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Marine Sciences Division

Stephen Breithaupt

Marine Sciences Laboratory
Pacific Northwest National Laboratory
1529 West Sequim Bay Road
Sequim, Washington 98382


Dr. Breithaupt is a senior scientist and lead modeler in the Integrated Coastal Modeling group at the Battelle Marine Sciences Laboratory. He has over 25 years of experience in the study and evaluation of water resource systems with 15 years conducting modeling studies of hydrodynamic, sediment, and water quality processes. His recent experience encompasses flooding studies and reviews of riverine and estuarine systems and hydrodynamic studies of wetlands (estuarine and riverine) for restoration and flooding potential. The reviews have included hydrologic and hydraulic analyses for nuclear power stations. He also has experience in sediment and contaminant transport, river and reservoir modeling for temperature and water quality, and hydrologic and hydraulic analyses. He also has 10 years of experience conducting field evaluation studies of water quality.

For the modeling studies, Dr. Breithaupt uses a range of 1-D, 2-D, and 3-D hydrodynamic, sediment transport, and water quality models. He has developed Lagrangian particle models to simulate fish larvae and effluent plume transport. For the estuarine wetlands and flood studies he has used the models FVCOM, RMA2, and RMA10. The flooding and restoration evaluations have included the use of the models HEC-HMS and HEC-RAS. For the evaluation of sediment transport, contamination, and natural recovery, he has used the models EFDC, TOXI5/WASP, and SEDCAM. Additionally, he used RMA11 for sediment transport analysis in the restoration evaluation of estuarine wetlands. He has conducted temperature and eutrophication water quality studies of river reservoir systems using the model CE-QUAL-W2 to evaluate changes in reservoir operations on water quality compliance. He has used the models RMA2 and RMA4Q to evaluate the effect of reservoir operations on river temperature and water quality. He has conducted groundwater modeling as a member of a team of engineers evaluating the impacts of reservoir operations on the Missouri River using MODFLO. He has done 3-D computational fluid dynamics (CFD) modeling on pump stations and reservoir fore bays using the models PHOENICS, Star-CD, and U2RANS. He developed a finite element benthic processes model to evaluate material fluxes between the benthos and the water column. He has developed graphical user interfaces for visualization of model results, for 2-D and 3-D models.

Research Interests

  • Inundation analysis during flooding and simulation of hydrodynamics of flooding processes
  • Simulation of ecological processes associated with wetlands restoration
  • Hydrodynamic analysis of wetlands restoration

Education and Credentials

  • Ph.D. Water Resources Engineering, University of California, Davis, CA
  • M.S. Environmental Science, Washington State University, Pullman, WA
  • B.S. Aquatic Biology, Texas State University, San Marcos, TX

Affiliations and Professional Service

  • American Society of Limnology and Oceanography

Awards and Recognitions

  • Recognition award from PNNL for contribution to Cumulative Effects analysis on the Columbia River

PNNL Publications


  • Breithaupt SA, AE Copping, J Tagestad, and JM Whiting. 2017. "Maritime Route Delineation using AIS Data from the Atlantic Coast of the US." The Journal of Navigation 70(2):379-394.  doi:10.1017/S0373463316000606


  • Copping AE, SA Breithaupt, JM Whiting, ME Grear, JD Tagestad, and GA Shelton. 2016. "Likelihood of a Marine Vessel Accident from Wind Energy Development in the Atlantic." Wind Energy 19(9):1557-1566.  doi:10.1002/we.1935


  • Diefenderfer HL, GE Johnson, JR Skalski, SA Breithaupt, and AM Coleman. 2012. "Application of the Diminishing Returns Concept in the Hydroecologic Restoration of Riverscapes." Landscape Ecology 27(5):671-682.  doi:10.1007/s10980-012-9713-8
  • Johnson GE, HL Diefenderfer, RM Thom, GC Roegner, BD Ebberts, JR Skalski, AB Borde, E Dawley, AM Coleman, DL Woodruff, SA Breithaupt, A Cameron, C Corbett, EE Donley, DA Jay, Y Ke, K Leffler, C McNeil, C Studebaker, and JD Tagestad. 2012. Evaluation of Cumulative Ecosystem Response to Restoration Projects in the Lower Columbia River and Estuary, 2010PNNL-20296, Pacific Northwest National Laboratory, Richland, WA. 
  • Yang Z, T Wang, T Khangaonkar, and SA Breithaupt. 2012. "Integrated Modeling of Flood Flows and Tidal Hydrodynamics over a Coastal Floodplain ." Environmental Fluid Mechanics 12(1):63-80.  doi:10.1007/s10652-011-9214-3


  • Breithaupt SA, and T Khangaonkar. 2011. "Effects of Wetland Restoration on Floodplain Hydrodynamics under Extreme Flooding Conditions." Ecological Restoration 29(1-2):161-172.  doi:10.3368/er.29.1-2.161



  • Khangaonkar TP, SA Breithaupt, and FC Kristanovich. 2006. "Restoration of Hydrodynamic and Hydrologic Processes in the Chinook River Estuary, Washington - Feasibility Assessment ." In Estaurine and Coastal Modeling Proceedings of the 9th International Conference held in Charleston, SC, Oct. 31-Nov.2, 2005, ed. M.L. Spaulding, pp. 734-751.  American Society of Civil Engineers, Reston, VA. 
  • Khangaonkar TP, SA Breithaupt, and FC Kristanovich. 2006. "Restoration of Hydrodynamic and Hydrologic Processes in the Chinook River Estuary, Washington - Feasibility Assessment." In 9th International Conference on Estuarine Coastal Modeling Conference, ed. ML Spaulding.  American Society of Civil Engineering, New York, NY. 

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Marine Sciences Laboratory
1529 W. Sequim Bay Road
Sequim, WA 98382
Phone: (360) 683-4151
Fax: (360) 681-3699