The purpose of the workshop was to provide a venue for open discussion among interested parties to identify data and science gaps and develop a scientific research framework to determine the role of ammonium and ammonia within the Sacramento-San Joaquin Delta (Delta) and Suisun Bay (Bay) ecosystem. This research framework is scientifically sound, was developed in an open forum, and thoroughly reviewed.



March 10-11, 2009
9:00 am-5:30pm
650 Capitol Mall, 5th Floor
Delta Room


A panel of national experts (Panel) in riverine and estuarine nutrient dynamics, food web processes, and ecotoxicology have assessed the best available science in a workshop setting. The Panel developed a draft Research Framework using input from local experts (invited scientists who are conducting research on ammonia/ammonium the Delta and Estuary ecosystem relative to the topic of interest in the workshop), stakeholders (invited interest groups and entities who have been engaged in the issue of ammonium-ammonia in the Delta and Estuary), and the interested public.

The research framework developed by the Panel represents a high level approach to direct investigations focused on ammonia and ammonium in the Delta and Bay. This research framework, combined with input from local experts and stakeholders during workshop discussions, will be used to develop a listing of specific research needs and priorities in a Data and Science Gap Analysis (DaSGA). The DaSGA is scheduled for completion in the Fall of 2009


The Panel prepared a draft outline of the Research Framework and offered it for the consideration of workshop participants (invited stakeholders, local experts, and public members). The Panel then prepared a draft Research Framework that took into consideration the comments of the workshop participants and identified key research questions and needs along with recommended methods and protocols to effectively address the key questions. CALFED made this draft report available for public comment. The Panel responded to the public comments and revised and finalized the report. Public comments, the Panel’s response to these comments and the final Research Framework are now posted on the CALFED Science Program’s web page.

The CALFED Science Program prepared a written summary of the workshop. This summary included key discussion points and the various positions presented on these points, and an overview of the scientific uncertainties. CALFED Science Program will coordinate all draft reports, comments, and final reports and post them on the CALFED Science website.

The DaSGA will identify, and possibly prioritize, the specific research needs that are not already being addressed and answer questions and uncertainties identified during the workshop. The DaSGA will be based on the high-level Research Framework and discussions during the workshop. Members of the workshop planning committee (Rich Breuer/DWR, Frances Brewster/Santa Clara Valley Water District, Cameron Irvine/CH2M HILL, and Karen Larsen/CVRWQCB) will prepare the draft DaSGA.This draft will be reviewed by the Panel. After addressing comments from the Panel, this living document will be provided to the POD-CWT (Contaminant Work Team) for distribution to POD investigators and funding agencies. The intent is that this document will be updated by the CWT as studies are completed, new understanding is generated, and new research questions are developed.


  • Patrick J. Mulholland, PhD: project lead for the Lotic Intersite Nitrogen eXperiment (LINX) that studied the fate of ammonium and nitrate in streams and rivers; nutrient biogeochemistry group in the Environmental Sciences Division of Oak Ridge National Laboratory.

  • Professor Hans Paerl, PhD: leading expert on nutrient loading effects on estuaries and the coastal ocean; William R. Kenan Professor at the Institute of Marine Sciences at the University of North Carolina at Chapel Hill.

  • Professor Amelia K. Ward, PhD: pioneering work on Microcyctis aeruginosa with Robert Wetzel; director of the Center for Freshwater Studies at the University of Alabama.

  • Joseph S. Meyer, PhD: 32 years of experience in applied limnology and the fate and effects of contaminants; professor emeritus, University of Wyoming.

Charge to the Panel of Experts

  • Prior to convening the workshop, review and assess summary papers and key studies conducted in the San Francisco Estuary related to ammonium and ammonia.
  • Conduct brief presentation at the workshop of their experience relevant to the role of ammonium-ammonia in freshwater and estuary ecosystems in the topic areas of fate and transport, and/or food web interactions, and/or ecotoxicology.
  • Participate in the workshop discussions.
  • Participate in the preparation of a draft Research Framework outline.
  • Prepare draft Research Framework that considers the information and input provided at the workshop and incorporates their expertise on the workshop topic.
  • Participate in the preparation of a response to comments to the draft Research Framework and the final production of the Research Framework.
  • Provide scientific review the stakeholder developed draft DaSGA and provide comments to the Panel Chair.
  • Panel Chair will synthesize Panel’s comments on the draft DaSGA and provide the synthesized comments to the preparers of the DaSGA report.

Schedule for Tasks and Deliverables – REVISED 5/21/2009

Task/Deliverable Schedule/Due Date
Public Workshop – Ammonia and Ammonium March 10 and 11, 2009
Draft Research Framework Outline – Oral Panel Presentation March 11, 2009
Draft Research Framework – written document March 20, 2009
Public Comment on Draft Research Framework April 3, 2009
Final Research Framework – written document April 13, 2009
Response to Public Comments on the Draft Research Framework – written document April 13, 2009
Draft DaSGA for Panel review Fall 2009
Review and comments of the Draft DaSGA by the Panel Fall 2009
Final DaSGA incorporating Panel input Fall 2009

Workshop Planning Committee

  • Karen Larsen – CA Central Valley Regional Water Quality Control Board
  • Adam Ballard – CA Central Valley Regional Water Quality Control Board
  • Rich Breuer – CA Department of Water Resources
  • Kevin Reece – CA Department of Water Resources
  • Tom Kimball – CA State Water Resources Control Board
  • Frances Brewster – Santa Clara Valley Water District
  • Cameron Irvine – CH2M Hill representing the Sacramento County Regional Sanitation District
  • Ladd Lougee - CALFED Science Program
  • Cliff Dahm - CALFED Lead Scientist
  • Anke Mueller-Solger - IEP Lead Scientist
  • Al Vargas - CALFED Science Program


March 10, 2009 - 9:00 a.m.

  1. Welcome
  2. Introduction - Dr. Cliff Dahm, CALFED Lead Scientist
  3. Ammonia/ammonium overview - Dr. Anke Mueller-Solger, IEP Lead Scientist
  4. Brief presentations by each Panel member on ammonia/ammonium related riverine and estuarine nutrient dynamics, food web processes, and ecotoxicology
  5. Facilitated discussion – Panel, local experts, and stakeholders organized into three sections: general fate and transport, food web interactions, and toxicity.

  6. 12:30 p.m. Lunch
  1. Continued facilitated discussion
  2. Public comment
  3. Summary of main points

  4. 5:30 p.m. Adjourn

March 11, 2009 - 9:00 a.m.

  1. Private deliberation by the panel to develop a Research Framework Outline
  2. Stakeholders, local experts, and the general public engaged in further facilitated discussion of issues. Discussions were framed around the following brief presentation by workshop participants.

  3. 12:30 p.m. Lunch
  1. Presentation of a draft Research Framework Outline by the Panel
  2. Panel discussion with key stakeholders
  3. Public comment

  4. 5:30 p.m. Adjourn

Background Papers – Ammonia and Ammonium Workshop

Background/Summary of Ammonium-Ammonia Investigations in the Delta and Suisun Bay.

The Chemical Stressors Conceptual Model as described in the Sacramento-San Joaquin Delta Regional Ecosystem Restoration Implementation Plan (DRERIP)

  • Camargo, J.A. and A. Alonso. 2006. Ecological and toxicological effects of inorganic nitrogen pollution in aquatic ecosystems: A global assessment. Environment International 32:831-849.

  • Dugdale, R.C., F.P. Wilkerson, V.E. Hogue, and A. Marchi. 2007. The role of ammonium and nitrate in spring bloom development in San Francisco Bay. Estuarine, Coastal and Shelf Science 73(1-2):17-29.

  • Eddy, F.B. 2005. Ammonia in estuaries and effects on fish. Journal of Fish Biology 67:1495-1513.

  • 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. Limnology and Oceanography, 47:698-712.

  • Jassby, A. 2008. Phytoplankton in the Upper San Francisco Estuary: Recent biomass trends, their causes and their trophic significance. San Francisco Estuary and Watershed Science 6(1): Article 2.

  • Lehman, P.W., G. Boyer, C. Hall, S. Waller and K. Gehrts. 2005. Distribution and toxicity of a new colonial Microcystis aeruginosa bloom in the San Francisco Bay Estuary, California. Hydrobiologia 541:87-99.

  • Lehman, P.W., G. Boyer, M. Satchwell, and S. Waller. 2008. The influence of environmental conditions on the seasonal variation of Microcyctis cell density and microcystins concentration in San Francisco Estuary. Hydrobiologia 600:187-204.

  • Passell, H.D., C.N. Dahm, and E.J. Bedrick. 2007. Ammonia modeling for assessing potential toxicity to fish species in the Rio Grande, 1989-2002. Ecological Applications 17(7):2087-2099.

  • Randall, D.J., and T.K.N. Tsui. 2002. Ammonia toxicity in fish. Marine Pollution Bulletin 45:17-23.

  • Sommer, T., C. Armor, R. Baxter, R. Breuer, L. Brown, M. Chotkowski, S. Culberson, F. Feyrer, M. Gingras, B. Herbold, W. Kimmerer, A. Mueller-Solger, M. Nobriga, and K. Souza. 2007. The collapse of pelagic fishes in the Upper San Francisco Estuary. Fisheries 32(6):270-277.

  • U.S. Environmental Protection Agency (US EPA). 1999. 1999 Update of Ambient Water Quality Criteria for Ammonia. EPA-822-R-99-014. Office of Water, Washington D.C.

  • Wilkerson, F.P., R.C. Dugdale, V.E. Hogue, and A. Marchi. 2006. Phytoplankton blooms and nitrogen productivity in San Francisco Bay. Estuaries and Coasts 29(3):401-416.