Puget Sound Oceanography:
Estuarine Processes

Winter Term 2011
OCN 506B Graduate(16678)
OCN 497B Undergraduate (16672)
3 credits

Dana Passage

Parker MacCready: Physical Oceanography
Julie Keister: Biological Oceanography (jkeister@u.washington.edu)

Meeting times: MWF 11:30-12:20
Location: Ocean Sciences Building 425 (map)

Many students have research projects in Puget Sound or other estuaries. Our goal is to give you a broad overview of all the interacting processes that shape estuarine ecosystems, particularly Puget Sound. Our second goal is to help you understand the global variation of estuaries, so that you can compare processes across different systems. Think of it as a class to help you write the Introduction and Conclusion sections of your thesis!

Click here for the SYLLABUS

Course Description: This class is intended for graduate and advanced undergraduate students from any scientific discipline. We will study the physical-biological coupling in a wide range of estuarine systems from around the world, with Puget Sound as a primary example. We focus on important estuarine processes and their consequences:

  • Effects of circulation and mixing on residence time and patterns of phytoplankton and zooplankton
  • Development of hypoxia and its effects on biology
  • Edges: the ETM (Estuarine Turbidity Maximum) and the intertidal zone
  • Harmful algal blooms
  • Effects of increasing urbanization and climate change, including Ocean Acidification

The course will consist of lectures, focused discussions of research papers, and discussions with local experts. Students will write a number of short response essays based on the reading, and a longer paper on a topic of their choice. Students will give a short presentation on their final paper in the last week. There will be no final exam.


  • 60% Reading Questions, due approximately weekly. These are 1-2 page written responses to the assigned readings. Formulate a question based on the reading, and attempt to answer it using reasoning, material from the reading, or outside sources. Quantitative approaches are encouraged. Typed, double-spaces, 12 pt., or neatly hand-written. There will also be discussions in class, typically formulated around these reading questions and the guest experts. Active participation in these discussions is an essential part of our expectations, and will be the basis of one-third of this 60%. Here are examples from a past class of a good and an excellent reading question response.
  • 40% Final Project, due the last day of class, at the start of class, Friday March 11th, 2011. This is a paper on a topic of your choosing; anything that pertains to estuaries. Expected paper lengths are at least 5 pages for undergrads and 9-11 pages for grad students. Quantitative analysis is encouraged, and it is expected that you will seek out and cite several outside referenced - particularly from the refereed literature. Typed, double-spaced, 12 pt. We like figures and diagrams, with explanatory captions. Comparison of your chosen topic across two or more different estuaries is strongly encouraged.
  • During the last 1.5 weeks the students in the class will give short talks on their projects to the class. Talk lengths will be 10 minutes for undergrads and 20 minutes for graduate students, and these include time for questions. Evaluation of this is included in the grading of the final project.
  • There is no final exam.

References (all links removed)

Chesapeake Bay

  • Elizabeth North's Research Page (ETM and Larval Processes): http://northweb.hpl.umces.edu/research/research.htm
  • Roman et al (2005) Plankton Patterns
  • Zhang et al (2006) More Plankton Patterns (with DO sections)
  • Chesapeake Bay Program: http://www.chesapeakebay.net/index.aspx?menuitem=13853
  • ...and their cool water quality maps: http://www.chesapeakebay.net/maps.aspx?menuitem=16828
  • Chesapeake EcoCheck: http://www.eco-check.org/summerreview/chesapeake/
  • EcoCheck Example Anoxia Map: http://www.eco-check.org/forecast/chesapeake/indicators/anoxia/#_Maps
  • Historical perspective on eutrophication in the Chesapeake: Brush et al. (2009)

Long Island Sound

  • LISS: the Long Island Sound Study

Hypoxia and the Gulf of Mexico Dead Zone

  • US Hypoxia Report (2010)
  • Great overview: OSTP Report 2000
  • Gulf Hypoxia LUMCON: http://www.gulfhypoxia.net/
  • Gulf Hypoxia EPA: http://www.epa.gov/msbasin/
  • Gulf Hypoxia USGS: http://toxics.usgs.gov/hypoxia/

San Francisco Bay

  • Conomos (1979) San Francisco Bay: The Urbanized Estuary: http://www.estuaryarchive.org/archive/conomos_1979/

Puget Sound

  • Babson et al (2006) Circulation and stratification box model
  • Cannon (1983) Circulation Overview
  • Cokelet et al (1990) The predecessor to Babson
  • Feelye et al. (2010) Ocean Acidification in Puget Sound
  • Newton (2007) HCDOP Overview
  • Lavelle et al (1988) Tides and the tidal model
  • Mofjeld and Larsen (1984) Tides
  • Sutherland et al. (2011) Numerical Model of Puget Sound and the Salish Sea
  • Winter et al (1975) Ecosystem Model
  • Hood Canal Nitrogen loading from rivers: http://pubs.usgs.gov/sir/2006/5073/index.html and http://pubs.usgs.gov/sir/2006/5106/index.html

Willapa Bay, WA

  • Banas et al (2004) Willapa Circulation and Stirring
  • Banas and Hickey (2005) Willapa residence Time
  • Banas et al. (2007) Tidal exchange, bivalve grazing, and patterns of primary production in Willapa Bay, Washington, USA

Estuarine Physics Overviews

  • MacCready (2004)
  • MacCready and Banas (2010) Estuary Treatise Chapter, "Residual Circulation, Mixing, and Dispersion
  • A review paper: MacCready, P. and W.R. Geyer (2010) Advances in Estuarine Physics. Annual Review of Marine Science, 2, 35-58, 10.1146/annurev-marine-120308-081015 [URL]

Estuarine Biology Overviews

  • Able (2005) A re-examination of fish estuarine dependence: Evidence for connectivity between estuarine and ocean habitats.
  • Cloern and Jassby (2010) Patterns and Scales of Phytoplankton Variability in Estuarine–Coastal Ecosystems.
  • Ray (2005) Connectivities of estuarine fishes to the coastal realm.


  • King County Water and Land Resources - Listing of External Resources: http://www.kingcounty.gov/environment/wlr/out-links.aspx
  • Ecology - Marine Waters PSAMP: http://www.ecy.wa.gov/programs/eap/mar_wat/mwm_intr.html
  • PSP - Puget Sound Partnership: http://www.psp.wa.gov/
  • PRISM - Puget Sound Regional Synthesis Model: http://www.prism.washington.edu/
  • NANOOS - Northwest Association of Networked Ocean Observing Systems: http://www.nanoos.org/
  • HCDOP Main page - Hood Canal Dissolved Oxygen Program: http://www.hoodcanal.washington.edu/


  • PRISM - Interactive plotter for cruise data: http://www.prism.washington.edu/cruiseData/cross-sections.jsp
  • PRISM Data Acces: http://www.prism.washington.edu/cruiseData/data_archive/
  • Ecology Marine Water Quality Data: http://www.ecy.wa.gov/apps/eap/marinewq/mwdataset.asp
  • HCDOP Data Access: http://www.hoodcanal.washington.edu/observations/dataaccessss.html
  • HCDOP Citizen CTD Data: http://www.hoodcanal.washington.edu/observations/dataaccessss.html
  • ORCA Data: http://orca.ocean.washington.edu/dataLogin.html
  • VENUS Observatory - Saanich Inlet and Strait of Georgia: http://www.venus.uvic.ca/
  • USGS - Washington Riverflow Data: http://waterdata.usgs.gov/wa/nwis/rt


  • PDF of Richard Strickland's Fertile Fjord: http://www.wsg.washington.edu/communications/online/fjord/index.html
  • NOAA PMEL Publications: http://www.pmel.noaa.gov/publications/search_get_ntis_list.php


  • Richard Strickland's website
  • Oceanography of Puget Sound, Fall 2006, Keil & Strickland, OCN 422