The purpose of this course is to provide beginning graduate students with a basic understanding of the principles and processes controlling the distribution and speciation of chemical constituents in the ocean and how these processes are studied.  The first part of the course provides an overview of the chemical composition of natural waters and is descriptive in nature.  A brief review of basic thermodynamics and chemical equilibria precede a discussion of the behavior of dissolved gases and carbonate equilibria and forms the basis for a more detailed examination of the distribution and speciation of nutrients, trace metals, trace organic compounds and isotopes.  During as well as in the last part of the course, the student is introduced to a number of “critical” processes that are of primary importance in controlling the distribution, transport and fate of chemicals in the aquatic environment including the consequences of the anthropogenic increase in atmospheric carbon dioxide.  It is assumed that the student is well prepared in chemistry (undergraduate courses at least through organic) and has at least some familiarity with the physical and biological dynamics of aquatic systems (Physical and Biological Oceanography preferred but not required).

Active participation and discussion is encouraged.  Resources include the primary text  (Emerson, S.R. and Hamme, R.C.., Chemical Oceanography; Elemental Fluxes in the Sea), selected texts, readings from the primary literature and other resources.  Student progress is assessed through performance on a combination of homework problem sets, mid-term and final exams, and participation in class discussions.


The course is offered in a distance learning on virtual format with lectures originating from either UMass Lowell or UMass Dartmouth.  Allt course materials are provided on this web site ( including copies of PowerPoint slides for each lecture, handout materials, homework assignments as well as audio and video recordings of previous class sessions.  Certain lectures may be provided in video format only.  Students will be notified in advance that they must watch the lecture video before participating in class.  Class time may then be used for a discussion of material, question and answer sessions, quizzes, sample calculations or other related activities.



  • Emerson, S.R. and Hamme, R.C. , Chemical Oceanography; Elemental Fluxes in The Sea, Cambridge University Press, 2022.  Some readings will be from the earlier edition (Emerson S.R. and Hedges J.I., Chemical Oceanography and the Carbon Cycle),  and available on this web site.

  Supplementary Reading:

  • Millero, Frank J. Chemical Oceanography, 3rd Edition, CRC Press 2006 or 2nd Edition, CRC Press, 1996.
  • Atkins, P.W. Physical Chemistry, 4th Edition, W.H. Freeman and Company, 1990.
  • Broecker, W.S. and Peng T.H. Tracers In The Sea, Eldigio Press, 1982.
  • Libes, Susan M. An Introduction to Marine Biogeochemistry, 2nd Edition, Wiley, John & Sons, 2009.
  • Morel, F.M.M. & Hering, Janet G. Principles and Applications of Aquatic Chemistry, Wiley-Interscience, 1993.
  • Pilson, Michael E.Q. An Introduction To The Chemistry Of The Sea, Prentice Hall Professional Technical Reference, 1998..
  • Schwarzenbach, Rene P., Gschwend, Philip M. & Imboden Dieter M. Environmental Organic Chemistry, Wiley, John & Sons, 2002.
  • Stumm, Werner & Morgan James J. Aquatic Chemistry, John Wiley & Sons, 1996.

A list of general references as well as specific reading assignments will be provided before each class.  Reading assignments will be generally provided a week in advance and can be viewed on the ‘Materials’ page of this web site.   Students should be prepared to discuss the content of the reading material assigned for each lecture. Lecture presentations assume you have read and digested the material before class.

In addition to the principal text (Emerson and Hamme) there will be frequent readings selected from other more advanced texts and the primary literature.  Those intending to go on to more advanced work in environmental and/or marine chemistry are strongly encouraged to purchase a copy of Stumm and Morgan (1996) and Schwarzenbach et al. (1993) for their libraries (see general reference list for full citations).   Those wishing to refer to a more basic text should consider purchasing Libes (2009) available through numerous web sites (try  This text is designed as an upper level undergraduate, beginning graduate level text.  In addition, where appropriate, references to useful Web sites will be provided.  It is assumed that you have access to a computer and to the internet.  You should be familiar with the use of word processors and spreadsheet software as well.


1) Descriptive Chemical Oceanography (fundamentals)

  • large scale circulation and water masses (conveyer belts) – 2 layer
  • vertical and horizontal distributions (basin scale)
  • nutrient-like behavior

2) Physical Chemistry of Seawater (elementary or basic chemistry

  • physicochemical properties
  • properties and structure of water
  • major, minor, trace components
  • units, types of concentration
  • macroscopic, colligative properties
  • salinity, chlorinity, density (influence on circulation), vertical stability – PSU
  • constancy of composition
  • optical properties

3) Equilibrium Concepts

  • remember your chemistry
  • chemical potential
  • activity and fugacity
  • Henry’s Law

4) Dissolved Gases and the Carbonate System

  • dissolved gases – solubility f(T,S,etc), AOU, Henry’s Law, gas exchange
  • basic carbonate system equations, alkalinity,
  • influence of master variables (pH, 3CO2, Alkalinity)
  • effects of organic production/decomposition
  • forcing of pCO2 variations
  • CCD and seafloor CaCO3 distributions
  • global carbon cycle

5) Geochemical and Biogeochemical Cycles 

  • residence time concept
  • controls on biological production and organic matter export
  • influence on atmospheric CO2
  • sources and sinks (weathering, atmospheric, hydrothermal, biosythesis)
  • organic production/decomposition (Redfield Stoichiometry)
  • nutrient biogeochemical cycles (N,P,Si)
  • iron limitation and HNLC regions
  • seasonal cycles (coastal processes)
  • eutrophication

6) Organic Geochemistry

  • basic organic chemistry of seawater
  • early diagenesis (humics)
  • production
  • degradation
  • preservation
  • modification
  • vertical transport
  • DOM and sediment organic matter

7) Trace Metals/Metal Geochemistry

  • biochemical rules
  • Fe limitation and HNLC region
  • speciation
  • toxicity
  • anthropogenic influence

8) Tracers (water column and sediment)

  • radioisotopes
  • stable
  • molecular

9) Special Topics (case studies from instructors research in a model construct)

  • detecting past climate change and impacts of global warming
  • early diagenesis
  • carbon sequestration


To help students understand the theory and application of powerful modeling and calculation tools, Virtual Labs or Workshops are planned.  The time of each Virtual lab session will be announced in class and posted on this website well in advance of its meeting.  Sessions are anticipated to last from 2 to 3 hours and will enable students to conduct hands-on problem solving exercises with the guidance of faculty instructors.  Each Virtual Lab will be scheduled around an assigned take-home Problem Set in order that students can perform necessary calculations in advance of the Lab meeting.  Additional details concerning Virtual Labs will be provided in class.


  • The Midterm and Final exam will be provided to students with a maximum of two hours to finish.
  • Midterm and final exam count for 25% each of total grade.  Four problem sets count for 40% of total grade. (see schedule page for details). The remaining 10% of your grade is based in class attendance and participation.


Students are encouraged to contact either of the instructors at any time to discuss any aspects of the course and course work.  Because of the rapid pace and broad nature of the course, students are strongly encouraged to seek help sooner rather than later to avoid getting too far behind.  Similarly it is strongly recommended that students stay abreast of the substantial reading assignments and bring questions regarding the readings to our attention in a timely fashion. Phone and email contacts are  posted below.


Dr. Mark Altabet Dr. David Ryan
(508) 999-8622 (SMAST)
(508) 542-0994 (CELL)
(978) 934-3698 (Tel)
(978) 934-3569 (FAX)
(617) 797-1997 (CELL)



  • Students are expected to attend class in order to be successful in this class. If you must miss a class due to an illness or emergency, you are responsible for notifying your primary instructor (or both instructors) in advance and for making up any missed work.
  • Class attendance in person is highly preferable given the benefits to students.  However, students for may reasonably request attendance via Zoom.  A note on Zoom participation: Keeping cameras on during class improves student engagement and helps faculty to better assess student learning. In this class students are expected to keep their cameras turned on during class unless you have a valid reason not to, which you should discuss with the instructors ahead of time. Only occasionally turning your camera off during class to attend to a distraction is acceptable.


  • Students are responsible for the honest completion and representation of their work and are held to the highest standards of integrity. Please review the University policy regarding academic integrity. If you choose to remain in this course, you must agree that you will neither give nor receive any unauthorized help on your homework, papers, exams, or other work.


  • Cell phones should be turned off or silenced during class to avoid being a distraction. Texting, talking on the phone, emailing or web browsing during class is strongly discouraged.


  • Federal definition of a credit hour requires that for every course credit awarded, a course must offer 15 hours of instructor-led course activities and 30 hours of out-of-class student work. This means that a standard 3 credit hour course requires 45 hours of instructor-led course activities and 90 hours of out-of-class student work.


  • If you or someone you know is experiencing mental health challenges, please contact Counseling Services, who are offering remote counseling via telehealth for all enrolled, eligible students. In addition, a crisis counsellor is available  at UMassD at 508-999-8648 and UML at 855-890-2879.


  • If you have a documented disability that will require classroom accommodations, please notify me as soon as possible, so that we might make appropriate arrangements. Please speak to me by making an appointment or send me an email, as I want to protect your privacy. Visit the Center for Access and Success webpage for further information and to register with that office if you require accommodations.


  • UMass Dartmouth and UMass Lowell recognize the importance of mutual trust between students and faculty. Neither faculty nor students may record video or audio of a course or private conversation without all parties’ consent. Massachusetts is a two-party consent state, which means it is illegal to record someone without their permission. Recordings of classroom lectures are the intellectual property of the instructor. Instructors have the right to prohibit audio and video recording of their lectures, unless the requesting student is registered with Disabilities Services and recording of class sessions is an approved accommodation. In addition, sharing of or selling recordings of classroom activity, discussions or lectures with any other person or medium without permission of the instructor is prohibited.