CICEET Progress Report for the period 9/02/07 Through 3/01/08

Project Title: Development of a Land Use Planning Tool for Estuarine Habitat Protection, Restoration and Cumulative Effects Assessment in North Puget Sound, WA
Principal Investigator(s): Tarang Khangaonkar (PNNL)
Additional Investigator(s): Zhaoqing Yang and Andrea Copping (PNNL); Kurt Fresh and Correigh Greene (NWMFS); Eric Beamer and Greg Hood (SRSC); Erick Grossman (USGS); Douglas Bulthuis (Padilla Bay ­ NERR)
Project Start Date: 7/01/2007

Figures

Figure 1

Figure 2

Figure 3

Figure 4

In general these efforts suffer from a lack of information about how to assess the feasibility of various restoration and protection options and the implications of proposed changes on key resources such as salmon and existing and alternate land uses. Project managers, scientists, land owners and engineers from various partnering agencies involved in Puget Sound nearshore restoration activities have repeatedly voiced concerns and expressed the need for more oceanographic information to help planning and decision-making. Nearshore restoration projects often lack the required hydrodynamic information necessary to make informed decisions on modifications to the topography and hydrology. However, the models/tools that are typically available through universities are larger scale oceanographic circulation models address broader circulation and transport but lack the scale required for simulating the exchange in the nearshore marshlands.

Objectives
In this study, development of a basin-scale hydrodynamic model with the required resolution along the shoreline for addressing the effects of land use decisions is proposed. The tool development will be conducted using a 3-D unstructured grid model such as FVCOM (Univ.Mass) which was tested and found to be particularly well suited for the simulation of complex shorelines and the associated shallow mud flats and tidal marshes, incorporating wetting and drying. With recovery of fish stock often one of the major goals of nearshore restoration projects; development of a module that would allow fish biologists to predict the movement of fish for various scenarios through a fish-like particle tracking model is also part of the scope of this project. This will help planners to better assess if proposed restoration actions will result in any benefit in terms of restoration of estuarine functions, recovery of habitat, and creation of conveyance pathways for migrating fish.

The overall objective of this project is to develop an interactive practical tool that will enable land-use planners to effectively address their concerns with respect to planning coastal development and restoration projects. The practical tool we proposed primarily consists of 1) hydrodynamic and constituent transport model and 2) an interactive user interface which land-use planner can easily use to examine movement of fish and particles and water quality constituents, integrated with a hydrodynamic solution for specific restoration project.

Tasks to meet objectives
The scope of this project was designed for completion through two phases over a two-year period. Year 1 focuses on the development, construction, testing and calibration of the Whidbey Basin-wide hydrodynamic model. Year 2 will focus on documentation and application of the model to a selected set of restoration projects in the basin and training of partner and other stakeholder staff in examining potential cumulative effects and impacts on planning. One of the underlying goals of this project is to get land use owners to understand and appreciate that restoration is a feasible option. Therefore communication and outreach is an important goal that will be carried out throughout the duration of the project. We expect to work with Padilla Bay NERR to conduct stakeholder outreach activities and solicit feedback to on the direction of the development of the Whidbey Basin Model (land use planning tool).

Specific tasks completed as of 2/28/2008 and subsequent tasks in progress and to be completed in each phase of the study are listed below.

Year 1 - Development of a Whidbey Basin Wide Hydrodynamic Model:
Task 1: Data Acquisition and Processing ­ (completed)
Task 2: Hydrodynamic Model Setup for Whidbey Basin ­ (completed)
Task 3: Model Calibration ­ (in progress)
Task 4: Land Use Planning Tool for Estuarine Restoration, Part 1 - Whidbey Basin Hydrodynamic Model Development Study Report ­ (in progress)
Task 5: Meetings, Presentations, and Outreach ­ (on going activity)

Year 2 ­Assessment of Cumulative Effects and Restoration Planning Tool Development
Task 6: Assessment of Cumulative Impacts of Restoration Projects.
Task 7: Fish-Like Particle Tracking Desktop Utility.
Task 8: Land Use Planning Tool for Estuarine Restoration, Part 2: Assessment of Cumulative Effects and Development of Fish-Like Particle Tracking Tool - Study Report:
Task 10: CICEET Metrics and Plan for Measurement

Progress on Tasks
Task 1: Data Acquisition and Processing: The project team collected and processed all data required for developing a Whidbey Basin hydrodynamic model and calibration. The data includes study domain geometry, bathymetry, shoreline definition, detailed LIDAR data, tidal marsh data, river flows and freshwater sources around the basin, tides and salinity, velocity distribution, and meteorological data. These data were processed and used in the development and calibration of the integrated Whidbey basin hydrodynamic model. Bathymetry data in the Whidbey basin were obtained from the several agencies. The bathymetry data includes University of Washington (UW) Puget Sound Digital Elevation Model (DEM), LIDAR from Puget Sound LIDAR Consortium and Counties, and cross-sectional data from USACE and counties. UW Puget Sound DEM data were used to define the main water body of Whidbey basin. The data have 30-ft by 30-ft spatial resolution. The LIDAR were used to accurately represent mudflats near the mouth of three major rivers. The cross-section data in the major rivers were used to define the bathymetry in the river sections of the model. Tidal elevations data for model open boundary conditions were obtained form the NOAA Xtide program because no measurement data were available during simulation periods. Wind data are required to specify wind stress at the water surface in the model. Wind data were obtained from the NOAA’s National Weather Service site at Everett/Paine Field (KPAE) Station near the study area.

The field-data for model calibration near the restoration sites in the Skagit Bay, Port Susan Bay, Snohomish Basin, Saratoga Passage and Possession Sound were collected, including velocity, tidal elevation, and salinity time histories and profiles. The calibration locations are shown in the map (see Figure 1).

Task 2: Hydrodynamic Model Setup for Whidbey Basin: The hydrodynamic model for Whidbey Basin was developed and set up for three different periods corresponding to the available data collection periods. The 3-D hydrodynamic model used in this study is the Finite Volume Coastal Ocean Model (FVCOM) developed by the University of Massachusetts at Dartmouth. FVCOM solves 3-D momentum, continuity, temperature, salinity, and density equations in an integral form by computing fluxes between non-overlapping horizontal triangular control volumes. This finite-volume approach combines the advantages of finite-element methods for flexibility in handling complex shorelines and the superior ability of finite difference methods for limiting numerical diffusion, handling simple discrete structures, and computation efficiency. A sigma-stretched coordinate system is used in the vertical plane to better represent the irregular bottom topography.

To simulate the tidal-wave propagation and salinity intrusion properly in the multi-channel and tidal mud-flat area, finer grid cells were specified in the marshlands between the tributary sloughs. The determination of land geometry and bottom bathymetry is one of the most important factors affecting the accuracy of model prediction of tidal circulation in estuaries. Because of the complexity of the braided estuary and the presence of a large tidal mud flat and surrounding tidal marshlands, high-resolution and accurate bathymetry data were required in the model setup.

The model grid covering the entire Whidbey basin and Padilla bay was developed (see Figure 2). The model grid resolution gradually decreases away from the estuarine delta to the open boundaries to maintain the computational efficiency of the model. Model grid sizes vary from 350 meters at the open boundaries to about 15 meters within the estuary marshland and river channels. The model grid was extended into diked tidal marshlands between river channels through openings in the dike breaches in the restoration areas. The total number of nodes and triangular elements in the model are 25,070 and 43,810 in the horizontal plane. Ten uniform vertical layers were specified in the water column in a sigma-stretched coordinate system. The combined model bathymetry data was interpolated onto the model grid (see Figure 3).

The model was setup for the calibration periods using forcing conditions such as tides at open boundaries, meteorological information, and river inflows at Skagit River, Stillaguamish River, and Snohomish River. The selected calibration stations and periods are as follow:

• Skagit bay ­ 6/6/2005 ~ 6/23/2005
• Port Susan bay ­ 10/10/2005 ~ 10/26/2005
• Snohomish basin ­ 10/12/2006 ~ 10/28/2006
• Whidbey Basin Joint Survey ­ October 2006

Model open boundary conditions specified were tidal elevations predicted using the XTIDE program based on National Oceanic Service algorithms. Tidal elevations were specified at the following three open boundaries: 1) Entrance of Possession Sound, 2) Deception Pass, and 3) Entrance of Padilla Bay. There were no salinity data available along the open boundaries. However, the salinity profiles measured in Whidbey Basin during oceanographic survey showed that salinities are quite uniform vertically, around 32 ppt. Therefore, salinity profiles along the open boundaries were specified as constant at 32 ppt. Field data also indicated that temperature variations in the study area were less than 5°C during the simulation period, and salinity variations near the restoration project site were more than 20 ppt. Therefore, the effect of temperature on density is likely not significant in comparison to the effect of salinity. The temperature effect on the density-induced currents thus was not simulated in this study.

Task 3: Model Calibration ­ (in progress): After model setup and initial testing, the project team is conducting the entire Whidbey basin model calibration task for each basin. The initial model results were examined to ensure reasonable results with numerical stability. Currently, the model calibration task is in progress and results are encouraging. A qualitative result in the form of a flow trace indicates that the model is up-and-running and general circulation patterns showing that most of the tidal flow passes through Saratoga Passage and connects Skagit Bay to Puget Sound (see Figure 4). The calibration of the entire study domain is being conducted by matching the model prediction to the observed data in the following format:

• Time series comparison of tide elevation
• Time series comparison of velocities
• Time series comparison of salinities
• Salinity profiles for available mooring stations.

Task 4: Land Use Planning Tool for Estuarine Restoration, Part 1 - Whidbey Basin Hydrodynamic Model Development Study Report ­ (in progress): The calibration results will be included in the Year 1 project study report. The report preparation work has been initiated.

Task 5: Meetings, Presentations, and Outreach ­ (on going activity)

Project Kickoff meeting
A “Kickoff Meeting” was held at Padilla Bay NERR on January 28, 2008. The purpose of the kickoff meeting was to provide a progress report on the tasks completed, an opportunity for the project partners to meet face to face, discuss the project scope, roles and responsibilities, schedule, budgets etc.

PNNL provided a project background and a historical perspective of how the various groups (SRSC, USGS, NMFS, and USGS) working in the Skagit delta came together to address the needs of nearshore restoration and fish stock recovery projects. PNNL project team showed preliminary results demonstrating that the model was up and running, thereby concluding Tasks1 and Task 2 of the scope of FY2008 work. Remainder of FY2008 work includes Task 3: Model Calibration, Task 4: Study Report and Task 5: Outreach.

A data gap identified was lack of high resolution bathymetry for Padilla Bay mudflats. The present bathymetry consisting of UW-DEM and 1950s hydrographic survey data is considered sufficient for this project.

Doug Bulthuis of Padilla Bay NERR and Andrea Copping from PNNL will lead the outreach activities starting with the list of planning partners included in the proposal. Also, new organizations recently identified such as City of Everett and Port of Everett who are also involved in nearshore restoration activities will be added to the list. The possibility of putting together a simple webpage for disseminating information (meeting notes, project progress presentations, memos, and biannual and annual reports) was discussed. Cathy Angell the Training Coordinator for Padilla Bay assessed the possibility of hosting the Webpage. Eric Beamer also offered SRSC web page as another possibility.

In preparation for FY2009, PNNL project team and SRSC provided their ideas on how to go about developing a fish migration/tracking tool. Although the Whidbey Basin hydrodynamic model is the real tool for assessing restoration feasibility, it is this fish tracking “software” which may be used by biologists and non-modelers which will be the product that will meet the “hand-on” tool requirement of the study. We are looking at NOAA GNOME particle tracking and other public domain software(s) for this application.

The project is on schedule and an all hands stakeholder meeting is being scheduled to be held at Padilla Bay, in September of this year. At that meeting the PI's will report on the status of the model or parts of the project and we will get feedback from the partners/stakeholders.

Difficulties
No unexpected difficulties were encountered

Data Generated to date
The following data required for model input and setup were generated as follow.

• Study domain geometry and bathymetry
• LiDAR flight data and analysis
• Model calibration data (tide elevation, velocity, salinity)
• Model open boundary conditions and river flow boundary conditions
• Meteorological forcing
• Model grid covering the entire Whidbey basin and Padilla Bay
• Preliminary model calibration results

Project Objectives for Next Reporting Period

Objectives
For the next reporting period, the objectives are as follows
(a) Completion of Task 3: Model Calibration,
(b) Completion of Task 4: Year 1 Study Report, and
(c) Continuation of Task 5 Meetings and Stake holder Outreach activities.

Work Plan to Meet Objectives
The study tasks are progressing on schedule and on budget. Our plan is to stay on track per schedule indicated below to ensure timely and on budget completion of Phase 1 activities.

Task 3: Model Calibration - Completion date: April 30, 2008
Task 4: Phase 1 Draft Study Report ­ Completion Date: July 30, 2008
Task 5: Meetings and Stakeholder Outreach ­ Periodic Meetings with project partners, stake holders, and other collaborators on an as needed basis.

We expect to submit a draft report to CICEET for review and comments in August 2008. Assuming that comments are received within two weeks, a final Phase I study report will be submitted to CICEET in September of 2008.

Expenditures
Expenditure to date is on track with proposed scope of work. Tasks 1 and 2 are complete and the budgets have been used completely. The budgets for Tasks 3 and 4 appear to be reasonable as work has just been initiated. The budget for Task 5 meetings and outreach activities was significantly underestimated. The project could benefit if additional funds were to become available in the future for improving the performance related to this activity.