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Title: Quantification of Off-Channel Inundated Habitat for Pacific Chinook Salmon (Oncorhynchus tshawytscha) along the Sacramento River, California, Using Remote Sensing Imagery

Journal Article · · Remote Sensing
DOI:https://doi.org/10.3390/rs14061443· OSTI ID:1981180

Off-channel areas are one of the most impacted aquatic habitats by humans globally, as extensive agricultural and urban development has limited them to roughly 10% of historical extent. This is also true for California’s Sacramento River Valley, where historically frequent widespread inundation has been reduced to a few off-channel water bodies along the mid-Sacramento River. This remaining shallow-water habitat provides crucial ecological benefits to multiple avian and fish species, but especially to floodplain-adapted species such as Chinook salmon (Oncorhynchus tshawytscha). Characterizing spatiotemporal off-channel dynamics, including inundation extent and residence time, is fundamental to better understanding the intrinsic value of such habitats and their potential to support recovery actions. Remote sensing techniques have been increasingly used to map surface water at regional and local scales, with improved resolutions. As such, this study maps off-channel inundation areas and describes their temporal dynamics by analyzing pixel-based time- series of multiple water indices, modified Normalized Difference Water Index (mNDWI) and the Automated Water Extraction Index (AWEI), generated from LandSat-8 and Sentinel-2 data between 2013–2021. Quantified off-channel area was similar with each water index and method used, but improved performance was associated with Sentinel-2 products and AWEI index to identify wetted areas under lower mainstem discharges. Results indicate an uneven distribution of off-channel habitat in the study area, with limited inundated areas in upstream reaches (<16% of total off-channel area for greater flows). In addition, much less habitat exists for flows under 400 m3/s, an important migration cue for endangered winter-run Chinook salmon, limiting juvenile access to areas with enhanced rearing conditions. Off-channel habitat residence times averaged between 7 and 16 days, primarily defined by the rate of receding flows, with rapid flow recession providing marginal off-channel habitat. This study shows reasonable performance of moderate resolution LandSat-8 and Sentinel-2 remote sensing imagery to characterize shallow-water inundated habitat in higher-order rivers, and as a method to inform restoration and native fish recovery efforts.

Research Organization:
Univ. of California, Oakland, CA (United States)
Sponsoring Organization:
USDOE Office of International Affairs (IA)
Grant/Contract Number:
IA0000018
OSTI ID:
1981180
Journal Information:
Remote Sensing, Vol. 14, Issue 6; ISSN 2072-4292
Publisher:
MDPICopyright Statement
Country of Publication:
United States
Language:
English

References (73)

An efficient method for mapping flood extent in a coastal floodplain using Landsat TM and DEM data journal January 2002
The use of remotely sensed data to detect channel hydromorphology; River Tummel, Scotland journal December 2004
An assessment of the use of remote sensing to map habitat features important to sustaining lamprey populations journal September 2008
Ecological connectivity in alluvial river ecosystems and its disruption by flow regulation journal September 1995
Shifting habitat mosaics and fish production across river basins journal May 2019
Modification of normalised difference water index (NDWI) to enhance open water features in remotely sensed imagery journal July 2006
A Riverscape Analysis Tool Developed to Assist Wild Salmon Conservation Across the North Pacific Rim journal July 2012
Adaptation to natural flow regimes journal February 2004
A Remote-Sensing, GIS-Based Approach to Identify, Characterize, and Model Spawning Habitat for Fall-Run Chum Salmon in a Sub-Arctic, Glacially Fed River journal September 2012
Analysis of Dynamic Thresholds for the Normalized Difference Water Index journal November 2009
Passive optical remote sensing of river channel morphology and in-stream habitat: Physical basis and feasibility journal December 2004
Riverine landscape diversity journal April 2002
The effect of water level on lateral movements of fish between river and off-channel habitats and implications for management journal January 2010
Relating wetland inundation to river flow using Landsat TM data journal January 2003
Evaluation of Landsat 8 OLI imagery for unsupervised inland water extraction journal April 2016
Zooplankton ecology and trophic resources for rearing native fish on an agricultural floodplain in the Yolo Bypass California, USA journal February 2017
Climate, Hydrologic Disturbance, and Succession: Drivers of Floodplain Pattern journal April 2007
One size does not fit all: variation in thermal eco-physiology among Pacific salmonids journal January 2021
Detecting, Extracting, and Monitoring Surface Water From Space Using Optical Sensors: A Review journal June 2018
Remote sensing analysis of physical complexity of North Pacific Rim rivers to assist wild salmon conservation journal July 2010
The science and practice of river restoration: THE SCIENCE AND PRACTICE OF RIVER RESTORATION journal August 2015
Size, growth, and origin-dependent mortality of juvenile Chinook salmon Oncorhynchus tshawytscha during early ocean residence journal July 2013
Validating alternative methodologies to estimate the regime of temporary rivers when flow data are unavailable journal September 2016
Unimpaired and Regulated Discharge in the Sacramento River Basin, California journal January 1995
Landfalling Atmospheric Rivers, the Sierra Barrier Jet, and Extreme Daily Precipitation in Northern California’s Upper Sacramento River Watershed journal July 2016
Mapping spatio-temporal flood inundation dynamics at large river basin scale using time-series flow data and MODIS imagery journal February 2014
Monitoring the effectiveness of floodplain habitat restoration: A review of methods and recommendations for future monitoring journal June 2019
Reach Scale Hydraulic Assessment of Instream Salmonid Habitat Restoration journal December 2004
Effects of flow variation on channel and floodplain biota and habitats of the Sacramento River, California, USA
  • Sommer, Ted R.; Harrell, William C.; Solger, Anke Mueller
  • Aquatic Conservation: Marine and Freshwater Ecosystems, Vol. 14, Issue 3 https://doi.org/10.1002/aqc.620
journal May 2004
Extending water resources performance metrics to river ecosystems journal July 2020
Juvenile Chinook salmon (Oncorhynchus tshawytscha) growth in off-channel and main-channel habitats on the Sacramento River, CA using otolith increment widths journal April 2009
The influence of flood cycle and fish predation on invertebrate production on a restored California floodplain journal June 2006
Effects of atmospheric river landfalls on the cold season precipitation in California journal March 2012
Modeling the effect of habitat availability and quality on endangered winter-run Chinook salmon (Oncorhynchus tshawytscha) production in the Sacramento Valley journal May 2021
Using optimization to develop a “designer” environmental flow regime journal February 2017
The California Environmental Flows Framework: Meeting the Challenges of Developing a Large-Scale Environmental Flows Program journal October 2021
Designing flows to resolve human and environmental water needs in a dam-regulated river journal December 2017
Automated Water Extraction Index: A new technique for surface water mapping using Landsat imagery journal January 2014
Ecologically Functional Floodplains: Connectivity, Flow Regime, and Scale 1 : E journal March 2010
Application of airborne multispectral digital imagery to quantify riverine habitats at different base flows journal January 2002
Riverine flood plains: present state and future trends journal September 2002
Estimate of flood inundation and retention on wetlands using remote sensing and GIS journal January 2014
Historical Abundance and Decline of Chinook Salmon in the Central Valley Region of California journal August 1998
The Mekong from satellite imagery: A quick look at a large river journal March 2007
Kinematic and Thermodynamic Structures of Sierra Barrier Jets and Overrunning Atmospheric Rivers during a Landfalling Winter Storm in Northern California journal June 2013
Regional scale flood modeling using NEXRAD rainfall, GIS, and HEC-HMS/RAS: a case study for the San Antonio River Basin Summer 2002 storm event journal June 2005
Priming the productivity pump: flood pulse driven trends in suspended algal biomass distribution across a restored floodplain journal August 2006
Analysis of Landsat-8 OLI imagery for land surface water mapping journal July 2014
Floodplain rearing of juvenile chinook salmon: evidence of enhanced growth and survival journal February 2001
Detection of Shallow Water area with Machine Learning Algorithms journal June 2019
Fish, Flows and Flood Plains: Links between Freshwater Fishes and their Environment in the Murray-Darling River System, Australia journal September 1999
Optimization tools for environmental water decisions: A review of strengths, weaknesses, and opportunities to improve adoption journal October 2016
Estimation of Juvenile Salmon Habitat in Pacific rim Rivers Using Multiscalar Remote Sensing and Geospatial Analysis journal October 2011
Oversummer growth and survival of juvenile coho salmon ( Oncorhynchus kisutch ) across a natural gradient of stream water temperature and prey availability: an in situ enclosure experiment journal February 2020
Functional Flows in Modified Riverscapes: Hydrographs, Habitats and Opportunities journal August 2015
Modelling spatial‐temporal change of Poyang Lake using multitemporal Landsat imagery journal September 2008
Linkages between flow regime, biota, and ecosystem processes: Implications for river restoration journal September 2019
Decision analysis for greater insights into the development and evaluation of Chinook salmon restoration strategies in California's Central Valley journal October 2020
Ephemeral floodplain habitats provide best growth conditions for juvenile Chinook salmon in a California river journal June 2008
Google Earth Engine: Planetary-scale geospatial analysis for everyone journal December 2017
Detrital food web contributes to aquatic ecosystem productivity and rapid salmon growth in a managed floodplain journal September 2020
Open Surface Water Mapping Algorithms: A Comparison of Water-Related Spectral Indices and Sensors journal April 2017
Open surface water index: a novel approach for surface water mapping and extraction using multispectral and multisensory data journal September 2020
Riverine landscapes: Biodiversity patterns, disturbance regimes, and aquatic conservation journal March 1998
Modelling stage—discharge relationships affected by hysteresis using the Jones formula and nonlinear regression journal June 2006
A functional flows approach to selecting ecologically relevant flow metrics for environmental flow applications journal January 2020
Accurate extraction of surface water in complex environment based on Google Earth Engine and Sentinel-2 journal June 2021
Migration Patterns of Juvenile Winter-run-sized Chinook Salmon (Oncorhynchus tshawytscha) through the Sacramento–San Joaquin Delta [Migration Patterns of Juvenile Winter-run-sized Chinook Salmon (Oncorhynchus tshawytscha) through the Sacramento–San Joaquin Delta] journal March 2013
The shifting habitat mosaic of river ecosystems journal March 2005
Hydromorphological attributes for all Australian river reaches derived from Landsat dynamic inundation remote sensing journal July 2019
Assessment of surface and sub-surface waterlogged areas in irrigation command areas of Bihar state using remote sensing and GIS journal July 2008
Application of time series of remotely sensed normalized difference water, vegetation and moisture indices in characterizing flood dynamics of large-scale arid zone floodplains journal March 2017
Dynamics of Surface‐Water Connectivity in a Low‐Gradient Meandering River Floodplain journal March 2019