Snohomish Estuary Restoration Effects on Temperature, Salinity, and Tides

From Salish Sea Wiki

Wiki Rules

Link to List of Workgroups Link to List of Topics Link to List of Places

Link to List of Efforts Link to List of Products Link to List of Documents Link to List of Graphics Link to List of Websites

Link to Delta Sites Link to Embayment Sites Link to Beach Sites Link to Rocky Headland Sites

Link to Headwater Sites Link to Lowland Watershed Sites Link to Floodplain Sites

Snohomish River Estuary CWS and CTD monitoring sites.

This study aims to evaluate the short and long-term impacts of estuary restoration to support development recommendations for restoration and resilience planning. This study will be completed in several phases. As part of Phase 1, water temperature, depth, and salinity data collected since 2012 were used to generate a post-restoration analysis of water conditions within the estuary, and the effects of the Qwuloolt and Smith Island restoration projects on water quality conditions. This included updating the existing Snohomish Estuary Model from the year 2007 effort to reflect current conditions circa 2014 and 2021 using water temperature, depth, and salinity data along with updated bathymetry. The model was used to simulate pre- and post-Qwuloolt and Smith Island restoration and set the stage for subsequent phases of model and scenario development. Phase 2 & 3 of the project will build on Phase 1 by taking the information learned from the Phase 1 modeling effort and developing model runs of the Snohomish estuary including integration of a three-dimensional hydro-heat flux numerical model to capture the effects of exposed tidal flats on water temperature (Phase 2), and modeling full restoration buildout (Phase 4). The final phase (Phase 5) of the project will look at water temperature, salinity, and tidal conditions utilizing the previously developed modeling components under future climate conditions in 2095. This page reports the results of Phase 1.

This study is the result of a combined effort by Cramer Fish Sciences in collaboration with the Tulalip Tribes, Salish Sea Modeling Center, NOAA NWFSC, and Snohomish County Surface Water Management Division.


Most large-scale estuary restoration projects involve removal, lowering, or breaching of dikes and levees to restore tidal flooding to lands previously used for agricultural purposes. This leads to decay of organic materials and subsidence of estuary habitat, creating predictable changes to the tidal prism and warmer, more variable conditions, especially in sites in the lower estuary. Given that elevation and inundation duration are strong drivers of vegetation establishment in estuary systems, subsided lands may remain unvegetated until sediment supply and transport processes can increase surface elevations sufficient to support vegetation establishment. The period in which recently restored tidal marshes remain unvegetated is of potential concern for restoration effectiveness.

Current restoration strategies assume sites will naturally transition toward offering the functional benefits of natural sites over time. However, the impacts of restoration actions on estuary conditions, which influence success expectations and management decisions, are less understood. The Snohomish River estuary  targeted for Chinook Salmon recovery[1] has seen extensive restoration, supported by a long-term monitoring framework deploying continuous water sensors since 2010 to measure salinity, temperature, and water level at 10-minute intervals. As part of the intensive restoration effectiveness monitoring program, water quality data were collected before and after the Qwuloolt (2015, Ebey Slough) and Smith Island (2018, Union Slough) restoration projects, which restored tidal flooding to 142 and 124 hectares, respectively. This included analyzing daily river flow data, extreme flow conditions, vertical water column profiles, and continuous sensor data to understand the short-term impact of restoration on estuary hydrology. The existing Snohomish Estuary Model was also updated to simulate pre- and post-Qwuloolt and Smith Island restoration conditions circa 2017 and 2021, respectively, and model system-scale responses to restoration.

Study Questions[edit]

  • ·        How does restoring tidal flooding to previously diked areas influence hydrology with respect to key parameters like salinity and temperature?
  • ·        What are the temporal and spatial extent of changes salinity and temperature related to restoration?
  • ·        How are these changes meaningful to juvenile Chinook rearing and restoration planning and evaluation in general?  


As part of the intensive system-wide restoration effectiveness monitoring program, a system-wide network of continuous water sensors and periodic collection of water column profile data were deployed to collect water quality data spanning the periods before and after implementation of the Qwuloolt and Smith Island restoration projects. We used data from these monitoring efforts and a series of hydrodynamic models to evaluate how implementation of these two projects has influenced hydrology.

Data collection

  • Daily river flow data from water years 1963 to 2022 for the mainstem Snohomish River USGS Station 1215080
    • Classified as extreme low flow, low flow, high flow, or flood conditions[2].
    • Attributed to CWS data.
  • Vertical water column profiles
    • Collected at the mid-channel of distributaries periodically from 2009 to 2022, and more intensively at the Qwuloolt breach site
    • Used to evaluate the maximum extent of salt intrusion and patterns of salinity, pH, turbidity, and dissolved oxygen.
  • Continuous water sensor data
    • Collected water level (pressure), temperature, and salinity (conductivity) at 10-minute intervals at 19 sensor locations from 2010 to 2021.
    • Used to evaluate conditions during peak juvenile Chinook presence in the estuary.
  • Snohomish Estuary Model
    • Updated previous 2014 pre-restoration model to conditions circa 2017, and to conditions circa 2021 to represent post-restoration conditions.
    • Used to compare pre- and post-restoration conditions in the Snohomish River estuary for water level, salinity, and velocities (temperature to be evaluated in later phases).


Field monitoring

  • Used system-wide water column profile surveys to determine changes in maximum extent of salt intrusion in the estuary during extreme low flow and spring tide conditions with restoration of Qwuloolt and Smith Island.
  • Used Qwuloolt intensive water column profiles to evaluate short term impacts to water quality with restoration of Qwuloolt.
  • Used long-term continuous water sensor data to evaluate changes in the time in mixohaline categories (freshwater (0-0.5 ppt), oligohaline (0.5-5.0 ppt), mesohaline (5.0-18.0 ppt), and polyhaline (18.0-30.0 ppt)), and changes in mean salinities before and after restoration of both Qwuloolt and Smith Island.
  • Used long-term continuous water sensor data to evaluate changes in the time in temperature ranges relevant to juvenile Chinook (sub-optimal temperatures for growth (<9°C), optimal temperatures for growth (9-16°C), above optimal temperatures for growth (16-19°C), and detrimental temperatures (>19°C)), and changes in mean temperatures before and after restoration of both Qwuloolt and Smith Island.
  • Used long-term continuous water sensor data to evaluate differences in temperatures above and below the Qwuloolt outlet during ebbing tides that followed a daytime high tide, where shallow surface waters could potentially be heated on unvegetated mudflats.


  • Modeled pre- and post-restoration conditions using a previously developed 3-D unstructured hydrodynamic model and historical topography and bathymetric survey data for Snohomish Estuary and 2014 (pre-) and 2021 (post-) CWS data to calibrate the model for salinity and water surface conditions.
  • Evaluated the local and direct effects of restoration projects due to physical shoreline and bathymetric alterations.
  • Tested the effects of restoration actions on water elevation, salinity, and currents by using identical meteorological, hydrological, and tidal conditions for pre- and post-restoration models.
Available salinity, temperature, and water level data for each CWS site
Snohomish river estuary model grid for pre- (2014 baseline) and post- (2021) restoration conditions

Key Findings[edit]

Monitoring results
We found evidence that the Qwuloolt and Smith Island restoration projects reduced the maximum extent of salt intrusion in the estuary (shifting from river kilometer 15.7 to 13.4 in the mainstem distributary) while also increasing the strength of salt intrusion in the lower estuary below the restoration projects.

  • Increases in salinities were strongest in the lower estuary and closest to the projects after each project was implemented (e.g., 0.5-7.1 ppt) and were not confined to the distributary in which the restoration occurred, with implementation of the Smith Island Restoration project resulting in a reduction in salinity near the Qwuloolt Restoration project.
  • We found evidence for significant shifts in temperature patterns, but the magnitudes of these shifts were low at the system and site scale compared to salinity (e.g., 0.3-1.3°C) and the results appear to be confounded by background variation in riverine and marine temperatures.
  • Prior to implementation of the Qwuloolt Restoration project, temperature differences above and below the breach location were relatively similar and we detected a significant increase in temperature differences post restoration when looking at low tides following daytime high tides from February – September. However, we also detected a significant decreasing trend in the temperature differences that we hypothesize could be related to increasing vegetation coverage inside the Qwuloolt over time. We also note that this finding is restricted to the ebbing tides following a daytime high tide, and additional analyses and monitoring are needed to determine the potential spatial extent and temporal duration of this thermal loading, which would ultimately inform our understanding of how or if this observation impacts juvenile salmon in the Qwuloolt or Ebey Slough.

Our results showed that implementation of subsequent projects can result in cumulative changes or additional shifts at system-scales and project impacts are not restricted to the distributaries in which the restoration sites are located. This supports the hypothesis that restoration projects have both a site-level and system-level effect on salinity patterns, and that the effects of restoration are cumulative over time.

Model results for salinity during low and high tide for pre- and post-restoration conditions.

Model results
The modeling successfully predicted tidal amplitudes, water surface elevations, and salinity fluctuations in pre- and post-restoration scenarios. When comparing water elevation, salinity, and currents for pre- and post-restoration scenarios, there was little difference in water surface levels or tidal amplitude and phase, indicating a minimal alteration of mean sea level and a minor change in tides following restoration.

An overall increase in tidal prism volume of 9.1% was modelled in the Snohomish Estuary following restoration, as well as an increase in periodic inundation and resumption of tidal exchange in and out of the restored area. The increased tidal prism that enters the estuary during each tide and associated salt flux resulted in an increase in saline conditions and intrusion of salt further into the estuary. The model indicated that the maximum extent of saltwater intrusion (0.5 ppt) increased from river kilometer 15.0 to 15.7 in the mainstem, as well as increases in the other distributaries (0.7-0.8 km). These results are opposite of the findings from the water column profiles and may be indicative of differences in conditions during field surveys that are controlled for in the hydrodynamic model.

Additionally, we observed significant changes in peak velocities downstream of restoration sites (≈40% increase in Union Slough below Smith Island, and ≈58% increase below Qwuloolt in Ebey Slough), and a corresponding increase in velocity/flow or volume flux through each distributary downstream of the project. This was paired with a reduction in velocity magnitudes of ≈55% in Ebey Slough and ≈40% in Union Slough upstream of the restoration sites. Changes in velocity were also observed throughout the network of distributaries in response to restoration (e.g., in Steamboat Slough) and to a lesser extent (<2% change) in the Upper and Middle Snohomish River mainstem distributary.

Overall, the effects of restoration actions on salinity and velocity were most pronounced at locations and reaches that are directly connected with restoration sites, but the results also highlight subtle yet significant estuary-wide effects on hydrodynamics due to increased tidal prism volumes.

This comprehensive approach to monitoring and modeling demonstrates the nuanced understanding required to evaluate and predict the outcomes of estuary restoration efforts, providing valuable insights for future planning and management decisions in the Snohomish River estuary and beyond.


Please contact Todd Zackey ( or Jason Hall ( with any questions regarding this project.

  1. Snohomish Basin Salmon Recovery Forum (SBSRF). 2013. Snohomish River basin 10-year salmon conservation plan and 3-year Work Plan. Snohomish County Department of Public Works, Surface Water Management Division, Everett, Washington,
  2. Indicators of Hydrological Alteration Software Version 7.1