Jonathan Warrick
My research focuses on the intersection of rivers and the sea. Topics include the movement of sediment within and from coastal watersheds, and how sediment can alter coastal landscapes and habitats. Recently these subjects have been addressed in my work on the Elwha River, Washington, where the largest dam removal project in U.S. history was completed in 2014.
In The News
2017, Los Angeles Times article, “Highway 1 was buried under a massive landslide. Months later, engineers battle Mother Nature to fix it”
2016, The Department of Interior and Lower Elwha Klallam Tribe, International RiverPrize Finalist
2015, New York Times article, “When Dams Come Down, Salmon and Sand Can Prosper”
2014, National Geographic news article, “World’s Largest Dam Removal Unleashes U.S. River After Century of Electric Production”
2013, Book, “Elwha: A River Reborn”
2012, Front-page Seattle Times article, “Dam gone, nature rebuilds Elwha River beach”
2009, Science Daily article, “Sediment Yield From The Tectonically Active Semiarid Western Transverse Ranges Of California”
2006, Environmental Science & Technology news article, “California’s Shifting Sands”
Professional Experience
Research Geologist, GS-15, 2016-present, USGS Pacific Coastal and Marine Science Center, Santa Cruz, California
Research Geologist, GS-14, 2008-2016, USGS Pacific Coastal and Marine Science Center, Santa Cruz, California
Research Geologist, GS-13, 2004-2008, USGS Pacific Coastal and Marine Science Center, Santa Cruz, California
Mendenhall Postdoctoral Fellow, GS-12, 2002-2004, USGS Coastal and Marine Geology Program, Menlo Park, California
Education and Certifications
Ph.D., 2002, University of California, Santa Barbara
M.Sc., 1995, University Wisconsin-Madison
B.Sc., 1993, California Polytechnic State University, San Luis Obispo
Science and Products
Mapping Land-Use, Hazard Vulnerability and Habitat Suitability Using Deep Neural Networks
Exploring the USGS Science Data Life Cycle in the Cloud
National Dam Removal Database: A living database for information on dying dams
Dam removal: synthesis of ecological and physical responses
Big Sur Coastal Landslides
Aerial Imagery of the North Carolina Coast: 2019-08-30 and 2019-09-02, Pre-Hurricane Dorian
Overlapping lakebed images and associated GNSS locations acquired near Dollar Point, Lake Tahoe, CA, March 2021
Geophysical and core sample data collected offshore San Francisco, California, during field activity 2019-649-FA from 2019-10-11 to 2019-10-18
Aerial Photogrammetry Data and Products of the North Carolina coast: 2018-10-06 to 2018-10-08, post-Hurricane Florence
Geophysical and core sample data collected offshore Oceanside to San Diego, southern California, during field activity 2018-638-FA from 2018-05-21 to 2018-05-26
Geophysical and sampling data collected offshore Oceanside, southern California during field activity 2017-686-FA from 2017-10-23 to 2017-10-31
Post-Hurricane Florence Aerial Imagery: Cape Fear to Duck, North Carolina, October 6-8, 2018
Bathymetry and acoustic-backscatter data collected in 2016 offshore the Elwha River mouth, Washington, during USGS Field Activity 2016-605-FA
Bathymetry and acoustic backscatter data collected in 2008 offshore Tijuana River Estuary, California during USGS Field Activity S-5-08-SC
SQUID-5 structure-from-motion point clouds, bathymetric maps, orthomosaics, and underwater photos of coral reefs in Florida, 2019
Bathymetry, topography, and sediment grain-size data from the Elwha River delta, Washington, July 2017
Topographic point clouds for the Mud Creek landslide, Big Sur, California from structure-from-motion photogrammetry from aerial photographs
Labeling poststorm coastal imagery for machine learning: Measurement of interrater agreement
Processing coastal imagery with Agisoft Metashape Professional Edition, version 1.6—Structure from motion workflow documentation
IntroductionStructure from motion (SFM) has become an integral technique in coastal change assessment; the U.S. Geological Survey (USGS) used Agisoft Metashape Professional Edition photogrammetry software to develop a workflow that processes coastline aerial imagery collected in response to storms since Hurricane Florence in 2018. This report details step-by-step instructions to create three-dimen
A survey of storm-induced seaward-transport features observed during the 2019 and 2020 hurricane seasons
Littoral sediment from rivers: Patterns, rates and processes of river mouth morphodynamics
Cliff Feature Delineation Tool and Baseline Builder version 1.0 user guide
Community for data integration 2018 funded project report
Accurate bathymetric maps from underwater digital imagery without ground control
Optical wave gauging using deep neural networks
Commentary: Variability in shelf sedimentation in response to fluvial sediment supply and coastal erosion over the past 1,000 Years in Monterey Bay, CA, United States
World’s largest dam removal reverses coastal erosion
Integrating structure from motion, numerical modelling and field measurements to understand carbonate sediment transport in coral reef canopies
Characterizing the catastrophic 2017 Mud Creek Landslide, California, using repeat Structure-from-Motion (SfM) photogrammetry
Along the rugged coast of Big Sur, California, the Mud Creek landslide failed catastrophically on May 20, 2017 and destroyed over 400 m of scenic California State Highway 1. We collected structure-from-motion (SfM) photogrammetry data using airborne platforms that, when combined with existing airborne lidar data, revealed that the area exhibited significant topographic change and displacement befo
Science and Products
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Mapping Land-Use, Hazard Vulnerability and Habitat Suitability Using Deep Neural Networks
Deep learning is a computer analysis technique inspired by the human brain’s ability to learn. It involves several layers of artificial neural networks to learn and subsequently recognize patterns in data, forming the basis of many state-of-the-art applications from self-driving cars to drug discovery and cancer detection. Deep neural networks are capable of learning many levels of abstraction, anExploring the USGS Science Data Life Cycle in the Cloud
Executive Summary Traditionally in the USGS, data is processed and analyzed on local researcher computers, then moved to centralized, remote computers for preservation and publishing (ScienceBase, Pubs Warehouse). This approach requires each researcher to have the necessary hardware and software for processing and analysis, and also to bring all external data required for the workflow over the intNational Dam Removal Database: A living database for information on dying dams
The United States has over 2 million dams on rivers and streams (Graf, 1999), and more than 84,000 of the larger dams are documented in the congressionally mandated National Inventory of Dams (U.S. Army Corps of Engineers, 2015). The average age of these National Inventory of Dams is 52 years; by the year 2030, over 80 percent will be at least 50 years old (American Society of Civil Engineers, 201Dam removal: synthesis of ecological and physical responses
Dam decommissioning is rapidly emerging as an important river restoration strategy in the U.S., with several major removals recently completed or in progress. But few studies have evaluated the far-reaching consequences of these significant environmental perturbations, especially those resulting from removals of large (>10-15 m tall) structures during the last decade. In particular, interactions bBig Sur Coastal Landslides
Information about USGS Pacific Coastal and Marine Science Center studies on coastal landslides in the Big Sur area - Data
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Aerial Imagery of the North Carolina Coast: 2019-08-30 and 2019-09-02, Pre-Hurricane Dorian
The U.S. Geological Survey (USGS) Remote Sensing Coastal Change (RSCC) project collects aerial imagery along coastal swaths, in response to storm events, with optimized endlap/sidelap and precise position information to create high-resolution orthomosaics, three dimensional (3D) point clouds, and digital elevation/surface models (DEMs/DSMs) using Structure-from-Motion (SfM) photogrammetry methods.Overlapping lakebed images and associated GNSS locations acquired near Dollar Point, Lake Tahoe, CA, March 2021
Underwater images were collected using a recently developed towed-surface vehicle with multiple downward-looking underwater cameras. The system is named the Structure-from-Motion (SfM) Quantitative Underwater Imaging Device with Five Cameras (SQUID-5). However, there were only 4 cameras operational for this collection due to a cable failure. Images were collected March 10th and 11th of 2021 by towGeophysical and core sample data collected offshore San Francisco, California, during field activity 2019-649-FA from 2019-10-11 to 2019-10-18
The U.S. Geological Survey (USGS) collected geophysical and core sample data aboard the R/V Bold Horizon in 2019 on cruise 2019-649-FA offshore San Francisco, California. The data were collected to assess sand and gravel resources in Federal and State waters for potential use in future beach nourishment projects along stretches of the coast where critical erosion hotspots have been identified. ThiAerial Photogrammetry Data and Products of the North Carolina coast: 2018-10-06 to 2018-10-08, post-Hurricane Florence
This data release presents structure-from-motion products derived from imagery taken along the North Carolina coast in response to storm events and the recovery process. USGS researchers use the aerial photogrammetry data and products to assess future coastal vulnerability, nesting habitats for wildlife, and provide data for hurricane impact models. This research is part of the Remote Sensing CoasGeophysical and core sample data collected offshore Oceanside to San Diego, southern California, during field activity 2018-638-FA from 2018-05-21 to 2018-05-26
The U.S. Geological Survey (USGS) collected geophysical and core sample data aboard the R/V Bold Horizon in 2018 on cruise 2018-638-FA offshore Oceanside to San Diego, southern California. The data were collected to assess sand and gravel resources in Federal and State waters for potential use in future beach nourishment projects along stretches of the coast where critical erosion hotspots have beGeophysical and sampling data collected offshore Oceanside, southern California during field activity 2017-686-FA from 2017-10-23 to 2017-10-31
This data release contains geophysical and sediment sample data that were collected aboard the R/V Snavely in 2017 on U.S. Geological Survey cruise 2017-686-FA offshore Oceanside, southern California. The goal of the survey was to provide high-resolution imaging, magnetic anomaly profiles and sediment analysis to characterize the surface and subsurface properties of the study area such as unconsolPost-Hurricane Florence Aerial Imagery: Cape Fear to Duck, North Carolina, October 6-8, 2018
The U.S. Geological Survey (USGS) Remote Sensing Coastal Change (RSCC) project collects aerial imagery along coastal swaths, in response to storm events, with optimized endlap/sidelap and precise position information to create high-resolution orthomosaics, three-dimensional (3D) point clouds, and digital elevation/surface models (DEMs/DSMs) using Structure-from-Motion (SfM) photogrammetry methods.Bathymetry and acoustic-backscatter data collected in 2016 offshore the Elwha River mouth, Washington, during USGS Field Activity 2016-605-FA
This data release provides bathymetry and acoustic-backscatter data collected during a 2016 SWATHPlus-M survey offshore the Elwha River mouth, Strait of Juan de Fuca, Washington. Data were collected and processed by the U.S. Geological Survey, Pacific Coastal and Marine Science Center during field activity 2016-605-FA. This survey, along with two other surveys (Cochrane and others, 2008, FinlaysonBathymetry and acoustic backscatter data collected in 2008 offshore Tijuana River Estuary, California during USGS Field Activity S-5-08-SC
In 2008 the U.S. Geological Survey (USGS), Pacific Coastal and Marine Science Center (PCMSC) collected bathymetry and acoustic-backscatter data offshore the Tijuana River Estuary, California. Mapping was conducted as part of the Tijuana Estuary Fine Sediment Fate and Transport Demonstration Project, which was developed by a number of State of California, federal, and private industry partners to pSQUID-5 structure-from-motion point clouds, bathymetric maps, orthomosaics, and underwater photos of coral reefs in Florida, 2019
The new structure-from-motion (SfM) quantitative underwater imaging device with five cameras (SQUID-5) was tested in July 2019 at Crocker Reef in the Florida Keys. The SQUID-5 was developed to meet the unique challenges of collecting SfM underwater imagery, including multiple cameras with different perspectives, accurate geographic locations of images, accurate and precise scaling of derived surfaBathymetry, topography, and sediment grain-size data from the Elwha River delta, Washington, July 2017
Two dams on the Elwha River, Washington State, USA trapped over 20 million m3 of sediment, reducing downstream sediment fluxes and contributing to erosion of the river's coastal delta. The removal of the Elwha and Glines Canyon dams between 2011 and 2014 induced massive increases in river sediment supply and provided an unprecedented opportunity to examine the response of a delta system to changesTopographic point clouds for the Mud Creek landslide, Big Sur, California from structure-from-motion photogrammetry from aerial photographs
This data release contains structure-from-motion (SfM) point cloud data from aerial surveys conducted over the Mud Creek landslide on Big Sur from 1967-2018. Data sources include scanned aerial photographs, digital images collected from fixed wing aircraft, and digital images collected from multirotor UAS. - Maps
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Labeling poststorm coastal imagery for machine learning: Measurement of interrater agreement
Classifying images using supervised machine learning (ML) relies on labeled training data—classes or text descriptions, for example, associated with each image. Data-driven models are only as good as the data used for training, and this points to the importance of high-quality labeled data for developing a ML model that has predictive skill. Labeling data is typically a time-consuming, manual procAuthorsEvan B. Goldstein, Daniel D. Buscombe, Eli D. Lazarus, Somya Mohanty, Shah N. Rafique, K A Anarde, Andrew D Ashton, Tomas Beuzen, Katherine A. Castagno, Nicholas Cohn, Matthew P. Conlin, Ashley Ellenson, Megan Gillen, Paige A. Hovenga, Jin-Si R. Over, Rose V. Palermo, Katherine Ratlif, Ian R Reeves, Lily H. Sanborn, Jessamin A. Straub, Luke A. Taylor, Elizabeth J. Wallace, Jonathan Warrick, Phillipe Alan Wernette, Hannah E WilliamsByProcessing coastal imagery with Agisoft Metashape Professional Edition, version 1.6—Structure from motion workflow documentation
IntroductionStructure from motion (SFM) has become an integral technique in coastal change assessment; the U.S. Geological Survey (USGS) used Agisoft Metashape Professional Edition photogrammetry software to develop a workflow that processes coastline aerial imagery collected in response to storms since Hurricane Florence in 2018. This report details step-by-step instructions to create three-dimen
AuthorsJin-Si R. Over, Andrew C. Ritchie, Christine J. Kranenburg, Jenna A. Brown, Daniel D. Buscombe, Tom Noble, Christopher R. Sherwood, Jonathan A. Warrick, Phillipe A. WernetteByEcosystems Mission Area, Natural Hazards Mission Area, Coastal and Marine Hazards and Resources Program, Maryland-Delaware-D.C. Water Science Center, Pacific Coastal and Marine Science Center, Southwest Biological Science Center, St. Petersburg Coastal and Marine Science Center, Woods Hole Coastal and Marine Science Center, Hurricane Florence, HurricanesA survey of storm-induced seaward-transport features observed during the 2019 and 2020 hurricane seasons
Hurricanes are known to play a critical role in reshaping coastlines, but often only impacts on the open ocean coast are considered, ignoring seaward-directed forces and responses. The identification of subaerial evidence for storm-induced seaward transport is a critical step towards understanding its impact on coastal resiliency. The visual features, found in the National Oceanic and AtmosphericAuthorsJin-Si R. Over, Jenna A. Brown, Christopher R. Sherwood, Christie Hegermiller, Phillipe Alan Wernette, Andrew C. Ritchie, Jonathan WarrickLittoral sediment from rivers: Patterns, rates and processes of river mouth morphodynamics
Rivers provide important sediment inputs to many littoral cells, thereby replenishing sand and gravel of beaches around the world. However, there is limited information about the patterns and processes of littoral-grade sediment transfer from rivers into coastal systems. Here I address these information gaps by examining topographic and bathymetric data of river mouths and constructing sediment buAuthorsJonathan WarrickCliff Feature Delineation Tool and Baseline Builder version 1.0 user guide
Coastal cliffs constitute 80 percent of the world’s coastline, with seacliffs fronting a large proportion of the U.S. West Coast shoreline, particularly in California. Erosion of coastal cliffs can threaten infrastructure and human life, yet the spatial and temporal scope of cliff studies have been limited by cumbersome traditional methods that rely on the manual interpretation of seacliff featureAuthorsAlexander C. Seymour, Cheryl J. Hapke, Jonathan WarrickCommunity for data integration 2018 funded project report
The U.S. Geological Survey Community for Data Integration annually funds small projects focusing on data integration for interdisciplinary research, innovative data management, and demonstration of new technologies. This report provides a summary of the 10 projects funded in fiscal year 2018, outlining their goals, activities, and accomplishments.AuthorsLeslie Hsu, Caitlin M. Andrews, John B. Bradford, Daniel D. Buscombe, Katherine J. Chase, Wesley M. Daniel, Jeanne M. Jones, Pam Fuller, Benjamin B. Mirus, Matthew E. Neilson, Hans W. Vraga, Jessica J. Walker, Dennis H. Walworth, Jonathan Warrick, Jake Weltzin, Daniel J. Wieferich, Nathan J. WoodAccurate bathymetric maps from underwater digital imagery without ground control
Structure-from-Motion (SfM) photogrammetry can be used with digital underwater photographs to generate high-resolution bathymetry and orthomosaics with millimeter-to-centimeter scale resolution at relatively low cost. Although these products are useful for assessing species diversity and health, they have additional utility for quantifying benthic community structure, such as coral growth and fineAuthorsGerry Hatcher, Jonathan Warrick, Andrew C. Ritchie, Evan T. Dailey, David G. Zawada, Christine J. Kranenburg, Kimberly K. YatesOptical wave gauging using deep neural networks
We develop a remote wave gauging technique to estimate wave height and period from imagery of waves in the surf zone. In this proof-of-concept study, we apply the same framework to three datasets: the first, a set of close-range monochrome infrared (IR) images of individual nearshore waves at Duck, NC, USA; the second, a set of visible (i.e. RGB) band orthomosaics of a larger nearshore area near SAuthorsDaniel Buscombe, Roxanne J Carini, Shawn Harrison, C Chris Chickadel, Jonathan WarrickCommentary: Variability in shelf sedimentation in response to fluvial sediment supply and coastal erosion over the past 1,000 Years in Monterey Bay, CA, United States
A commentary on: Variability in Shelf Sedimentation in Response to Fluvial Sediment Supply and Coastal Erosion Over the Past 1,000 Years in Monterey Bay, CA, United States. by Carlin J., Addison J., Wagner A., Schwartz V., Hayward J., Severin V. (2019) Front. Earth Sci., 7:113. doi: 10.3389/feart.2019.00113AuthorsJonathan Warrick, Amy E. East, Curt D. Storlazzi, James E. ConradWorld’s largest dam removal reverses coastal erosion
Coastal erosion outpaces land generation along many of the world’s deltas and a significant percentage of shorelines, and human-caused alterations to coastal sediment budgets can be important drivers of this erosion. For sediment-starved and erosion-prone coasts, large-scale enhancement of sediment supply may be an important, but poorly understood, management option. Here we provide new topographiAuthorsJonathan Warrick, Andrew W. Stevens, Ian M. Miller, Shawn R Harrison, Andrew C. Ritchie, Guy R. GelfenbaumIntegrating structure from motion, numerical modelling and field measurements to understand carbonate sediment transport in coral reef canopies
Reef canopies are complex and extremely variable across a range of spatial scales. This variability affects the velocity above as well as within the canopy, and directly impacts the transport of sediment along the bed as well as suspended in the water column. How a canopy affects the transport of sediment is important to understand and predict changes in the position of the adjacent shoreline, parAuthorsAndrew Pomeroy, Curt D. Storlazzi, Kurt J. Rosenberger, Gerry Hatcher, Jonathan WarrickCharacterizing the catastrophic 2017 Mud Creek Landslide, California, using repeat Structure-from-Motion (SfM) photogrammetry
Along the rugged coast of Big Sur, California, the Mud Creek landslide failed catastrophically on May 20, 2017 and destroyed over 400 m of scenic California State Highway 1. We collected structure-from-motion (SfM) photogrammetry data using airborne platforms that, when combined with existing airborne lidar data, revealed that the area exhibited significant topographic change and displacement befo
AuthorsJonathan Warrick, Andrew C. Ritchie, Mark E. Reid, Kevin M. Schmidt, Joshua B. Logan - Software
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