Salish Sea Modeling Center » Salish Sea Model » History & SSM Versions

History & SSM Versions

Whidbey Basin of the Puget Sound. PNNL initially began applying FVCOM on several projects within this region from 2003-2007.

As Pacific Northwest National Laboratory (PNNL) at the U.S. Department of Energy implemented numerous sub-basin scale models within Puget Sound over a period from 1997 through 2003, it became clear that simulation of hydrodynamic circulation and water quality in Puget Sound sub-basins would be best conducted using a region wide model to ensure accounting of inter-basin exchange and elimination of errors associated with boundaries in close proximity of the river plume mixing zones. However, accomplishing this goal using popular structured grid models was a challenge due to the complexity of the Puget Sound shoreline, with its deep bathymetry with steep side slopes and the presence of several mid-Channel Islands. By mid-2000s, finite volume methods became available and tools such as Finite Volume Coastal Ocean Model (FVCOM) with excellent mass conservation capability and the ability to operate in parallelized mode on a multi-processor Linux cluster made the objective of a Puget Sound-Wide Model attractive and feasible.

PNNL initially began applying FVCOM on several projects within the Whidbey Basin of Puget Sound, mostly funded by Salmon Restoration Funding Board and Estuary Salmon Restoration and Protection grants from 2003-2007. In 2007, through an internally funded Laboratory Directorate Research and Development (LDRD) grant, the effort to develop a Puget Sound wide model was initiated. Subsequently, the model development was supported by U.S. EPA through a National Estuary Program grant. From 2009 through 2012, PNNL developed the Puget Sound Model (PSM) in collaboration with Washington State Department of Ecology with funding from U.S. EPA. The Puget Sound Model boundaries were set at the entrance to the Strait of Juan De Fuca to the west and at the entrance to Georgia Strait to the north. Since the domain covered Puget Sound and Georgia Strait including the Straits surrounding San Juan Islands, collectively known as the Salish Sea, the name of the model was updated to the Salish Sea Model (SSM). From 2012 through 2016, PNNL continued efforts to improve the model capabilities. Specifically, sediment diagenesis and carbonate chemistry modules were added. In 2017, PNNL also expanded the model domain to the continental shelf and encompassed Vancouver Island to the north and included Columbia River and Yaquina Bay in Oregon to the south.

As a result of these improvements, a robust diagnostic model of the Salish Sea has now been established with the ability to reproduce characteristic oceanographic features such as two-layer density-driven circulation and exchange with Pacific Ocean and annual biogeochemical cycles of algal growth, nutrient consumption, pH, and dissolved oxygen response. A milestone accomplishment of the model in 2018 was the ability to reproduce observed hypoxia in Hood Canal and other sub-basins such as Penn Cove and East Sound while maintaining heathy DO levels in other parts of Puget Sound.

Salish Sea Model Versions

The table below provides a listing of SSM releases along with associated hydrodynamic and water quality code versions.

Model Year Model / Code Development Publications Description / Features Hydrodynamics Model Code


(U. of Mass)

Water Quality Model Code


PSM 2012 Khangaonkar et al. (ECSS 2011, Ocean Dynamics. 2012) Original model also referred to as the Puget Sound version. Domain limited to Puget Sound and Georgia Basin FVCOM_v2.7

(Chen et al. 2003)


(Kim and Khangaonkar 2012)

PSM 2013 Khangaonkar and Wang (Applied Ocean. Res. 2013) Addition of a floating structure / bridge module FVCOM_v2.7a FVCOM-ICM_v1
PSM 2014 Wang and Khangaonkar et al. (JMSE 2014) Addition of a kelp module FVCOM_v2.7b FVCOM-ICM_v1
PSM 2016 Khangaonkar et al. (Northwest Science 2016) Addition of embedded fine resolution, wetting and drying, plus intertidal nearshore salinity and temperature module revisions FVCOM_v2.7c FVCOM-ICM_v1
PSM 2017 Bianucci, Long, Khangaonkar et al. (Elementa Science of the Anthropocene, 2018) Addition of sediment diagenesis, and pH modules to the water quality model. (Documentation in Pelletier et al. 2017a, b) FVCOM_v2.7ecy FVCOM_ICM_v2
SSM 2017 Khangaonkar et al. (Ocean Modelling 2017) Expanded Salish Sea Model domain past continental shelf. Exchange flow and circulation computation FVCOM_v2.7d FVCOM-ICM_v2
SSM 2018 Khangaonkar et al. (JGR 2018) Finalized SSM domain to shelf break, finalized, hypoxia and net heat flux calibration FVCOM_v2.7d FVCOM-ICM_v2
SSM 2021 Khangaonkar et al. (Ecological Modelling 2021) Updated ocean boundary forcing to HYCOM, new Re-aeration formulation, recalibration for harmonization of pH and DO (V3). Addition of turbidity, zooplankton, and submerged aquatic vegetation modules (V4) FVCOM_v2.7d FVCOM-ICM_v3


SSM 2021 Khangaonkar et al. (Frontiers in Marine Science 2021)

In Progress

Improved currents and water surface elevation calibration using distributed bed friction and meteorology and FVCOM version upgrade FVCOM_v4.3a

(updated v4.3 to match v2.7 improvements PNNL)


SSM Version References

Khangaonkar, T., A. Nugraha, S. Yun, L. Premathilake, J. E. Keister, and J. Bos. (2021). Propagation of the 2014–2016 northeast pacific marine heatwave through the Salish Sea. Frontiers in Marine Science, Coastal Ocean Processes. Front. Mar. Sci. 8:787604. .

Khangaonkar, TK, L Premathilake, A Nugraha, J Keister, A Borde. (2021) Projections of algae, eelgrass, and zooplankton ecological interactions in the inner Salish Sea – for future climate, and altered oceanic states, Ecological Modelling, Volume 441, 2021, 109420, ISSN 0304-3800,

Bianucci L, W Long, T Khangaonkar, G Pelletier, A Ahmed, T. Mohamedali, M Roberts, C. Figueroa-Kaminsky. (2018). Sensitivity of the regional ocean acidification and the carbonate system in Puget Sound to ocean and freshwater inputs. Elementa Science of the Anthropocene, 6(1): 22. doi: 10.1525/elementa.151

Khangaonkar T, A Nugraha, W Xu, W Long, L Bianucci, A Ahmed, T Mohamedali, and G Pelletier. 2018. Analysis of Hypoxia and Sensitivity to Nutrient Pollution in Salish Sea. Journal of Geophysical Research – Oceans, 123(7): 4735-4761. doi: 10.1029/2017JC013650

Khangaonkar T., W. Long, and W. Xu.  2017.  “Assessment of Circulation and Inter-Basin Transport in the Salish Sea including Johnstone Strait and Discovery Islands Pathways.”  Ocean Modelling, Volume 109, 2017, Pages 11-32, ISSN 1463-5003,

Pelletier G, L Bianucci, W Long, T Khangaonkar, T Mohamedali, A Ahmed, and C Figueroa-Kaminsky. 2017a. Salish Sea Model Sediment Diagenesis Module. Washington State Department of Ecology. Publication No. 17-03-010, Olympia, WA.

Pelletier G, L Bianucci, W Long, T Khangaonkar, T Mohamedali, A Ahmed, and C Figueroa-Kaminsky. 2017b. Salish Sea Model Ocean Acidification Module and the Response to Regional Anthropogenic Nutrient Sources. Washington State Department of Ecology. Publication No. 17-03-009, Olympia, WA.

Khangaonkar, T., W. Long, B. Sackmann, T. Mohamedali , and A. Hamlet.2016  Sensitivity of Circulation in the Skagit River Estuary to Sea Level Rise and Future Flows. Northwest Science 90(1): 94-118. 2016.

Wang , T., T. Khangaonkar, W. Long and G. Gill. 2014. Development of a Kelp-Type Structure Module in a Coastal Ocean Model to Assess the Hydrodynamic Impact of Seawater Uranium Extraction Technology. J. Mar. Sci. Eng. 2014, 2, 81-92; doi:10.3390/jmse2010081.

Khangaonkar, T. and T. Wang. 2013. Potential alteration of fjordal circulation due to a large floating structure—Numerical investigation with application to Hood Canal basin in Puget Sound, Applied Ocean Research, Volume 39, January 2013, Pages 146-157, ISSN 0141-1187, 10.1016/j.apor.2012.11.003.

Khangaonkar, T. , B. Sackmann, W. Long, T. Mohamedali , and M. Roberts. 2012. Simulation of annual biogeochemical cycles of nutrient balance, phytoplankton bloom(s), and DO in Puget Sound using an unstructured grid model. Ocean Dynamics. (2012) 62:1353–1379. DOI 10.1007/s10236-012-0562-4

Kim, T. and T. Khangaonkar. 2012. An Offline Unstructured Biogeochemical Model (UBM) for Complex Estuarine and Coastal Environments.  Environmental Modelling & Software 31 (2012) 47-63

Khangaonkar, T.,  Z. Yang, T. Kim, and M. Roberts. 2011.  Tidally Averaged Circulation in Puget Sound Sub-basins:  Comparison of Historical Data, Analytical Model, and Numerical Model.  Journal of Estuarine Coastal and Shelf Science, Volume 93, Issue 4, 20 July 2011, Pages 305-319.