Automating Landscape Connectivity for Puget Sound River Deltas and Pocket Estuaries

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Cramer Fish Sciences will complete development of an automated landscape connectivity tool and dataset with landscape connectivity scores for all Puget Sound large river deltas and small embayments features between 2023 and 2025. This work will support future recovery and restoration planning by producing a standardized and readily available approach to calculate landscape connectivity across the Puget Sound region.

Snohomish distributary network bifurcation order and landscape connectivity scores.
Snohomish distributary network bifurcation order and landscape connectivity scores.


Landscape connectivity describes the accessibility of estuarine habitat as a function of distance and complexity of pathways juvenile salmon must follow to reach estuarine or nearshore habitats [1]. Habitat connectivity decreases as the complexity of migration routes (i.e., number of bifurcations) and pathway distance increases along bifurcations to natal estuary habitats, non-natal nearshore habitats (e.g., pocket estuaries, lagoons, or other embayments), or other non-natal estuaries. Previous studies have shown that landscape connectivity is a significant predictor of juvenile salmon densities and can be used to evaluate the effects of changing connectivity through restoration or natural processes [1] [2]. However, current methods rely on manual remote sensing, which introduces variance in mapping of connectivity scores, and increases the time it takes to generate data layers to support research and planning.

Goals and Objectives

The primary aim of this project is to develop an automated tool designed to consistently calculate landscape connectivity that employs various metrics believed to describe the relationship between landscape connectivity and juvenile Chinook distribution and density. This tool will facilitate the testing of multiple landscape connectivity models as well as enable the comparison of these model scores with observed distribution and densities to help fine-tune the selection and weighting of model parameters. A key feature of the tool will be its ability to generate the necessary input metrics autonomously and consistently, requiring minimal input from the user. The tool will provide landscape connectivity scores along the distributary network or to specific points, accompanied by comprehensive documentation describing how the model was configured to produce the results. Additionally, the project will include thorough documentation on how to use the tool, along with detailed descriptions of the underlying methodologies and assumptions. Overall, our goal is to facilitate and standardize the estimation of landscape connectivity scores to allow managers and practitioners the ability incorporate these values into further analyses, recovery planning, and restoration planning.

Key Questions

  • What factors of landscape connectivity best predict observed fish abundance?
  • How does landscape connectivity play out in different regions? How well do formulations for one distributary network apply to others?
  • Are there other additional factors that should be included when considering calculating landscape connectivity scores?


Data layers, connectivity indices, and metrics: Landscape connectivity layers and scores for all Puget Sound large river deltas and small embayment features. This will include alternate formulations and supporting metrics developed as part of this project and analyses, as well as all standardized input datasets that can be used to run the tool/analyses.

Automated tool and GUI: An automated tool and GUI for calculating landscape connectivity scores, which will be hosted online and made readily available.

User guide and tool documentation : User guides and documentation describing how to use the automated tool. Connectivity layers will be developed as spatial data layers that will include connectivity scores to natal and non-natal habitats (e.g., other deltas or nearshore habitats like pocket estuaries) for all large river deltas that have input data available. Given that these results will be based on input layers that represent a static snapshot in time, the automated GIS tool is an important deliverable for restoration planners and comanagers given that the tool can be used to develop connectivity score outputs based on restoration scenarios or changing landscape conditions (e.g., like avulsions observed in the Skagit River estuary).

Project report: A draft and final project report, formatted as scientific paper (Introduction, Methods, Results, Discussion) with an executive summary, a preferred bibliographic citation for the final report, and an appendix providing the tool documentation and user guide material.


  1. 1.0 1.1 Beamer, E., A. McBride, C. Greene, R. Henderson, G. Hood, K. Wolf, K. Larsen, C. Rice and K. L. Fresh. 2005. Delta and nearshore restoration for the recovery of wild Skagit River Chinook salmon: linking estuary restoration to wild Chinook salmon populations. Supplement to Skagit Chinook Recovery Plan, Skagit River System Cooperative. La Conner, Washington.
  2. Greene, C.M., E. Beamer, J. Chamberlin, G. Hood, M. Davis, K. Larsen, J. Anderson, R. Henderson, J. Hall, M. Pouley, T. Zackey, S. Hodgson, C. Ellings, and I. Woo. 2021. Landscape, density-dependent, and bioenergetic influences upon Chinook salmon in tidal delta habitats: Comparison of four Puget Sound estuaries. ESRP Report 13-1508.