Puget Sound Oceanography:
Estuarine Processes

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

Dana Passage

Parker MacCready: Physical Oceanography (parker@ocean.washington.edu)
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 & Links

Chesapeake Bay

Long Island Sound

Hypoxia and the Gulf of Mexico Dead Zone

San Francisco Bay

Puget Sound

Willapa Bay, WA

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.