay, Wetlands, 28(3), 841–851, doi:10.1672/07-190.1.
187. Thompson, J. K. (2005), One estuary, one invasion, two responses: Phytoplankton and benthic community dynamics determine the effect of an estuarine invasive suspension feeder, in The Comparative Roles of Suspension Feeders in Ecosystems, edited by S. Olenin and R. Dame, pp. 291–316, Springer, Amsterdam, doi:10.1007/1-4020-3030-4_17.
188. Thomson, J. R., W. J. Kimmerer, L. R. Brown, K. B. Newman, R. M. Nally, W. A. Bennett, F. Feyrer, and E. Fleishman (2010), Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary, Ecol. Appl., 20(5), 1431–1448, doi:10.1890/09-0998.1.
189. Twardowski, M. S., and P. L. Donaghay (2001), Separating in situ and terrigenous sources of absorption by dissolved materials in coastal waters, J. Geophys. Res., 106, 2545–2560, doi:10.1029/1999JC000039.
190. U.S. Department of Agriculture (2010), California Agricultural Statistics 2009 Crop Year, report, Washington, D. C. [Available at http://www.nass.usda.gov/Statistics_by_State/California/Publications/California_Ag_Statistics/Reports/2009cas-all.pdf.]
191. U.S. Environmental Protection Agency (2000), Progress in Water Quality. An Evaluation of the National Investment in Municipal Wastewater Treatment, report, Washington, D. C. [Available at http://water.epa.gov/polwaste/wastewater/treatment/upload/2002_06_28_wquality_cover.pdf.]
192. Van Drecht, G., A. F. Bouwman, J. Harrison, and J. M. Knoop (2009), Global nitrogen and phosphate in urban wastewater for the period 1970 to 2050, Global Biogeochem. Cycles, 23, GB0A03, doi:10.1029/2009GB003458.
193. vanGeen, A., and S. N. Luoma (1999), The impact of human activities on sediments of San Francisco Bay, California: An overview, Mar. Chem., 64, 1–6, doi:10.1016/S0304-4203(98)00080-2.
194. Vasseur, D. A., and P. Yodzis (2004), The color of environmental noise, Ecology, 85(4), 1146–1152, doi:10.1890/02-3122.
195. Vericat, D., and R. Batalla (2006), Sediment transport in a large impounded river: The lower Ebro, NE Iberian peninsula, Geomorphology, 79(1–2), 72–92, doi:10.1016/j.geomorph.2005.09.017.
196. Vitousek, P. M., C. M. D'Antonio, L. L. Loope, and R. Westbrooks (1996), Biological invasions as global environmental change, Am. Sci., 84(5), 468–478.
197. Vitousek, P. M., H. A. Mooney, J. Lubchenco, and J. M. Melillo (1997), Human domination of the Earth's ecosystems, Science, 277, 494–499, doi:10.1126/science.277.5325.494.
198. Vollenweider, R. A. (1975), Input-output models with special reference to the phosphorus loading concept in limnology, Schweiz. Z. Hydrol., 37, 53–84.
199. Vörösmarty, C., M. Meybeck, B. Fekete, K. Sharma, P. Green, and J. Syvitski (2003), Anthropogenic sediment retention: Major global impact from registered river impoundments, Global Planet. Change, 39(1–2), 169–190, doi:10.1016/S0921-8181(03)00023-7.
200. Walters, R. A., R. T. Cheng, and T. J. Conomos (1985), Time scales of circulation and mixing processes of San Francisco Bay waters, Hydrobiologia, 129, 13–36, doi:10.1007/BF00048685.
201. Wasson, K., C. Zabin, L. Bedinger, M. Cristina Diaz, and J. Pearse (2001), Biological invasions of estuaries without international shipping: The importance of intraregional transport, Biol. Conserv., 102(2), 143–153, doi:10.1016/S0006-3207(01)00098-2.
202. Werner, I., and J. T. Hollibaugh (1993), Potamocorbula amurensis: Comparison of clearance rates and assimilation efficiencies for phytoplankton and bacterioplankton, Limnol. Oceanogr., 38(5), 949–964, doi:10.4319/lo.1993.38.5.0949.
203. Whitall, D., S. Bricker, J. Ferreira, A. M. Nobre, T. Simas, and M. Silva (2007), Assessment of eutrophication in estuaries: Pressure-state-response and nitrogen source apportionment, Environ. Manage. N. Y., 40(4), 678–690, doi:10.1007/s00267-005-0344-6.
204. Wickham, H. (2009), ggplot2: Elegant Graphics for Data Analysis, Springer, New York.
205. Williams, S. L., and E. D. Grosholz (2008), The invasive species challenge in estuarine and coastal environments: Marrying management and science, Estuaries Coasts, 31(1), 3–20, doi:10.1007/s12237-007-9031-6.
206. Winder, M., and A. D. Jassby (2011), Shifts in zooplankton community structure: Implications for food-web processes in the upper San Francisco Estuary, Estuaries Coasts, 34(4), 675–690, doi:10.1007/s12237-010-9342-x.
207. Winder, M., A. D. Jassby, and R. Mac Nally (2011), Synergies between climate anomalies and hydrological modifications facilitate estuarine biotic invasions, Ecol. Lett., 14, 749–757, doi:10.1111/j.1461-0248.2011.01635.x.
208. Wolff, W. (1998), Exotic invaders of the meso-oligohaline zone of estuaries in the Netherlands: Why are there so many?, Helgol. Mar. Res., 52(3), 393–400.
209. Wright, S. A., and D. H. Schoellhamer (2004), Trends in the sediment yield of the Sacramento River, California, 1957–2001, San Francisco Estuary Watershed Sci., 2(2), 1–14. [Available at http://escholarship.ucop.edu/uc/item/891144f891144.]
210. Xu, J., J. H. W. Lee, K. Yin, H. Liu, and P. J. Harrison (2011), Environmental response to sewage treatment strategies: Hong Kong's experience in long term water quality monitoring, Mar. Pollut. Bull., 62(11), 2275–2287, doi:10.1016/j.marpolbul.2011.07.020.
211. Yang, S. L., J. D. Milliman, P. Li, and K. Xu (2011), 50,000 dams later: Erosion of the Yangtze River and its delta, Global Planet. Change, 75(1–2), 14–20, doi:10.1016/j.gloplacha.2010.09.006.
212. Yasuhara, M., H. Yamazaki, A. Tsujimoto, and K. Hirose (2007), The effect of long-term spatiotemporal variations in urbanization-induced eutrophication on a benthic ecosystem, Osaka Bay, Japan, Limnol. Oceanogr., 52, 1633–1644, doi:10.4319/lo.2007.52.4.1633.