2020 High Definition Fish Survey: Upper Delaware River, Hancock, NY

Threatened and Endangered Species Sampling

The Upper Delaware River is a component of the National Wild and Scenic Rivers System and a unit of the national park system. The National Park Service (NPS) is responsible for protecting threatened and endangered (T&E) species in this area. The Upper Delaware River watershed is host to a T&E species of fish known as the bridle shiner, Notropis bifrenatus. A member of the minnow family, the bridle shiner is vulnerable to poor water quality and high turbidity, particularly in agricultural areas. The NPS requested a High Definition Fish Survey (HDFS) to sample for the presence of bridle shiners in a small, highly vegetated and intermittently floodplain pond next to the Delaware River. The HDFS provided a rapid way to gather geo-referenced video to document the species occurring within the pond. The video results were sent to species experts and confirmed the presence of the bridle shiner in these areas. HDFS proved ideal for T&E species sampling because it is rapid, verifiable and much less disruptive to aquatic life than other sampling methods such as electro-shocking or seine-netting.

High Definition Fish Surveys, Habitat Assessments

Shehawken Creek and Equinunk Creek are tributary streams flowing into the main stem of the Delaware River downstream of the confluence between the Eastern and Western branches of the Delaware River. Both streams are important reproduction streams for wild rainbow and brown trout. The Shehawken Chapter of Trout Unlimited was interested in the High Definition Fish Survey (HDFS) technique to develop citizen science program that would conduct periodic fish surveys in these creeks and other waters in the Upper Delaware watershed. Trutta worked with the Shehawken Chapter of Trout Unlimited to inform members about the HDFS and High Definition Stream Survey (HDSS) techniques and provided the opportunity to complete the HDFS methods on Equinunk Creek. In coordination with the volunteer surveys, Trutta conducted high definition stream surveys of approximately two miles of both Shehawken and Equinunk Creeks using a backpack-mounted system. The surveys took about 1.5 hours each. Trutta subsequently completed a High Definition Fish Survey of Shehawken Creek, documenting underwater aquatic habitat and fish at approximately 100 sites over a 1.5 mile stretch of stream, starting at the confluence with the main stem of the Delaware. The combination of HDSS and HDFS on the streams will allow habitat use, availability and suitability results to be developed and the results will allow TU members to interact with and support fisheries managers in protecting the trout habitat in these important spawning creeks. This project was made possible with funds from the Shehawken chapter of Trout Unlimited and the Embrace-A-Stream program hosted by the national headquarters of Trout Unlimited.

Habitat Availability, Mitigation Prioritization, Bathymetric Cross-Sections

The Upper Delaware River is a premier wild-trout fishery in the eastern United States and flows through New York and Pennsylvania. The New York Department of Environmental Conservation, the Pennsylvania Fish and Boat Commission and the Friends of the Upper Delaware River wanted to document habitat availability and suitability for wild trout in the Upper Delaware River system. Key objectives included: 1) determining the habitat conditions for wild brown trout and rainbow trout; 2) providing information to help prioritize future river projects related to the preservation and maintenance of trout habitat, and 3) providing a baseline of information that will be used to measure the impacts of future projects on the health of the river system. Trutta completed a High Definition Stream Survey (HDSS) of approximately 80 miles of the Upper Delaware River in approximately 5 days using a combination of inflatable rafts and kayaks. The survey area covered the West Branch from Deposit, NY to Hancock, NY; the East Branch from Downsville, NY to Hancock, NY; and the main river from the confluence of the East and West branches at Hancock south to Callicoon, PA. The HDSS involved two rafts to ensure documentation of the conditions of both stream banks, the streambed, and stream conditions. Trutta also completed cross-sectional transects at 1-mile increments for bathymetric modeling purposes. This project was funded with as part of a National Fish and Wildlife Foundation Contract aimed at enhancing the New York-Pennsylvania Joint Fisheries Investigation Plan.

Habitat Quality Assessment & Suitability Modeling

Stream Erosion Susceptibility

Stream Corridor Assessment: Barriers, Infrastructure, Point/Non-Point Source Pollution

The Bear Creek survey collected 64 miles of streambank data at one-second intervals. BESI (Connell 2012) was applied to tie into a simultaneously running bridge and culvert study of over 650 crossings that was using the BEHI (Rosgen, 2001). The ability to rank stream sections and entire watersheds will reduce subjectivity when prioritizing future restoration areas. Combining the results of these surveys with data on other important factors such as land ownership, land use, geology, and jurisdictional boundaries using a GIS approach will allow further prioritization of restoration sites. A key advantage of collecting geo-referenced video of streambank conditions along an entire survey section is the ability to review conditions at any site within the watershed at a later date. Thus, changes over time can be easily documented for sites throughout the watershed. The data can be shared as a data table (in spreadsheet or database format), as a shapefile for use in mapping software, or as video files to directly review the survey information. Importantly, the bank condition survey data can be combined with various other data sets to create new and novel analyses of conditions and management actions, which will support the long-term goals of improving water quality, habitat and species within the Bear Creek River system.

Habitat Quality Assessment & Suitability Modeling

Stream Erosion Susceptibility

Stream Corridor Assessment: Barriers, Infrastructure, Point/Non-Point Source Pollution

Understanding the quality and distribution of stream habitat is important to managing stream biota. Traditional stream habitat survey methods are often spatially-limited, time-consuming, expensive, and collect limited amounts of data. Using the HDSS system, 53 continuous miles of the Paint Rock River and its tributaries were surveyed in 3 field days. Each GPS point was assigned an associated bank condition score and habitat type (pool, riffle, run), and was used to develop GIS habitat quality maps. The survey results can be used in four ways; 1) As a tool for monitoring the results of previous restoration activities; 2) a tool to prioritize future restoration efforts and action areas; 3) baseline characterization of river bank conditions in 2014 for future review; and 4) to provide easily shared GIS data for numerous agencies to benefit from.

HDSS results all you to efficiently find and prioritize locations with high streambank erosion and viewing the associated georeferenced video allow you to see instream conditions at the location.

Habitat Quality Assessment & Suitability Modeling

Stream Erosion Susceptibility

Stream Corridor Assessment: Barriers, Infrastructure, Point/Non-Point Source Pollution

A mining company has a claim along the Weogufka Creek and needed to document baseline conditions prior to the mine opening. Many times this type of baseline documentation takes the form of a few transects near the project site and spot surveys at access locations in the larger area. Using traditional methods, the access points were too few and far between in this remote location to gain reliable data. This lack of access to appropriate sites would have made it difficult to pinpoint any direct impact on the creek due to the mining practices. In only one day, the HDSS techniques were used to collect a fully integrated suite of stream and streambank metrics for 17 miles of Weogufka Creek around the project location. Now regulators and the mining company can see any future direct impacts from the mining operation and work quickly and effectively to remedy any negative problems that may arise. An additional benefit arose from using the HDSS approach in that the survey video forms a highly useful archive of the conditions when the mining company first began operations. Over time, as other development occurs within this stream reach, impacts such as increased sedimentation resulting from bank clearing by farmers or homeowners will not be attributed to the mining operation by default as the largest project in the area. The geo-video survey allows site-specific impacts to be separated from cumulative impacts associated with general on-going development.

Instream habitat delineation for the HDSS project on Weogufka Stream, Al.

Habitat Suitability Modeling

Instream Flow Modeling

Fish & Invertebrates


For large dam operators, assessing the impacts of management actions on all of the competing uses for water can be a complex task. For the Alabama Power Company (APC), understanding the impact of a reservoir drawdown on potential habitat of endangered mussel species was one such problem. Bathymetry data was collected utilizing a sonar-based kayak-mounted depth profile system integrated with RTK-GPS to calculate surface areas exposed by reservoir drawdowns for defined contour intervals in the 6-mile Coosa River reach. Collected hydrographic data and overbank elevations from the National Elevation Dataset were imported into ArcGIS and merged into a unified geodatabase. Channel elevations were characterized in areas not represented in the survey by importing the data into HEC-RAS and interpolating missing cross-sections. The cross-sectional data was then exported into HEC-RAS and interpolated cross-sections were modeled at 10 m intervals. Interpolated cross-sections were incorporated with the survey data in an elevation geodatabase, and utilizing geospatial kriging techniques, an elevation surface was generated. This surface was utilized to generate contours for specific elevation ranges to support calculation of endangered snail habitat.

HEC-RAS output associated with the Coosa River bathymetry project.

Habitat Quality Assessment & Suitability Modeling

Fish & Invertebrates

Streambank Erosion Susceptibility

Stream Corridor Assessment


Goodwin’s Mill Dam was removed from the Big Canoe Creek in order to eliminate a barrier to fish and mussel movement. Given the high cost of dam removal and subsequent stream restoration, it is important to monitor stream conditions to assure that improved habitat conditions have resulted from the dam removal actions. One problem when attempting to document changes resulting from dam removal using traditional transect surveys is that the changes to the stream can occur over a broad area up and downstream from the removal site. This makes determining the placement and number of transects extremely subjective. More transects over a wider area will likely document changes more effectively, but this come with a high cost to the annual monitoring budget. To solve this problem, we used the High Definition Stream Survey method. In only 2 1/2 hours, this technique allowed us to quickly collect 1-meter resolution data of both stream banks and the stream bottom for over 3 miles of stream centered on the dam site. The geovideo surveying method was used to delineate pool-riffle-run sequencing, substrate type and embeddedness, depth, bank full depth, bank angle and height, bank erosion potential, and riparian diversity. This information will help show trends in sediment movement, stream geometry, and habitat conditions by comparing the results of annual surveys and to document (hopefully) improving conditions resulting from the dam removal effort.

Dashboard view from the Big Canoe Creek Survey before removal of Goodwin’s Mill Dam.

The Duck River is the most biologically diverse river in the United States and is also the source of drinking water for 250,000 people in Middle Tennessee. In recent years, Trutta has completed 155 miles of High Definition Stream Survey (HDSS). Completing this would have been impossible if not for the partnerships. We have partnered with a group of collaborators from various organizations (Duck River Agency, Tennessee Department of Environment and Conservation (TDEC), Columbia Power and Water Systems (CPWS), South Central Tennessee Development District (SCTDD), Tennessee State Parks, Stantec, O’Brien & Gere, and InfloDesign). These surveys collected a huge amount of valuable data to assist managers in making good decisions to achieve their goals, while keeping the Duck River healthy.

Flow Modeling

Our work began below Normandy Dam with TDEC. They were interested in cross-sections data for TMDL flow modeling at one-mile increments. The Cities of Lewisburg and Columbia each funded additional high-density cross-sections in their respective reservoirs for both drinking water and wastewater purposes.

Drinking Water

Since then, that data has been used by Columbia Power and Water to estimate current reservoir capacities for various water needs including drought planning. Engineering firms, such as O’Brien and Gere, Stantec, and InfloDesign have used the data for monitoring current drinking water intakes, as well as siting new drinking water intakes in collaboration with different municipalities and the Duck River Agency.

River Corridor Data

While collecting bathymetric data throughout the years, we also ran the HDSS system to collect longitudinal river corridor data. Every mile of river has StreamView video, depth data, and side scan sonar imagery that can be used for numerous different water resource management purposes. MS4 stormwater permitting, streambank restoration prioritization, and habitat suitability modeling are just some of the ways that this data could be used today. With the surveys already completed, this data can be made available to you at a reduced cost.

Other Uses for HDSS Data

Trutta has also been in discussions with Tennessee Wildlife Resource Agency (TWRA) to help determine habitat for endangered mussel species, with the National Resources Conservation Service (NRCS) about suitable locations for streambank plantings, and Tennessee State Parks about using the video for information and education.

Habitat Assessment, Mitigation Accounting, Scenario Testing, Habitat Suitability Modeling, Flood Control Modeling, Barrier Assessment, Infrastructure Assessment

The goal of the USACE Ala Wai Canal Flood Mitigation Project was to reduce the risk of flooding within in the Manoa area of Honolulu, HI. The project was focused on holding back or diverting peak flood flows to lessen the impact of a flooding event. The infrastructure needed to do this was expected to have an impact on aquatic habitat and native Hawaiian stream animals. We used the Hawaiian Stream Habitat Assessment Procedure (HSHEP) model to determine the impact and quantify mitigation scenarios. In addition to supporting the HSHEP model, long stretches of Manoa, Palolo and Makiki streams were surveyed using the High Definition Stream Surveys (HDSS) approach to better understand instream conditions both at the impact sites and throughout the stream in general. The application of the HSHEP model and HDSS approach to habitat quantification for the assessment of current conditions with project impacts and mitigation scenarios proved very successful. HDSS habitat availability data were collected throughout the streams and allowed very detailed understanding of where and what type of habitat was present in different stream segments. Prior to the HDSS fieldwork, the presence of over-hanging drops within Manoa and Palolo Streams were unknown. Covering extensive stream reaches also allowed us to see that the upper reaches of all of the streams still have suitable habitat for native amphidromous species and in many locations in the highly developed lower and middle reaches suitable habitat still exists.

HDSS stream documentation video showing erosion damage to water line crossing on Manoa Stream, Oahu, HI.

The 125 mile long Harpeth River flows northwest around the southern and western portions of the greater Nashville metropolitan area in Middle Tennessee. Much of the Harpeth River’s watershed is rural, but the area is experiencing rapid growth in suburban development especially in the area around Franklin, TN. Partially due to the area’s rapid growth, sections of Harpeth River have been listed as impaired on the State’s 303(d) list with stormwater runoff, non-point source pollution, sanitary wastewater, and water withdrawals all contributing to its water quality problems.

To better understand the location and extent of the issues within the Harpeth River, the High Definition Stream Survey (HDSS) method was used in March of 2016 to record important river channel information. The primary objective of the survey was to collect high-resolution, geo-referenced longitudinal and cross-sectional surveys on 77.8 miles of the main channel of the Harpeth River. The survey began at the Trinity Road bridge (upstream of Hwy 65) and continued downstream past the Narrows of the Harpeth area. Averaging about 16 miles per day, we gathered 22 hours of video, sonar and other data for each second during the survey resulting in over 75,000 lines of data representing the river channel conditions. The information was used to determine habitat type (pool, riffle, run), water depth, and left and right bank condition for the full extent of the survey length.

In all, 82 cross-sectional transects were surveyed in the Harpeth River and at the mouth of some of its major tributaries. For the longitudinal surveys, the multiple video concurrent streams were processed and assembled into a single video to provide a “first person” point-of-view of the entire survey path. From the HDSS results, we delineated 471 distinct habitat type units for the survey area. Runs were the most frequent habitat type, followed by pools and riffles. In terms of their overall length, the pool habitat type occupied most of the river length and riffles were a very small portion. As expected, pools were deeper on average than runs and riffles, and we did not see any difference between bank conditions scores associated with habitat types. We observed that much of the Harpeth River has incised stream banks and the potential for streambank erosion is moderate to high throughout large sections of the river. Encroaching development from both agriculture and housing developments restricts the riparian zone in many areas. Some of the specific issues discussed included the impacts of powerlines, log jams, livestock, and point-source runoff.

The High Definition Stream Survey (HDSS) approach proved to be a rapid method to collect a wide range of useful information about the Harpeth River. The resulting data will be highly useful for a range of river management issues. The cross-section transect information is useful to help better understand the quantity of water available at different discharges, while the longitudinal information can be used to support targeted restoration and habitat improvement projects. Along with the report, the field data and results from the Harpeth River HDSS project were provided in digital format.

An example screen capture of the three-view video from the Harpeth River. The time and GPS location are embedded in the video.

Habitat Quality Assessment, Habitat Suitability Modeling, Barrier Assessment, Infrastructure Assessment, Point Source Pollution, Non-point Source Pollution

Using the HDSS system, 68 continuous miles were surveyed on the Choccolocco and Cheaha Creeks in 4 field days. In addition to documenting baseline conditions and habitat types, large woody debris and man-made structures were also assessed and geo-referenced. Illegal water withdrawal, illegal dumping, un-fenced cattle, and man-made fish barriers were geo-referenced so that further legal action can be taken. Using the locations and density of woody debris, correlations can be observed when compared to areas of high bank erosion. This information can also be used with IBI’s and the abundance of macroinvertebrates to better understand overall stream health.

HDSS video imagery of the worst location documented during the Choccolocco Creek Survey. Note the large failing stream bank and lack of riparian vegetation.

Due in part to the growth of the area, sections of Falling Water River have been listed as impaired on the State’s 303(d) list with stormwater runoff, non-point source pollution, sanitary wastewater, and water withdrawals all contributing to its water quality problems. Effectively managing water resource issues associated with the Falling Water River requires high quality data of the current conditions in river corridor. This primary goal of this project, funded by Tennessee Department of Environment and Conservation (TDEC), was to collect state-of-the-art, high-resolution, geo-referenced longitudinal and cross-sectional surveys on 23 miles the main channel of the Falling Water River, 5 miles of Pigeon Roost Creek and 2.6 miles of Hudgens Creek to enable efficient characterization of stream channel conditions and provide geomorphic data for modeling purposes. We accomplished this goal by completing four main objectives:

collecting high-resolution, geo-referenced longitudinal and cross-sectional surveys on the main channel of Falling Water River, Pigeon Roost Creek and Hudgens Creek to document baseline river bank and instream conditions during June/July 2016,
producing stream-view HDSS video, classifying habitat and bank condition and creating a database of collected information,
analyzing data by creating aquatic habitat GIS layers for depth, habitat type (pool, riffle, run), and left and right bank condition scores, and
making assessments and identifying other potential applications of the HDSS results to support river management.
The HDSS project resulted in over 65,000 lines of data covering the survey area. We collected 28 cross-sectional transects to support water management modeling applications. From the longitudinal survey, we assessed the left and right bank condition as a metric of the potential for shoreline erosion. In general, approximately 15% of the stream banks of the Falling Water River were in good or optimal condition. Conversely approximately 26% were in the poor or very poor categories. Most of the Falling Water River system was in average condition. From a distribution perspective, it appears that Hudgens Creek is in poorest overall condition and the upper and lower segments of Falling Water River are in the best condition. We also observed issues associated with losing water reaches, log jams, and livestock management.

The High Definition Stream Survey (HDSS) approach proved to be a successful method to rapidly collect a wide range of useful information about the Falling Water River and the HDSS video of the river system will allow decision makers and other parties to see high-definition video of the streambank conditions of the entire survey area from June/July 2016 and have the high resolution classified data to make specific comparisons for different projects.

Habitat by type for upper portion of Falling Water River and all of Pigeon Roost Creek and Hudgens Creek.

Habitat Quality Assessment, Habitat Suitability Modeling, Barrier Assessment, Infrastructure Assessment, Point Source Pollution, Non-point Source Pollution, Mitigation

The proposed 52 mile Birmingham Northern Beltline crosses numerous creeks, and as part of minimizing the environmental impact of the project, documenting instream conditions within the affected creeks is a fundamental component. To aid in documenting the current conditions within the stream channels of Turkey Creek, our team used HDSS to provide up-to-date, geo-referenced video and develop spatially continuous maps of bank and stream conditions. The survey data can be used in many ways but this report will focus on the method’s ability to: 1) provide a baseline characterization of river bank and instream conditions in during the survey, 2) develop aquatic habitat GIS layers for depth, habitat type (pool, riffle, run), substrate type, percent embeddedness, and left and right bank condition scores, 3) document areas of high habitat suitability for endangered darter species, and 4) identify areas that are most suitable for mitigation restoration. Rather than restore streambanks where no darters will benefit from the investment, we used the HDSS data to locate areas with the greatest instream habitat combined with poor streambank condition.

Locations scored by combining the worst streambank condition with the highest instream habitat to optimize mitigation efforts.

Stream Condition Assessment, MS4, Fish Habitat, Fish Distribution, Rapid Surveys, Habitat Quality Assessment

Timber Run, a long-term monitoring, reference stream in Maryland was surveyed using the High Definition Stream Survey (HDSS) and High Definition Fish Survey (HDFS). The survey was completed by a single surveyor using the HDSS Backpack setup in a single day and covered over 3.7 km. The habitat assessment included stream channel geomorphology, bank condition, instream habitat, and infrastructure and was completed in only 2.2 hours. The fish surveys were completed on a wide range of habitats throughout the stream. This long-term reference stream had been surveyed numerous times over the past 19 years, but the traditional survey methods only covered 100m and required 4-6 people to complete. The combination of the HDSS and HDFS approach proved much faster and more spatially complete than past traditional surveys and provided new insights into this reference stream.

Timber Run in MD was surveyed using the HDSS and HDFS methods in less than 1/80 the time when compared to the traditional survey methods.

Fish surveys, Fish distribution, Habitat Use, Habitat Suitability Modeling, Rapid Assessment, Fish Passage, Native Species, Introduced Species

High Definition Fish Surveys (HDFS) were conducted to better understand the current distribution and habitat use of fish with the Ala Wai Watershed streams. The results were used in the USACE Flood Mitigation Project impact assessment on the loss of instream habitat from proposed flood control structures. The HDFS approach allow for very rapid documentation of fish species presence in a wide range of urban stream conditions that were difficult to survey with other survey methods. The HDFS method easily integrates with the High Definition Stream Surveys (HDSS) method providing an excellent understanding of the distribution of habitat and fish species within a stream system.

Locations scored by combining the worst streambank condition with the highest instream habitat to optimize mitigation efforts.


HDSS in MS4 Permitting

HDSS in Dam Removals

HDSS Integration with Google Earth

HDSS & Tennessee Wildlife Resources Agency

HDSS – Turkey Creek, AL

HDSS – Turkey Creek, AL (2)

HDSS/HDFS Hawaiian Streams

HDFS Manoa Stream, HI

HDSS Manoa Stream, HI

The above video shows the use of High Definition Stream and Fish Surveys in Hawaiian Streams (narration coming soon)

Here is example footage from our High Definition Fish Surveys (HDFS) from a project in Manoa Stream in Hawaii. In addition to the video footage, the underwater fish surveys have location (GPS) and time associated with each second of the video so that we know exactly where and when the video was collected. The information gathered in the video about species present, their sizes or number, and habitat can be easily integrated with the High Definition Stream Survey (HDSS) results that capture the overall stream channel conditions.


Here is a short clip for the overall HDSS for Manoa Stream. It shows various habitats in a short section and also a you can see a large section of retaining wall collapsing into the stream. This stream section is also the area with the High Definition Fish Surveys for Manoa stream.

 HDSS Waiawa Stream, HI

 HDSS Waiawa Stream, HI

 HDSS Waiawa Stream, HI

This is a High Definition Stream Survey (HDSS) of Waiawa Stream on Oahu. This stream segment lies adjacent to one of the high speed railway stations being constructed to help alleviate traffic congestion in the Honolulu area. The HDSS will help document instream conditions prior to the railway station construction and hopefully aid in appropriate mitigation decisions to help protect the stream.

This is just the first step in the analysis process for the HDSS information. We still need to classify the habitat and stream channel conditions and provide dashboard overlays of the resulting data to the video.

In addition to the habitat mapping shown here, we also completed water quality samples throughout the stream segment and fish surveys using the High Definition Fish Surveys (HDFS). The water quality information and fish surveys are not shown here.

I would like to thank Glenn Higashi (Hawaii Division of Aquatic Resources), Michael Tauchen and Jorge Felix (Honolulu Authority for Rapid Transportation), and Kevin Foster (U.S. Fish and Wildlife Service) for their assistance during these surveys.

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