US Environmental Protection Agency (EPA), Region 10, October 2021 – September 2024
Video of Portage Bay sunset on January 1, 2023
Coastal shellfish growing areas are threatened by poor water quality which can lead to a change in their classification and subsequent closures due to contamination from wastewater effluent plumes from land-based sources. Shellfish harvesting areas in the Salish Sea, often experience exposure to fecal bacteria which results in seasonal closures for harvesting due to the potential human health risk. Freshwater streams from the surrounding watersheds carrying agricultural runoff and wastewater effluent are hypothesized to be the major sources of fecal bacteria contamination impacting critical shellfish habitats in the Salish Sea including those in Whatcom and Skagit Counties. Although pollution prevention and source control actions have been implemented by regulators and stakeholders in these areas, the fecal bacteria pollution in the shellfish beds continues to persist requiring repeated closures of shellfish beds
Whatcom and Skagit counties are working with U.S. EPA through the National Estuary Program’s Shellfish Strategic Initiative to conduct numerous pollution identification and correction (PIC) activities to reduce bacteria levels in freshwater and marine waters affecting shellfish beds. Fecal bacteria do not only come from on-site sewage systems and agricultural farms, but also from pet waste, recreationalists, urban wildlife, waterfowl etc. There is a longstanding need to better understand marine circulation of pathogens in connection with shellfish beds with questions as following.
- Whether the freshwater streams are the major loading sources of fecal bacteria to critical shellfish habitats?
- How currents driven by tides and winds move freshwater and pollutants from rivers, streams and outfalls to the shellfish beds areas?
Figure 1. DOH map of shellfish bed closures at Samish Bay, Portage Bay and Drayton Harbor
Through an interagency agreement with the Pacific Northwest National Laboratory (PNNL) and U.S. EPA, Salish Sea Model (SSM) was applied to address the existing fecal bacteria pollution concerns in Samish Bay, Portage Bay, and Drayton Harbor. The SSM was regionally refined with better representation of local shoreline, intertidal bathymetry and incorporation of local streams and sources impacting the shellfish growing areas. A simplified new fecal bacteria module (SSM-fb) was developed and incorporated with existing water quality model to simulate the fate and transport of fecal bacteria from different sources.
The Portage Bay portion of the study is used below as an example to illustrate the research processes and findings. Portage Bay is located approximately 8-km southwest of Nooksack River delta, between the Lummi Peninsula and the Portage Island and hosts Lummi Nation’s shellfish growing area. A detailed analysis of hydrodynamics and circulation under different freshwater inflow, tides and wind conditions was conducted using locally refined grid of Portage Bay area embedded within SSM grid which includes local streams such as Lummi River, Squalicum Creek, Whatcom Creek, Padden Creek, Chuckanut Creek and point sources in the surrounding marine waters. Flushing time of Portage Bay area under different flow conditions was using a numerical dye to compute flushing time. It serves as a proxy for estimating the time needed for the Bay to be flushed out with clean water before it may be re-opened for shellfish growing operations. The numerical dye was also released from different streams and coastal outfalls to identify the transport time scales and to help estimate relative contributions of major sources of pollution to the Portage Bay.
Figure 2. SSM-Portage model simulation of freshwater plumes distribution in Bellingham Bay and Portage Bay during high and low freshwater flow periods
Animation 1: Simulation of freshwater plumes in Bellingham Bay during high flow period
Animation 2: Simulating flushing of instantaneously introduced tracer in Portage Bay during high flow period
In SSM-Portage fecal bacteria (FB) simulation, the FB inputs were determined based on 11 monitoring stations on 8 major streams and tributaries provided by Whatcom County. Data from additional 10 coastal stormwater outfalls surrounding Portage Bay were acquired from Lummi Natural Resources Department. Model simulation results were validated and calibrated with 12 DOH stations in Portage Bay shellfish beds and nearby Hale Passage with approximately monthly sampling frequency. Year 2021 was selected as the initial target year for the simulations based on the pronounced flooding events that occurred in November of 2021 accompanied by high levels of fecal bacteria observed at the monitoring sites.
Figure 3. SSM-Portage model inputs of fecal bacteria sources from streams stations (black triangles) and coastal outfalls (red dots). Monitoring data were acquired from Whatcom County and Lummi Natural Resources Department
The leading hypothesis is that FB contamination in Portage Bay is dominated by FB load in the Nooksack River discharge. Model successfully predicted the time variation of observed FB concentrations over the shellfish beds in Portage Bay. The FB peaks at DOH stations generally followed the timing of observed high FB concentrations in Nooksack River, which confirmed the dominant influence of Nooksack River discharge. However, hotpots of high FB levels were also observed along the west shoreline of Portage Bay. These also occurred when loading from Nooksack River was low. To test the hypothesis that these hotspots may be from local stormwater outfalls, sensitivity tests were conducted during low river inflow period (i.e., September) with additional FB inputs from coastal outfalls (SW035). These were not included in the baseline previously due to lack of data associated with these outfalls. The simulation successfully reproduced the high FB level at DOH stations close to the coastline (DOH050, DOH051) during the low flow season in mid-September. The hotspot in observed FB concentrations was at station DOH050 near Hermosa Beach adjacent to stormwater outfall SW035. These tests indicated that the coastal stormwater outfalls likely had strong local impact and may be significant pollution sources during the dry flow period of Nooksack River.
Figure 4. SSM-Portage model simulations of FB concentrations at DOH marine monitoring stations in comparison with observed data in 2021. The red dots, grey line and black line represented observation data, baseline simulation and sensitivity test respectively. The contour plot on the right showed the FB concentration distribution during survey in mid-September 2021.
Project Highlights for the Portage Bay study
- Flood tide, high freshwater flow and northeasterly winds favor the freshwater plumes spreading into Portage Bay; the north and west part of Portage Bay is most impacted by freshwater plumes; the possible longest flushing time for Portage Bay is ~32 hours which occurs during low freshwater flow period; Nooksack River input dominates the pollutant concentrations in Portage Bay, especially during the high freshwater inflow periods.
- The SSM-fb model simulation successfully reproduced the magnitude and seasonal variation of FB concentrations in the Portage Bay. The results show that the Nooksack River is a dominant source for FB in the Portage Bay. However, during the dry flow period, the coastal stormwater outfalls likely have strong local impact and may be significant during storm/high runoff events.
- The results also imply that frequent field surveys in the downstream part of watershed (especially during and after raining event) and at stormwater outfalls may be required to provide an early indication of FB contamination in the shellfish beds area. The future integration of a separate watershed bacteria transport model (i.e., EPA-VELMA) with SSM will not only be an alternate to high frequency monitoring data, but also be able to provide real-time operational forecast of FB contamination in the marine environment.
Results for the Samish Bay and Drayton Harbor portions of this study are summarized the Ni et al. 2022 and Ni et al. 2023 technical memorandums listed below.
Contacts and Project Team
Wenfei Ni, Pacific Northwest National Laboratory
Tarang Khangaonkar, Pacific Northwest National Laboratory
Technical Memorandum
[1] Ni W., T.P. Khangaonkar, and M. Premathilake. 2023. Whatcom and Skagit County Shellfish Beds Fecal Bacteria Exposure Assessment using SSM: Drayton Harbor Circulation, Freshwater Plume Simulations, and Flushing Analysis & Fecal Bacteria Calibration Exposure Assessment. PNNL-34775. Richland, WA: Pacific Northwest National Laboratory.
[2] Ni W., T.P. Khangaonkar, and M. Premathilake. 2022. Whatcom and Skagit County Shellfish Beds Fecal Bacteria Exposure Assessment using SSM: Samish Bay – Circulation, Freshwater Plume Simulations, and Flushing Analysis. PNNL-xxxx. Richland, WA: Pacific Northwest National Laboratory.
[3] Ni W., T.P. Khangaonkar, and M. Premathilake. 2022. Whatcom and Skagit County Shellfish Beds Fecal Bacteria Exposure Assessment using SSM: Samish Bay Fecal Bacteria Calibration and Exposure Assessment. PNNL-xxxx. Richland, WA: Pacific Northwest National Laboratory.
[4] Ni W., T.P. Khangaonkar, and M. Premathilake. 2023. Whatcom and Skagit County Shellfish Beds Fecal Bacteria Exposure Assessment using SSM: Portage Bay – Circulation, Freshwater Plume Simulations, and Flushing Analysis. PNNL-xxxx. Richland, WA: Pacific Northwest National Laboratory.
[5] Ni W., T.P. Khangaonkar, and M. Premathilake. 2023. Whatcom and Skagit County Shellfish Beds Fecal Bacteria Exposure Assessment using SSM: Portage Bay Fecal Bacteria Calibration and Exposure Assessment. PNNL-xxxx. Richland, WA: Pacific Northwest National Laboratory.
Presentations
[1] Ni W., T.P. Khangaonkar, and M. Premathilake. 06/20/2023. “Whatcom and Skagit County Shellfish Beds Fecal Bacteria Exposure Assessment using SSM: Drayton Harbor circulation and fecal bacteria modeling.” Presented by W. Ni at Whatcom Clean Water Program Core Team Meeting, Online Conference, United States. PNNL-SA-186575
[2] Gockel C., T.P. Khangaonkar, W. Ni and M. Premathilake. 01/23/2023. “Whatcom and Skagit County Shellfish Beds Fecal Bacteria Exposure Assessment using SSM – Portage Bay Circulation and Fecal Bacteria Modeling.” Presented by T.P. Khangaonkar, C. Gockel, W. Ni at Whatcom Clean Water Program Core Team Meeting, Online, Washington. PNNL-SA-181265.
[3] Gockel C., T.P. Khangaonkar, M. Premathilake, and W. Ni. 05/24/2022. “Whatcom and Skagit County Shellfish Beds Fecal Bacteria Exposure Assessment using SSM YR1 (Q1, Q2, Q3) Progress Presentation to Shellfish Growers.” Presented by T.P. Khangaonkar, C. Gockel, M. Premathilake at Presentation to Shellfish Growers Association led by Taylor Shellfish, Online Conference, Washington. PNNL-SA-173548.