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Monitoring the Cape Fear River Ecosystem
This program is examining the effects of the Cape Fear River Harbor dredging project on selected physical, chemical, and biological parameters in the river and adjacent wetlands. Eleven data collection platforms have been constructed in the Cape Fear and Northeast Cape Fear Rivers. Each platform houses water level sensors, conductivity instruments, and data loggers that record changes in tidal amplitude and salt water excursion up river. These data are retrieved using telemetry. Additional conductivity sensors and piezometers are used to measure fortnightly salinity and water level changes, respectively, along transects in swamp and marsh sites. These fortnightly surveys are conducted in the winter and summer. Standard methods are used to asses impacts on benthic and fish populations along selected river edge locations. Pore water samples are collected at selected swamp sites in the summer and in the winter. These samples are analyzed to determine sulfate, chloride and methane concentrations. All data are provided to the US Army Corps of Engineers annually.

A description of the scope of work follows. Dr. Lynn Leonard at the University of North Carolina, Wilmington is conducting the investigation. For more information and data, see

Description of Work

Monitoring Effects of a Potential Increased Tidal Range in the Cape Fear River Ecosystem
Due to Deepening Wilmington Harbor, North Carolina
Year 1: 7 August 1, 2000 – July 31, 2001

The contractor will be responsible for performing all the sample collection and analysis, monitoring, routine equipment maintenance, and data management associated with the activities indicated below.


a.            Monitoring Associated with Data Collection Platforms (DCP):  Under a separate contract, DCP’s have been installed at the eleven (11) station locations indicated in the March 1999 CZR Report (P1, P2, P3, P6, P7, P8, P9, P11, P12, P13, & P14).  Instruments installed on each DCP were a water level recorder (Unidata Water Level Monitor) and a programmable data logger (Unidata Star Logger).  The water level recorder is tied into the logger along with probes for salinity (from conductivity), and temperature.  The primary water level sensor is a shaft-encoder instrument installed in a stilling well.  The water level sensor was leveled directly to local benchmarks that provide absolute measurements referenced to local water level datums.  These sensors have an accuracy of 1/100 ft over a 10-foot water level range.  Data will be retrieved from the logger via a cellular communication system every 1-2 weeks.  The entire package is contained in a watertight housing and powered by a 12-volt battery, recharged with solar panels.


In addition, a Unidata Star Logger with probes for conductivity and temperature was installed at the existing NOAA tide gauge at the Corps of Engineer Yard.  No telemetry is available for this site; therefore, the data must be manually downloaded every 1-2 weeks.


Water level monitoring will follow the sampling protocol established by the NOS (1998).  The data loggers are programmed to collect measurements at 6-minute intervals with each measurement consisting of a set of 181 1-second-interval water level samples centered on each tenth of an hour.  The mean of 181 are reported along with the maximum and minimum over the measurement period.  The reported measurements have 0.01-foot resolution and are stored in the system memory of the data logger.  To ensure quality data, it will be necessary to conduct monthly maintenance of DCP’s.  Each DCP and its sensors will be cleaned and visually inspected for damage. 


Standard National Oceanic and Atmospheric Administration (NOAA) routines will be used to calculate tidal harmonics.  Statistical evaluation of computed amplitudes and phases will be conducted at a confidence level of alpha=0.05.  Tidal phase differences between stations will be used to establish a baseline tidal lag time over the length of the study area.  Mean amplitudes and harmonic amplitudes will be determined for each station.  These data will establish amplitude differences currently existing between sites.  Pre-project water level data will further be used to evaluate maximum background fluctuations.


Supplementary conductivity and temperature measurements will be collected by hand at the surface and at the maximum depth of the stilling basin once per month at each station.  These measurements will be used to assess variability in conductivity and temperature in the water column and to verify instrument calibrations.  Conductivity sensors will be calibrated each day before and after water column measurements are made.


The monitoring period for this work will be from contract award through July 31, 2001.


b.   Benthic Invertebrates:  At Eight (8) of the stations indicated in the March 1999 CZR Report [P2, P3a&b (on both sides of Town Creek combined as one station), P6, P7, P8, P11, P12, & P13], benthic invertebrates will be sampled at two subsites (high intertidal and low intertidal) along each of two transects running perpendicular to the river/creek's edge.  Three benthic cores will be taken at each of these four locations per station (two transects X two subsites).


Sampling at all stations for benthos will be done in June 2001.  Samples will be taken with a 0.007 m2 area by 10 cm deep corer.  The contents will then be sieved through a 0.5 mm screen, fixed in 10% formalin, and subsequently transferred to 70 percent isopropanol.  Sorting will be required to separate fauna from root matrices and detrital debris before enumeration and identifications is done.  Then all benthic fauna will be identified to the species or genus level where possible.  Benthic fauna will also be classified into functional guilds based on living position and life history type (Fauchald and Jumars 1979, Posey 1990), including classifications considering dispersal mode and salinity tolerances.


Under a separate contract, sampling was also performed for benthic invertebrates in June 2000 at the same 8 locations and using the same sampling procedure.  These previous samples were just sieved through a 0.5 mm screen, fixed in 10% formalin, and subsequently transferred to 70 percent isopropanol. These previous samples will also be sorted and identified using the same methods indicated in the previous paragraph.


c.            Epibenthic Fish and Decapods:  Monitoring of epibenthic fish and decapods will be conducted at the same eight (8) stations indicated for monitoring for benthic invertebrates [(P2, P3 on both sides of Town Creek combined as one station), P6, P7, P8, P11, P12, & P13].  Monitoring will be done twice per year, once during September-October 2000 and once during March-April 2001.  At each sampling station, epibenthic fish and decapod use of wetland habitats will be monitored at three subsites along each of two transects running perpendicular to the river's edge (2 transects x 3 subsites=6 subsites per station).  The three subsites per transect will correspond to shallow subtidal, mid-intertidal, and high intertidal elevations, and exact locations will be determined from site characteristics, elevation surveys, and coordination with other monitoring efforts.  Juvenile fish and decapod abundances will be monitored through a combination of Breder and drop trap sampling.  Both sampling methods have been used in other studies of wetland fish and decapod use in the Cape Fear region (Townsend 1991; Griffitt, Posey, and Alphin 1999).


Both Breder and drop trap sampling are conducted at high tide when the area is covered by water.  Five Breder traps will be set simultaneously at each subsite on each sampling date for a total of 30 per site.  The traps are constructed of clear acrylic, 31 cm long x 15 cm wide x 16 cm high, with clear acrylic leader wings.  Traps are placed facing downstream of prevailing currents with at least 1 m between traps.  The traps will be left in place for 1.5 hours.


Nine drop samples will be conducted at the shallow subtidal subsite on each sampling date for a total of 18 per site.  The drop traps are one meter aluminum squares that are deployed by hand and all fish and decapods removed with a sweep net.


All fauna will be counted, measured, and identified to the species or genus level where possible.


d.      Porewater Salinity, Sulfate and Methane:  At the nine (9) belt transects indicated in the March 1999 CZR Report (P3 on only one side of the Town Creek, P6, P7, P8, P9, P11, P12, P13, & P14), sediment pore water samples for chloride, sulfate, and methane determination will be collected using a Hesslein‑type peeper (Hesslein 1976).  The peepers are deployed in the substrate for 1-2 weeks while the concentrations of the analytes in the peeper chambers water equilibrates with the surrounding porewater.  The concentration of all parameters are determined after removing samples from peeper cells with a syringe equipped with a needle.  Sulfate and chloride concentrations are determined with an ion chromatograph (Hoehler et al. 1994).  Salinity is calculated from the chloride concentrations of the equilbrated peeper chamber water.  Sulfate reduction in indicated by a departure from seawater ratios of chloride and sulfate.  Samples for porewater methane analysis are prepared by extraction of porewater methane into an inert helium headspace within a gas-tight syringe.  The headspace gas is then injected into a gas chromatograph equipped with a flame ionization detector (Kelly et al. 1995) for quantitative determination of methane concentration.  The presence of elevated methane concentrations indicates that sulfate concentrations are too low for sulfate reduction to occur and that the sediment has not been recently influenced by salt water intrusion.


      One peeper is located at each of six substations per transect with the substations generally equally spaced along the long axis of each transect.  Where feasible, the peepers will be located in the area with sensitive vascular herbaceous vegetation as described in paragraph “f” below.  Each substation is accessed by boardwalks that were installed under a separate contract.  The porewater sampling will be conducted during each of two sampling periods:  December -February 2000/2001 and June-August 2001.  One station will be monitored monthly to determine the maximum-minimum pattern.


To determine pore water sulfate concentrations, a small amount of concentrated acid will be added and samples shaken to remove any volatile sulfide compounds that otherwise would be converted to sulfate under oxic conditions.  Sulfate concentrations are stable under oxic conditions and can be stored in serum vials until analysis.  Sulfate concentrations will be determined with an ion chromatograph following the method of Hoehler et al. (1994).


Porewater methane concentrations are also derived from water extracted from peeper cells into airtight glass syringes equipped with a three-way stopcock and a needle.  Contact with air is minimized to prevent oxidation of methane.  Samples will be transported back to the laboratory on ice.  A known quantity of air will be drawn into the syringe and the sample shaken vigorously to extract the highly insoluble methane gas into the headspace of the syringe.  The headspace will then be injected into a gas chromatograph equipped with a flame ionization detector to determine methane concentration.  The porewater methane concentration will be calculated from the amount of porewater and headspace in the syringe following Kelley et al. (1995).


Salinity concentrations will be reported to the nearest tenth of a part per thousand, and methane and sulfate concentrations will be reported to the nearest 100 micromoles and 2 micromoles, respectively.


e.   Belt Transects Surface Water Levels and Salinity:  At the nine (9) belt transects indicated in the March 1999 CZR Report (P3 on only one side of the Town Creek, P6, P7, P8, P9, P11, P12, P13, & P14), water level (RDS WL20s and WL40s) and salinity (Unidata Star Logger with conductivity probe) data will be collected.  One WL20s or 40s and one salinity probes will be located at each of six substations per transect with the substations generally equally spaced along the long axis of each transect.  Each substation is accessed by boardwalks that were installed under a separate contract.  These are the same substations indicated in paragraph “d” above.  The equipment will be deployed over fortnightly sampling periods at each transect during each of two sampling periods:  August-December 2000 and February-June 2001.  Fortnightly sampling will account for spring/neap variability.  One-minute averages of water level and salinity (conductivity) will be recorded once every 6 minutes during inundation.  The data will be manually download every 1-2 weeks.


Data will need to be recorded to the nearest hundredth (1/100) of a foot for water level measurements and nearest tenth of a part per thousand for salinity.


f.            Vegetation:  At the nine (9) belt transects indicated in the March 1999 CZR Report (P3 on only one side of the Town Creek, P6, P7, P8, P9, P11, P12, P13, & P14), major plant communities or cover types will be described along with approximate widths (i.e. the same procedure as in the March 1999 CZR Report).  In addition within each belt transect, areas of sensitive vascular herbaceous vegetation will have their perimeter mapped (at an appropriate scale) and area determined using GPS technology with sub-meter accuracy.  Also for sensitive vascular herbaceous vegetation, percent cover will be estimated within these perimeters.  Sensitive vascular herbaceous vegetation is defined as non-woody vegetation intolerant to changes in soil chemistry, inundation regime, or salinity that may be caused by the deepening project.  This work will be performed in June-July of 2001. 


g.   Quality Assurance and Control:  Quality Assurance and Control will be performed in accordance with Section 2.10 of the May CZR 1998 Report.


h.   Data Collection and Data Analysis Protocols:  Manuals will be prepared detailing data collection and data analysis monitoring protocols for paragraphs “a-g” above.  The manuals will contain sufficient information so that an independent party could duplicate the monitoring efforts.


i.            Horizontal and Vertical Control.  Horizontal and vertical controls have been established at all locations indicated below.  The contractor will not alter any of these controls or structures associated with these controls indicated below without first obtaining written consent from the contracting officer.  If any of these control are altered by the contractor, they will be reestablished by the contractor at no cost to the government.


1)        the water level sensors on the DCP’s,

2)       conductivity and temperature sensors at each DCP location and at the Corps of Engineer Yard,


 For each of the 9 belt transects:


3)       one fix on the top of a solid steel rod > 1.0 cm in diameter and at least 2.5 meters long driven at least 2 meters vertically into the substrate, and

4)       all belt transect water level monitoring locations


2.  Monthly and Annual Reports:


         a.  Monthly Status Report:  By the fifth working day of each month, a written letter report is required for the previous month’s activities.  This report will summarize sampling activities, preliminary results, and important observations.  These status reports shall also be used to discuss potential problems and solutions related to contract performance or conditions which may affect performance.  Monthly status reports must accompany requests for partial payment.


         b.  Annual Project Report:  Upon completion of all work tasks under the contract, the Contractor shall submit a draft report for review.  The report and findings shall be objective and fully substantiated by documentation.  The report shall follow the format required by reputable scientific periodicals, including abstract, summary, introduction, methods, results, discussion, conclusions and recommendations, references, and appendices.  The appendices will contain tabulations of all physical, biological, and statistical data and a list of all participating technical staff and their respective responsibilities on the project.  The report shall contain appropriate summary tables and figures.  In addition, the report must include:


(1)             equipment maintenance and data collection procedures, equipment replacement and malfunctions, and problems with lost or questionable data;

(2)            description of monitoring methodology, results and any problems;

(3)            discussion of the results including habitat value and apparent difference in sites from downstream to upstream.


Text material shall be typed or printed with a letter quality printer (dot matrix printing is not acceptable) on 8-1/2" by 11" bond paper with 1-1/2" margins on the left for binding.  All pages must be consecutively numbered.  Drawings or plates bound in the report shall be no larger than 11" by 17" and shall include a graphic bar scale for control during reduction or enlargement.  Additional larger maps or drawings shall be provided on standard 30" by 42" sheets, unless the Contracting Officer and the Contractor agree otherwise. The Contracting Officer will provide written comments on the accepted draft report.  The Contractor will revise the report in accordance with these comments and, then, submit the report as final.


            Ten copies of the draft report including the Data Collection and Data Analysis Protocols must be submitted by November 1, 2001, to the U.S. Army Corps of Engineers, Wilmington District, for review.  A draft report requiring extensive proofreading or incomplete draft reports will be returned to the Contractor as unacceptable. Twenty-five copies of the final report must be submitted to the Corps within 30 working days after the date the Corps provides comments on the draft to the contractor.


            The cover of the project report must bear the title "Monitoring Effects of a Potential Increased Tidal Range in the Cape Fear River Ecosystem Due to Deepening Wilmington Harbor, North Carolina, Year 1:  August 1, 2000 – July 31, 2001”, "Prepared for the Wilmington District, US Army Corps of Engineers.", and Contract Number.  In addition, the title page shall bear an inscription stating Project Manager: (Name).  If the document has been prepared by someone other than the Project Manager, this inscription will, instead, state Prepared Under the Supervision of (Name), Project Manager.  The original copy of the final report shall be signed by the Project Manager.


            The Contractor shall provide one copy of the entire final report text, including all tables, charts, and  appendices, on IBM Personal Computer readable floppy disks or compact disk.  The enclosure indicates the format required for all electronic files delivered to the District.






CZR, Incorporated.  1999.  Location of Permanent Stations, Background Stations, and Substations for Monitoring Potential Effects of Increased Tidal Range on the Cape Fear River Ecosystem Due to Deepening Wilmington Harbor, North Carolina.  Prepared for U.S. Army Corps of Engineers, Wilmington District, Wilmington, North Carolina.  March 1999.


CZR, Incorporated.  1998.  A Monitoring Plan to Determine Potential Effects of Increased Tidal Range on the Cape Fear River Ecosystem Due to Deepening Wilmington Harbor, North Carolina.  Prepared for U.S. Army Corps of Engineers, Wilmington District.  May 1998.


Fauchald, K. and P.A. Jumars. 1979. The diet of worms: a study of polychaete feeding guilds. Oceanography and Marine Biology Annual Reviews 17:477-489.


Griffitt, B.J, M.H. Posey, and T.D. Alphin.  1999.  Effects of edge fragmentation on oyster reef utilization by transient nekton.  J. of Elisha Mitchell Scientific Society 115:98-103


Hesslein, R.H. 1976. An in situ sampler for close interval pore water studies.  Limnology             and Oceanography 21:912‑914.


Hoehler, T.M., M.J. Alperin, D.B. Albert and C.S. Martens.  1994.  Field and laboratory studies of methane oxidation in an anoxic marine sediment: Evidence for a methanogen‑sulfate reducer consortium.  Global Biogeochemical Cycles 8:451‑463.


Kelley, C.A., C.S. Marten, and W. Ussler III.  1995.  Methane dynamics across a tidally flooded riverbank margin.  Limnology and Oceanography  40:1112‑1129.


National Ocean Survey. 1998. The New Water Level Measuring System. Oceanographic Products and Services Division.


Posey, M.H.  1990.  Functional approaches to soft-substrate communities:  How useful are they?  Reviews in Aquatic Science 2/3:343-356.


Sargent, W.B. and P.R. Carlson, Jr.  1987.  Utility of Breder traps for sampling mangrove and high marsh fish assemblages.  Proceedings from the Fourteenth Annual Conference on Wetland Restoration and Creation.  PP 194-205.


Townsend, E. C.  1991.  Depth Distribution of grass shrimp (Palaemonetes pugio) in Two Contrasting Tidal Creeks in North Carolina and Maryland.  MS Thesis, University of North Carolina at Wilmington.



Wilmington District Corps of Engineers, Geospatial Data and Systems Standards



The following paragraphs represent the format for electronic files being delivered as part of any contract.  These paragraphs do not specify content or what the electronic files should contain.  The content or data represented should be specified in the basic Scope of Work.



1.  Specifications For Digital Data.  Any maps, drawings, figures, sketches, databases, spreadsheets, or text files prepared under the terms of this contract shall be provided in both hard copy and digital form, unless otherwise specified in the Scope of Work.  The hard copy deliverables shall be defined in the body of the basic Scope of Work.


2.  Text, Spreadsheet, and Database Files:  The U.S. Army Corps of Engineers, Wilmington District standard computing software is Microsoft Office.  Reports and other text documents shall be provided in Microsoft Word 97 format.  Spreadsheet files shall be provided in Microsoft Excel format.  Databases shall be provided in Microsoft Access format, unless otherwise specified in the basic Scope of Work.  Prior to database development, the contractor shall provide the Government with a Technical Approach Document for approval which describes the contractor's technical approach to designing and developing the database.  All text, spreadsheet, and database files shall be delivered on 3.5 inch, high density diskettes, 100mb ZIP Disks, or compact disk read-only memory (CD-ROM) with ISO-9660 format.


3.                   Digital Mapping and Data Standards:  The U.S. Army Corps of Engineers, Wilmington District utilizes Microstation for Computer Assisted Drafting and Design CADD.


4.  Geographic Information System (GIS) Data Delivery Format:


a.  Digital geographic maps and the related digital information shall be developed using double precision and delivered in uncompressed ARC/INFO export file format (.e00) using ARC/INFO Release 7.2 or higher.  ARC/INFO is a geographic information system software application produced by the Environmental Systems Research Institute of Redlands, California, and is the software used by U.S. Army Corps of Engineers, Wilmington District.


b.  Digital geographic maps and the related digital information shall be usable on a IBM compatible personal computer system using the Windows NT 4.0 operating system.  This data shall be provided on compact disk read-only memory (CD-ROM) with ISO-9660 format.  Digital information may alternatively be delivered on 100mb ZIP Disks.


5.  General Digital Standard for CADD and GIS Files


a.  Geographic data shall be provided in feet and projected into the North Carolina State Plane coordinate system.  The maps shall use the GRS 1980 spheroid and the North American Datum 1983 (WGS-84).  No offsets shall be used.  Each map layer or coverage shall have a projection file.  Map or drawing scales will be determined by the Contracting Officer's Representative for the contract.  Mapping accuracy for the agreed scales will conform to the American Society for Photogrammetry and Remote Sensing (ASPRS), "Accuracy Standards for Large-Scale Maps" and “Interim Accuracy Standards for Large-Scale Maps” (ASPRS, 1991).  Copies of the ASPRS Accuracy Standards can be obtained by contacting:


American Society for Photogrammetry and Remote Sensing

5410 Grosvenor Lane, Suite 210

Bethesda, MD 20814-2160


ASPRS accuracy standards can also be found on the Internet at:


b.  Geographic data must be provided in a form that does not require translation, preprocessing, or postprocessing before being used in the U.S. Army Corps of Engineer’s System.  However, the Contractor shall consult with the Government (specifically the Geographic Information Systems Office) concerning the use of alternative delivery formats such as MicroStation SE or higher to provide design drawings, sketches, or figures.  The Government may approve the use of AutoCAD when it is determined that the format will not compromise the spatial accuracy or structure of the delivered data and that the data will easily integrate with the U.S. Army Corps of Engineers, Wilmington District’s System.  All digital files provided in Microstation shall be in the same projection and use the same coordinate system, datum, and units as stated above, and shall be provided on 3.5 inch, high density diskettes, 100mb Zip Disks, or CD-ROMs.


c.  Geographic Data Structure:  All geographic information shall be developed in a structure consistent with the Spatial Data Standards (SDS), Version 1.9, released in December 1999, or a higher version if available at the time of this project.  The Contractor shall consult with the Government concerning modifications or additions to the SDS.  The Government may approve modifications to the Standard if it is determined that SDS does not adequately address subject data sets.  Copies of the SDS may be obtained by contacting:


Director, U.S. Army Engineer Waterways Experiment Station

Tri-Service CADD/GIS Technology Center

Attn:  CEWES-IM-DA/Smith

3909 Halls Ferry Road

Vicksburg, MS  39180-6199


Electronic copies of the Standards are also available from the Tri-Service CADD/GIS

Technology Center's Internet homepage at URL address:


d.  Geographic Data Documentation: For each digital file delivered containing geographic information (regardless of format), the Contractor shall provide documentation consistent with the "Content Standards for Digital Geospatial Metadata, June 1998" published by the Federal Geographic Data Committee.  The documentation shall include but is not limited to the following:  the name and description of the map layer or coverage, the source of the data and any related data quality information such as accuracy and time period of content, the type of data coverage (point, line, polygon, etc.), the field names of all attribute data and a description of each field name, the definition of all codes used in the data fields, the ranges of numeric fields and the meaning of these numeric ranges, the creation date of the map layer and the name of the person who created it.  A point of contact shall be provided to answer technical questions.  A metadata generation software, called Document.aml, is available from ESRI for use with ARC/INFO to help in the production of the required metadata.  Copies of the FGDC metadata standard can be obtained by contacting:


FGDC Secretariat

c/o U.S. Geological Survey

590 National Center

Reston, Virginia  22092

(703) 648-5514


FGDC metadata standards can also be found on the Internet at:


e.  Geographic Data Review:  The digital geographic maps, related data, and text documents shall be included for review in the draft and final contract submittals.  The reviews may include a visual demonstration of the geographic data on the Windows NT computer system in the Environmental Resources Section GIS Unit’s.  Actual installation of the digital data from the CD-ROM onto the computer will be conducted by GIS Unit personnel.  However, the Contractor shall have a technical consultant available at each review to assist with any digital data discrepancies.  The data will be analyzed for subject content and system compatibility.  Review comments to data and text shall be incorporated by the Contractor prior to approval of the final submittal.


f.  Ownership:   All digital files, final hard-copy products, source data acquired for this project, and related materials, including that furnished by the Government, shall become the property of U.S. Army Corps of Engineers, Wilmington District and will not be issued, distributed, or published by the Contractor.


Prepared by the Environmental Resources Section GIS Team (910/251-4755)