Prepared in cooperation with the U.S. Fish and Wildlife Service

User’s Manual to Update the National Wildlife Refuge 

System Water Quality Information System (WQIS)

Chapter 8 of 

Section C, Geographic Information Systems tools and applications

Book 11, Collection and Delineation of Spatial Data 

Techniques and Methods 11–C8

U.S. Department of the Interior

U.S. Geological Survey

User’s Manual to Update the National 

Wildlife Refuge System Water Quality 

Information System (WQIS)

By Kimberly A. Chojnacki, Chad J. Vishy, Jo Ellen Hinck, Susan E. Finger, Michael 

J. Higgins, and Kevin Kilbride

Chapter 8 of 

Section C, Geographic Information Systems tools and applications

Book 11, Collection and Delineation of Spatial Data 

Prepared in cooperation with the U.S. Fish and Wildlife Service

Techniques and Methods 11–C8

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

U.S. Geological Survey, Reston, Virginia: 2013

For more information on the USGS—the Federal source for science about the Earth, its natural and living 

resources, natural hazards, and the environment, visit http://www.usgs.gov or call 1–888–ASK–USGS.

For an overview of USGS information products, including maps, imagery, and publications, 

visit http://www.usgs.gov/pubprod

To order this and other USGS information products, visit http://store.usgs.gov

Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the 

U.S. Government.

Although this information product, for the most part, is in the public domain, it also may contain copyrighted materials 

as noted in the text. Permission to reproduce copyrighted items must be secured from the copyright owner.

Suggested citation:

Chojnacki, K.A., Vishy, C.J., Hinck, J.E., Finger, S.E., Higgins, M.J., and Kilbride, Kevin, 2013, User’s manual to update 

the National Wildlife Refuge System Water Quality Information System (WQIS): U.S. Geological Survey Techniques 

and Methods, book 11, chap. C8, 24 p. 
iii

Contents

Abstract...........................................................................................................................................................1

Introduction.....................................................................................................................................................1

Project Background.......................................................................................................................................2

Purpose and Scope .......................................................................................................................................3

Water Quality Information System Database............................................................................................3

Required Geospatial Datasets.....................................................................................................................4

Data Acquisition and Preparation...............................................................................................................4

Spatial Overlay ...............................................................................................................................................9

Prepare the Analysis Areas File.........................................................................................................9

Prepare NHDPlus Flowlines Dataset...............................................................................................11

Prepare the Water-Quality Datasets ...............................................................................................16

Reproject the NHD Flowlines and Water-Quality Datasets.........................................................16

Export Tables .......................................................................................................................................16

Prepare the Parameter Attribute Tables.........................................................................................16

Refreshing the WQIS Database ................................................................................................................18

Optimize the Database................................................................................................................................18

Troubleshooting ...........................................................................................................................................20

References Cited..........................................................................................................................................23

Figures

1. Screen capture of the U.S. Fish and Wildlife Service Geospatial Services 

webpage.........................................................................................................................................5

2. Screen capture of the NHDPlus Web site showing the NHDPlus Data link.......................6

3. Screen capture of the NHDPlus Version 1 archive Web site................................................6

4. Screen capture of the NHDPlus regions ..................................................................................7

5. Screen capture of the NHDPlus version 1 datasets...............................................................7

6. Screen capture of the U.S. Environmental Protection Agency Reach Address

Database Download Web site....................................................................................................8

7. Screen capture of the National Geospatial Datasets webpage...........................................8

8. Screen capture of the Clean Water Act Section 303(d) Listed Impaired Waters

Download webpage .....................................................................................................................9

9. Screen capture showing the creation of a new file geodatabase in ArcCatalog .............9

10. Screen capture of adding the FwsApproved and FwsInterest data layers to 

ArcMap.........................................................................................................................................10

11. Screen capture of the Query Builder expression used to display only National

Wildlife Refuges..........................................................................................................................10

12. Screen capture of the Select by Attributes tool used to select the approved

boundaries for all Refuges EXCEPT the four large Refuges in the FwsApproved 

data layer .....................................................................................................................................11

13. Screen capture of the Select by Attributes tool used to select the boundaries 

of the four Refuges in the FwsInterest data layer.................................................................11
iv

14. Screen capture of the Merge tool used to combine boundaries from both the

FwsApproved and FwsInterest data layers............................................................................12

15. Screen capture of the NDHflowline data layer within a NHDPlus geodatabase ............12

16. Screen capture of the Clip tool used to clip the NHDflowlines from each 

National Hydrography Dataset region to refuge boundaries using the Analysis

Areas data layer created previously .......................................................................................13

17. Screen capture of the Merge tool to combine the clipped NHDflowlines from 

each National Hydrography Dataset region into one seamless national 

NHDflowlines layer.....................................................................................................................14

18. Screen capture of the Spatial Join function to add refuge attributes to the

NHDflowline data layer..............................................................................................................14

19. Screen capture of the Select by Attributes tool used to select stream segments

with null values in the GNIS_Name column...........................................................................15

20. Screen capture of the Query Builder expression used to eliminate artificial path,

coastline, and pipeline features from the NHDflowline dataset representation in

ArcMap.........................................................................................................................................15

21. Screen capture of the Project tool used to convert the prepared datasets to a

projected coordinate system....................................................................................................16

22. Screen capture of Exporting the attribute table for the prepared files;

NHDflowlines, Clean Water Act Section 303(d) listed impaired waters, and total

maximum daily load data layer.................................................................................................17

23. Screen capture of saving the data table exported from ArcGIS as a .dbf file .................17

24. Screen capture of the parameter attribute table for Clean Water Act Section 

303(d) impaired waters within the U.S. Environmental Protection Agency 

RAD_303(d) geodatabase..........................................................................................................18

25. Screen capture showing the side-by-side comparison of fields contained in the 

old Impaired and new Impaired1 versions of the table........................................................19

26. Screen capture showing the Dates table within the WQIS database...............................19

27. Screen capture of the Performance Analyzer tools in Microsoft Access........................20

28. Screen capture of the Performance Analyzer results .........................................................21

29. Screen capture of the Access Options to configure Microsoft Access to

successfully run the WQIS database......................................................................................21

30. Screen capture of the Access Options box in Microsoft Access......................................22

31. Screen capture of the Macro Settings within the Microsoft Access Trust Center.........22

32. Screen capture of the Enable Data Execution Prevention setting in the Microsoft

Access Trust Center...................................................................................................................23

Tables

1. Water-quality standard attainment categories based on U.S. Environmental

Protection Agency guidance ......................................................................................................2

2. Data tables contained in the Water Quality Information System database .......................3

3. Geospatial datasets and their sources used to summarize water-quality issues 

on National Wildlife Refuges ......................................................................................................4
User’s Manual to Update the National Wildlife Refuge 

System Water Quality Information System (WQIS)

By Kimberly A. Chojnacki, Chad J. Vishy, Jo Ellen Hinck, Susan E. Finger, Michael J. Higgins, and Kevin 

Kilbride

Abstract 

National Wildlife Refuges may have impaired water 

quality resulting from historic and current land uses, upstream 

sources, and aerial pollutant deposition. National Wildlife 

Refuge staff have limited time available to identify and evaluate potential water quality issues. As a result, water quality–

related issues may not be resolved until a problem has already 

arisen. The National Wildlife Refuge System Water Quality 

Information System (WQIS) is a relational database developed 

for use by U.S. Fish and Wildlife Service staff to identify 

existing water quality issues on refuges in the United States. 

The WQIS database relies on a geospatial overlay analysis 

of data layers for ownership, streams and water quality. The 

WQIS provides summary statistics of 303(d) impaired waters 

and total maximum daily loads for the National Wildlife 

Refuge System at the national, regional, and refuge level. 

The WQIS allows U.S. Fish and Wildlife Service staff to be 

proactive in addressing water quality issues by identifying and 

understanding the current extent and nature of 303(d) impaired 

waters and subsequent total maximum daily loads. Water quality data are updated bi-annually, making it necessary to refresh 

the WQIS to maintain up-to-date information. This manual 

outlines the steps necessary to update the data and reports in 

the WQIS. 

Introduction

The National Wildlife Refuge System (NWRS) is a 

network of public lands and waters managed by the U.S. Fish 

and Wildlife Service (FWS). The mission of the NWRS is to 

conserve, protect and enhance biological resources and habitat 

for the benefit of present and future generations of Americans (U.S. Fish and Wildlife Service, 2011). Many National 

Wildlife Refuges (refuges) have water quality impairments 

resulting from previous and current land uses, transport of 

pollutants from off-refuge, upstream sources, and aerial pollutant deposition. These new and existing impairments often 

elude refuge staff until a problem arises, as much of their 

time is spent on daily resource management duties. Legal 

mandates on National Wildlife Refuge System lands include 

the amended National Wildlife Refuge System Administration Act for Refuge purpose and water quality protection (16 

U.S.C. 668dd–668ee; Code of Federal Regulations, 2012a); 

the Migratory Bird Treaty Act (16 U.S.C. 703–711), the 

Endangered Species Act (16 U.S.C. 11 1531–1544, December 

28, 1973, as amended 1976–1982, 1984 and 1988), and the 

Marine Mammal Protection Act (16 U.S.C. 1361–1471h) for 

addressing FWS biological resources (Code of Federal Regulations, 2012a); and FWS Manual Chapter 601 FW 3-Biological Integrity, Diversity, and Environmental Health for 

maintaining and restoring biological integrity, diversity, and 

environmental health (U.S. Fish and Wildlife Service, 2012a). 

The Clean Water Act was established in 1972 to restore 

and maintain the chemical, physical, and biological integrity of surface waters in the United States (Code of Federal 

Regulations, 2012b). Water-quality standards, the conceptual 

basis for the surface-water pollution control program of the 

Clean Water Act, define the goals for a water body by designating its uses (for example, drinking water supply, primary or 

secondary contact recreation, aquatic life use support), setting 

criteria to protect those uses, and establishing antidegradation 

provisions. Under Clean Water Act Section 305(b), states are 

required to prepare biennial water-quality assessment reports 

that identify where and why navigable water bodies are not 

meeting state water-quality standards. The term “navigable 

waters” includes; (1) all navigable waters of the United States, 

as defined in judicial decisions before the passage of the 1972 

Amendments of the Federal Water Pollution Control Act, also 

known as the Clean Water Act, and tributaries of such waters 

as, (2) interstate waters, (3) intrastate lakes, rivers, and streams 

that are used by interstate travelers for recreational or other 

purposes, and (4) intrastate lakes, rivers, and streams from 

which fish or shellfish are taken and sold in interstate commerce (Code of Federal Regulations, 2008).

 Water bodies that do not meet water-quality standards are 

considered ‘‘water quality-limited’’ and placed on the impaired 

waters list in the Clean Water Act Section 303(d), hereinafter 

known as 303(d). Impaired water bodies are placed into one 

of five categories representing different levels of water-quality 

standard attainment based on U.S. Environmental Protection Agency (EPA) guidance (table 1; U.S. Environmental 
2 User’s Manual to Update the National Wildlife Refuge System Water Quality Information System (WQIS)

Table 1. Water-quality standard attainment categories based on U.S. Environmental Protection Agency guidance.

[From Guidance for 2004 assessment, listing, and reporting requirements pursuant to Sections 303(d) and 305(b) of the Clean Water Act (U.S. Environmental 

Protection Agency, 2003)]

Category Description

1 All designated uses are met.

2 Some designated uses are met but insufficient data for remaining designated uses.

3 Insufficient data to determine if any designated uses are met.

3B Insufficient data but some data indicate nonattainment of applicable water-quality standards have been approved.

4A All total maximum daily loads needed for attainment of applicable water-quality standards have been approved.

4B Other pollution control requirements are expected to address all pollutants and will attain water-quality standards.

4C Impairment is not caused by a pollutant.

5 Water is impaired or threatened and a total maximum daily load is needed.

Protection Agency, 2003). Once a water body is listed as 

303(d) impaired, the Clean Water Act requires the state to 

develop a total maximum daily load (TMDL) for the impaired 

water to protect beneficial uses by minimizing further degradation. After the TMDL is approved by the EPA, an implementation plan is prepared and initiated by the state. A TMDL is an 

estimate of the maximum amount of a pollutant that a water 

body can receive and still meet the water-quality standards. It 

is calculated as the sum of (1) waste load allocation, which is 

the amount of pollutant from all existing point sources (such 

as, sewage treatment plant; industrial facility), (2) load allocation, which is the amount of pollutant from existing nonpoint 

sources and natural background (for example, runoff or atmospheric deposition), and (3) a margin of safety that reflects 

uncertainty associated with the TMDL estimate. A TMDL 

commonly targets anthropogenic sources such as agriculture, 

silviculture, industry, and urban centers (such as, stormwater 

runoff). In addition, discharges from natural and managed wetlands or other aquatic habitats also are affected by load-limit 

regulations. Because reporting on the status of implementation 

is currently (2012) not required under the Clean Water Act or 

by EPA, it is often difficult to assess progress toward meeting 

a TMDL (Hinck and others, 2011). 

The regulatory requirements associated with a TMDL 

represent one of the ultimate challenges for adaptive management on refuges. States prepare and apply TMDL implementation plans that allocate contaminant load limits among all 

discharges within a watershed (including wetlands) to maintain or improve water quality. Although wetland and water 

management on refuges may be affected by or contribute 

to the establishment and implementation of a TMDL, many 

refuges are not prepared to adapt to an existing or proposed 

TMDL. Specifically, a TMDL may force alterations of refuge 

water-management programs (for example, limiting wetland 

drawdowns) that can affect the quantity and quality of refuge 

aquatic habitats. A TMDL also may affect FWS-coordinated 

efforts for resource management with conservation partners in 

larger landscapes beyond refuge boundaries.

Project Background

This project builds on a cooperative project initiated in 

2008 (Hinck and others, 2011) involving FWS, U.S. Geological Survey (USGS), and EPA. In the initial project, USGS 

developed a geospatial approach to identify and prioritize 

water-quality issues affecting resources of concern within 

refuge boundaries (Hinck and others, 2011). The nature of 

303(d) impaired waters and TMDLs within individual refuges were assessed with a geospatially-based application for 

two pilot states in FWS Region 1 (Oregon and Washington). 

Products from this project included; summary statistics of 

303(d) impaired waters and TMDLs for the region, as well as 

a Geographic Information System (GIS) based module that 

included all pertinent geospatial data layers. Individual refuge 

summaries allow for FWS staff to be proactive in addressing 

water-quality issues by identifying and understanding the current extent and nature of 303(d) impaired waters and TMDLs. 

With this information, refuge staffs can evaluate the effect of 

current management actions on 303(d) impaired waters and 

subsequent TMDLs, as well as identify best management practices to protect and enhance water quality. 

The concept of the initial project in Oregon and Washington was then applied to create a national database (Water 

Quality Information System; WQIS), which included summary statistics of 303(d) impaired waters and TMDLs for 

the NWRS at the national, regional, and refuge level using 

linear stream-segment geospatial data. Such information is 

useful to develop Water Resource Inventory and Assessment 

reports, Comprehensive Conservation Plans, and Contaminant 

Assessment Process reports. Information on using the WQIS, 

including frequently asked questions and troubleshooting, is 

contained within the database itself. The WQIS was developed 

for ultimate inclusion as a module in the Environmental Conservation Online System of FWS.
Water Quality Information System Database 3

Purpose and Scope

The WQIS is a relational database developed for use by 

FWS staff to identify existing water-quality impaired streams 

on refuges in the United States, excluding Alaska. The WQIS 

provides summary statistics of 303(d) impaired waters and 

TMDLs for the NWRS at the national, regional, and refuge 

level. The WQIS also generates a National Score Card report 

that provides an abbreviated summary of water-quality issues. 

This version of the WQIS database includes data for refuges 

only, not Wetland Management Districts or Waterfowl Production Areas.

The WQIS database relies on a geospatial overlay 

analysis of data layers for land ownership, streams, and water 

quality. The EPA water-quality data required for this project 

are updated bi-annually, making it necessary to refresh the 

analysis to maintain up-to-date reports. This User’s Manual 

documents and describes the methods used to identify 303(d) 

listed impaired streams and streams with established TMDLs 

within approved refuge boundaries. It is important to note that 

impairments for nonlinear water features (such as, lakes and 

wetlands) are NOT included in this version of the WQIS database. Additionally, this document describes the development 

of the WQIS database and the method to update the database 

and the reports contained therein. 

Water Quality Information System 

Database

The WQIS database was developed by USGS using 

Microsoft Access (Microsoft Corporation, Seattle, Wash.) to 

provide a flexible and portable database platform. Each table 

in the database is designed to store a specific and defined set 

of data, in which each record has a mutually exclusive identifier. Data stored in one table can be linked (related) to data in 

another table using the mutually exclusive identifiers. These 

linkages are established and maintained within the database, 

making it possible to combine data from multiple tables into 

one report. These linkages are maintained even when the 

data tables are updated, as long as the table and field names 

involved in the relationship remain constant in the database. 

The Microsoft Access platform also provided the opportunity to develop a user interface, allowing users to quickly 

view a series of custom reports summarizing information 

from multiple tables. Reports providing summary statistics 

of 303(d) impaired waters and TMDLs for refuges at the 

national, regional and refuge level have been made easily 

accessible through the custom WQIS user interface. 

The WQIS consists of nine tables (table 2). Table names 

are italicized to improve readability. The NHD, Impaired 

and TMDL tables are derived from a spatial overlay analysis 

in a GIS. The Impatt and TMDLatt are attribute tables providing detailed information about the parameters for each 

303(d) impairment and established TMDL. The Dates table 

contains publication dates for the FWS cadastral dataset and 

Table 2. Data tables contained in the Water Quality Information System database. 

[TMDL, total maximum daily load]

Table name Description

Dates Table containing the publication dates for the U.S. Fish and Wildlife Service cadastral and U.S. Environmental Protection Agency water-quality data.

Impatt Additional descriptive attribute information for each Clean Water Act Section 303(d) listed impairment, linked in a oneto-many relationship to the impaired table using the SourceFeatureID.

Impaired Table containing data for Clean Water Act Section 303(d) listed impaired stream segments within refuge boundaries. 

Extracted from spatial overlay analysis.

NHD Table containing data for National Hydrography Dataset flowline stream segments within refuge boundaries. Extracted 

from spatial overlay analysis.

TMDL Table containing data for TMDL on impaired stream segments within refuge boundaries. Extracted from spatial overlay 

analysis.

TMDLatt Additional descriptive attribute information for each established TMDL linked in a one-to-many relationship to the 

TMDL table using the SourceFeatureID.

RankImp Table containing top five Clean Water Act Section 303(d) impairment parameters per U.S. Fish and Wildlife Service 

region. Created by the Water Quality Information System database.

RankTMDL Table containing top five TMDL parameters per U.S. Fish and Wildlife Service region. Created by the Water Quality 

Information System database.

States Table containing the name and state(s) of each refuge, used to link with the cycle date in each EPA water-quality tables 

(Impaired and TMDL).
4 User’s Manual to Update the National Wildlife Refuge System Water Quality Information System (WQIS)

EPA water-quality datasets. This information is incorporated 

into the header of all the summary reports, providing the user 

information on the publication date of the data being reported. 

The States table includes a complete refuge name list and 

the state(s) in which each refuge is contained. These data are 

linked to the Impaired and TMDL tables to provide the reporting-cycle year information. The EPA reporting-cycle year is 

included in the summary reports so that the user understands 

how current the data are. The RankImp and RankTMDL tables 

provide the top five 303(d) impairment parameters and TMDL 

parameters, respectively, for each FWS region. These two 

tables are created dynamically by the WQIS database and are 

necessary for the generation of the National Score Card report. 

Required Geospatial Datasets

Required geospatial datasets include FWS cadastral geodatabase, NHDPlus datasets, and water-quality datasets from 

EPA (table 3). The FWS cadastral geodatabase contains FWS 

Approved, FWS Interest, and Special Designation data layers. 

The FWS Approved dataset represents the external boundaries of lands and waters that are approved for acquisition by 

FWS. The FWS Interest dataset represents fee title lands and 

less-than fee lands (for example, easements) and may include 

inholding lands within acquisition boundaries. The Special 

Designation dataset represents other designations, such as Wilderness and Wild and Scenic Rivers on FWS managed lands. 

NHDPlus data were obtained for all hydrologic regions 

within the contiguous United States and Hawaii. These data do 

not yet exist for Alaska. The NHDPlus is an integrated suite 

of geospatial datasets incorporating many features from the 

National Hydrography Dataset (NHD), the National Elevation 

Dataset (NED), the National Land Cover Dataset (NLCD) and 

the Watershed Boundary Dataset (WBD) (NHDPlus Team, 

2010). The NHDPlus data provides a comprehensive stream 

centerline network based on the medium resolution NHD 

(1:100,000). Linkages have been developed by EPA between 

the NHDPlus and numerous EPA water-quality databases 

by assigning NHD stream reach addresses (NHDPlus Team, 

2010). NHDPlus Version 1 was used for the initial development of the WQIS, as NHDPlus Version 2 had not yet been 

released. The data structure of the NHDPlus Version 2 has 

only minor modifications and could therefore be used in lieu 

of Version 1. Make note that the Version 2 data has not been 

released for Hawaii (2012). 

Water-quality datasets are available from the EPA including 303(d) listed impaired waters and TMDLs data layers 

(table 3). The 303(d) impaired waters dataset includes waters 

identified as Attainment Category 5 (table 1). Geospatial data 

on waterbodies in Categories 2-4c (table 1) are not currently 

(2012) available from EPA. The TMDL dataset represents 

waters that are not supporting their designated uses. The 

303(d) impaired waters and TMDL datasets have additional 

attributes maintained in separate tables inside their respective 

geodatabases. The spatial representation and descriptive attribute tables can be related (linked) using an associated identifier. These relationships are defined in the WQIS database. 

Data Acquisition and Preparation

Updating the WQIS requires downloading all the requisite geospatial datasets, performing the GIS processing, and 

importing the new tables into the existing WQIS database. The 

updated version of the database or the reports produced by the 

database can then be made available to other users.

Requirements for successful data preparation include: 

• ArcGIS (ESRI, Inc., Redlands, Calif.) suite of GIS 

products 

• Microsoft Access (Microsoft Corporation, Seattle, 

Wash.)

• Datasets described in the Required Geospatial Datasets section (table 3) 

It is assumed that a user attempting to refresh the data 

developed for the WQIS is familiar with GIS and database 

utilization, specifically the ArcGIS suite of products, and 

Microsoft Access. Methods described herein utilize ArcGIS 

10.0 and Access 2010, but could be performed using other 

software packages. 

The WQIS requires several datasets described in the 

Required Geospatial Datasets section. It is advisable to 

Table 3. Geospatial datasets and their sources used to summarize water-quality issues on National Wildlife Refuges. 

Dataset Online Linkage1 Description

FWS cadastral http://www.fws.gov/GIS/data/CadastralDB/index.htm Datasets representing U.S. Fish and Wildlife Service 

Approved, Interest and Special Designation layers.

NHDPlus http://www.horizon-systems.com/nhdplus/ Datasets uniquely identifying water bodies in the 

United States.

303(d) impaired waters http://epamap32.epa.gov/radims/ Datasets representing Clean Water Act Section 303(d) 

impaired waters of the United States.

Waters with TMDLs http://epamap32.epa.gov/radims/ Datasets representing waters with established total 

maiximum daily loads. 

1

Links valid as of September 1, 2012.
Data Acquisition and Preparation 5

develop a file location to maintain all datasets downloaded for 

this project. This will help maintain the integrity of the datasets as originally downloaded and provide a backup copy of the 

data should mistakes occur during the processing steps. 

Many spatial analysis operations can be performed by 

using several, slightly different methods. This manual presents 

one method, but this method could be altered and still provide 

the same results. Naming conventions for datasets, especially 

those created during the spatial overlay data processing, have 

been suggested throughout the manual. Some suggestions 

are simply a matter of keeping track of the processing step(s) 

and are not necessary to duplicate; however, the final tables 

imported into the WQIS database MUST be given the 

specific names provided or the database queries will not 

function properly. 

Download and save the FWS Cadastral Geodatabase 

(fig. 1) from http://www.fws.gov/GIS/data/CadastralDB/index.

htm (U.S. Fish and Wildlife Service, 2012b) by clicking on the 

FWS Cadastral Geodatabase link. These data provide the necessary spatial representations of refuge boundaries. Make note 

of the date on which the data were updated and published 

(fig. 1). This information will be needed during the refresh of 

the WQIS database. 

Download the NHDPlus, National Hydrography Dataset 

for each of the regions within the contiguous United States 

and Hawaii (regions 1–18 and 20) from http://www.horizonsystems.com/nhdplus/index.php (Horizon Systems Corporation, 2012) by clicking on the NHDPlus Version 1 (Archive) 

link (fig. 2). These data provide a stream centerline network 

based on the medium resolution (1:100,000) NHD. Click on 

the Data link on the NHDPlus Version 1 (Archive) Web site 

(fig. 3). Click on a NHD region (fig. 4) to view all the available datasets for that region (fig. 5). The only dataset required 

for this analysis is the National Hydrography Dataset (see 

example in fig. 5). 

Obtain the EPA water-quality datasets from http://

epamap32.epa.gov/radims/ (U.S. Environmental Protection 

Agency, 2012) by clicking on the National Geospatial Datasets Extractions link (figs. 6 and 7). Download the ESRI File 

Geodatabase for both the 303(d) listed impaired waters and 

TMDLs (fig. 8). These datasets provide line segments representing impaired waters, impaired waters with established 

TMDLs, and the associated parameter attribute tables. Make 

note of the extraction date for the EPA water-quality data 

(fig. 8). This information will be needed during the refresh of 

the WQIS database. 

Figure 1. Screen capture of the U.S. Fish and Wildlife Service Geospatial Services webpage (May 22, 2012).
6 User’s Manual to Update the National Wildlife Refuge System Water Quality Information System (WQIS)

Figure 2. Screen capture of the NHDPlus Web site showing the NHDPlus Data link (November 1, 2012).

Figure 3. Screen capture of the NHDPlus Version 1 archive Web site (November 1, 2012).
Data Acquisition and Preparation 7

Figure 4. Screen capture of the NHDPlus regions (November 1, 2012).

Figure 5. Screen capture of the NHDPlus version 1 datasets. The National Hydrography Dataset needed for the Water Quality 

Information System analysis is circled in red (November 1, 2012).
8 User’s Manual to Update the National Wildlife Refuge System Water Quality Information System (WQIS)

Figure 6. Screen capture of the U.S. Environmental Protection Agency Reach Address Database Download 

Web site. The National Geospatial Datasets extractions web link is circled in red (May 22, 2012).

Figure 7. Screen capture of the National Geospatial Datasets webpage. The web links to download the Clean 

Water Act Section 303(d) listed impaired waters and impaired waters with total maximum daily load datasets are 

circled in red (May 22, 2012).
Spatial Overlay 9

Figure 8. Screen capture of the Clean Water Act Section 303(d) Listed Impaired Waters Download webpage. The link to download the 

The FWS Cadastral, NHDPlus, and EPA water-quality 

datasets are downloaded as compressed zip files. Unzip each 

downloaded dataset using WinZip (WinZip Computing, Mansfield, Conn.) or similar software. 

ESRI File Geodatabase is circled in red (May 22, 2012).

Spatial Overlay

Spatial overlay will be used to extract NHD stream segments, 303(d) impaired waters, and waters with established 

TMDLs within refuge boundaries. It is advisable to create a 

new geodatabase to contain the data layers created to refresh 

the WQIS database. 

Open ArcCatalog and create a File Geodatabase by right 

clicking on the folder where the new file geodatabase will be 

created, click New, click File Geodatabase (fig. 9), and name 

the new geodatabase WaterQuality.

Prepare the Analysis Areas File

In an ArcMap map document, add the FwsApproved and 

FwsInterest data layers from the FwsCadastral.gdb, FwsBoundary Feature Dataset (fig. 10). 

Figure 9. Screen capture showing the creation of a new file geodatabase in ArcCatalog.
10 User’s Manual to Update the National Wildlife Refuge System Water Quality Information System (WQIS)

To filter the FwsApproved boundaries layer to display 

only National Wildlife Refuges, open the FwsApproved 

layer properties, click on the Definition Query tab, and use 

the Query Builder to create the following expression: “RSL_

TYPE” = ‘NWR’ (fig. 11). 

The FwsApproved layer contains four large and inclusive 

refuges (Dakota Grassland, Driftless Area, Northern Tallgrass 

Prairie, and Silvio O. Conte). These refuges span multiple 

States and overlap with other refuge boundaries (for example, 

Agassiz, Big Stone, and Rydell Refuges are 

included within the Northern Tallgrass Prairie 

NWR boundary). This overlap would result in 

double counting streams and impaired waters 

that are within both boundaries (for example, 

stream length would be summarized once for 

Agassiz NWR and once for Northern Tallgrass 

Prairie NWR, which would account for the 

stream length inside Agassiz twice when summarized for the region and Nation). To address 

this issue, the approved boundaries for Dakota 

Grassland, Driftless Area, Northern Tallgrass 

Prairie, and Silvio O. Conte need to be replaced 

with boundaries from the FwsInterest dataset 

so that they would not be included in the data 

analysis. This process is accomplished by 

Figure 10. Screen capture of adding the FwsApproved and FwsInterest data layers to ArcMap.

creating an Analysis Area data layer as documented in the following paragraphs.

To prepare an Analysis Areas data layer, click Selection, click Select By Attributes, and ensure that the FwsApproved layer is selected in the Layer dropdown menu (fig. 12). 

Select all NWR’s EXCEPT Dakota Grassland, Driftless Area, 

Northern Tallgrass Prairie, and Silvio O. Conte using the 

following expression: “ORGNAME” NOT IN (‘DAKOTA 

GRASSLAND CONSERVATION AREA’, ‘DRIFTLESS 

Figure 11. Screen capture of the Query 

Builder expression used to display only 

National Wildlife Refuges.
Spatial Overlay 11

Figure 12. Screen capture of the Select by Attributes tool used 

to select the approved boundaries for all Refuges EXCEPT the four 

large Refuges in the FwsApproved data layer.

AREA NATIONAL WILDLIFE REFUGE’, ‘NORTHERN 

TALLGRASS PRAIRIE NATIONAL WILDLIFE REFUGE’, 

‘SILVIO O. CONTE NATIONAL FISH AND WILDLIFE 

REFUGE’) (fig. 12). Tip: copy and paste the expression into 

the expression box.

Next click Selection, click Select By Attributes, and ensure 

that the FwsInterest layer is selected in the Layer dropdown 

menu. Select the four NWR’s named above using the following expression: “ORGNAME” IN (‘DAKOTA GRASSLAND 

CONSERVATION AREA’, ‘DRIFTLESS AREA NATIONAL 

WILDLIFE REFUGE’, ‘NORTHERN TALLGRASS PRAIRIE NATIONAL WILDLIFE REFUGE’, ‘SILVIO O. CONTE 

NATIONAL FISH AND WILDLIFE REFUGE’) (fig. 13). 

Use the Merge tool (in ArcToolbox, Data Management 

Tools, General) to combine the selected areas from both 

the FwsApproved and FwsInterest data layers, producing 

the Analysis Areas data layer. Select the FwsApproved and 

FwsInterest data layers as the Input Datasets, and define the 

Output Dataset as Analysis Areas in the newly created WaterQuality geodatabase (fig. 14). The “Analysis Areas” name is 

not required; it is simply a means of keeping track of datasets 

created during the spatial overlay analysis process. Examine 

the new boundary layer to ensure the results are as expected. 

The geospatial boundaries of the FWS Cadastral data 

may change with time, making it necessary to reevaluate 

the refuges included during this step of the spatial overlay 

analysis. The above procedure can be modified at any time to 

include or exclude certain properties or types of properties to 

suit the needs of the users. 

Prepare NHDPlus Flowlines Dataset

To maintain manageable datasets, ArcGIS will be used to 

clip the NHD flowlines for each region to the extent of areas 

within the Analysis Areas data layer (from the Prepare the 

Analysis Areas File section) before assembling the NHD flowlines from each NHDPlus region into one national dataset. The 

clipped NHD flowlines will then be merged into one dataset 

representing only NHD flowlines within the Analysis Areas 

defined for this project. 

Add the NHDflowline dataset for each of the National 

Hydrography Dataset region (1–18 and 20) files to the ArcMap 

document. The NHDflowline datasets can be found in the 

Hydrography folder (fig. 15) once the zip files have been 

extracted. 

Figure 13. Screen capture of the Select by Attributes tool used 

to select the boundaries of the four Refuges in the FwsInterest 

data layer.
12 User’s Manual to Update the National Wildlife Refuge System Water Quality Information System (WQIS)

Figure 14. Screen capture of the Merge tool used to combine 

boundaries from both the FwsApproved and FwsInterest data 

layers.

Figure 15. Screen capture of the NDHflowline 

data layer within a NHDPlus geodatabase.
Spatial Overlay 13

Use the Clip tool from the ArcToolbox, Analysis Tools, 

Extract toolset to clip the NHDflowlines from each particular 

NHD region (1–18 and 20) to the extent of the refuge boundaries within the Analysis Areas data layer (fig. 16). The clip 

procedure must be repeated for each of the regions. Clipping 

the NHDflowlines of each NHD region prior to combining the 

flowlines into one large data layer for overlay with the Analysis Areas data layer reduces the processing time by limiting the 

number of unnecessary features in the overlay analysis. Tip: 

ArcGIS ModelBuilder can be used to expedite this repetitive 

task. 

Once the NHDflowlines from each NHD region have 

been clipped to include only flowlines within refuge boundaries, use the Merge tool in the ArcToolbox, Data Management 

Tools, General toolset to combine all the clipped NHD files 

into one NHDflowline dataset (fig. 17). Name this data layer 

NHDflowlines_NWRS and save it into the WaterQuality 

geodatabase. 

A Spatial Join will be utilized to join important attributes 

from the Analysis Areas data layer (for example, refuge name) 

to the NHDflowlines data layer. Right click on the merged 

NHD flowline data layer in the ArcMap table of contents, 

select Joins and Relates, then select Joins. Select “Join data 

from another layer based on spatial location”, choose the 

Analysis Areas as the layer you wish to join, select the “each 

line will be given all the attributes of the polygon that it falls 

completely inside” option (fig. 18). Name the new data layer 

NHDflowline_NWRS_Join and save it to the WaterQuality 

geodatabase. 

Several unnecessary fields are added to the NHDflowline dataset during processing. These extra fields can cause 

confusion and even errors in the final database if they are not 

removed before importing the resultant data into the WQIS 

database. Open the attribute table for the newly created 

NHDflowline_NWRS_Join data layer. Delete the fields named 

LENGTHKM, and SHAPE_LENG by right clicking the field 

column name and selecting Delete Field. Use caution during 

this step as deleting columns cannot be undone. 

All stream-segment records must have a value in the 

GNIS_Name column to be properly parsed by the WQIS 

database (“null” values must be replaced). With the NHDflowline_NWRS_Join attribute table open, select records with 

“null” value in the GNIS_Name column by clicking Select By 

Attributes under the Table Options menu, then enter the following expression: “GNIS_NAME” = ‘’ (fig. 19). 

Figure 16. Screen capture of the Clip tool used to clip the NHDflowlines from each National Hydrography Dataset region to 

refuge boundaries using the Analysis Areas data layer created previously.
14 User’s Manual to Update the National Wildlife Refuge System Water Quality Information System (WQIS)

Figure 17. Screen capture of the Merge tool used to combine the clipped 

NHDflowlines from each National Hydrography Dataset region into one 

seamless national NHDflowlines layer.

Figure 18. Screen capture of the Spatial Join 

function to add refuge attributes to the NHDflowline 

data layer.
Spatial Overlay 15

Figure 19. Screen capture of the Select by Attributes tool used to select stream segments with null values in the GNIS_Name 

column.

Use the Field Calculator to populate these records with 

“Unnamed stream(s)”, by right clicking on the “GNIS_

NAME” field, then clicking on Field Calculator, and entering 

“Unnamed stream(s)” as the expression. 

The NHDflowline datasets contain line segments representing features that are outside the scope of the 

WQIS (artificial path, coastline, and 

pipeline). To eliminate these features 

from the WQIS, open the NHDflowline_NWRS_Join layer properties, 

click on the Definition Query tab, 

and use the Query Builder to create 

the following expression to eliminate the artificial path, coastline, and 

pipeline line segments: “FTYPE” 

NOT IN (‘ArtificialPath’, ‘Coastline’, ‘Pipeline’) (fig. 20). Artificial 

path line-segments represent flow 

through an open waterbody, such 

as a lake, to facilitate hydrologic 

modeling (NHDplus Team, 2010). Coastline is defined as 

a contact line between the open sea and the land. Pipeline 

is defined as a closed conduit for long-distance transport of 

gases, fluids or finely divided solids.

Figure 20. Screen capture of the 

Query Builder expression used to 

eliminate artificial path, coastline, and 

pipeline features from the NHDflowline 

dataset representation in ArcMap.
16 User’s Manual to Update the National Wildlife Refuge System Water Quality Information System (WQIS)

Prepare the Water-Quality Datasets

In the ArcGIS map document, add the impaired waters 

data layer by navigating to the rad_303d geodatabase, then 

add the rad_303d_l feature class. Add the TMDL data layer 

by navigating to the Rad_impwtmdl geodatabase, then adding 

the rad_impwtmdl_l feature class. Use the Clip tool from the 

ArcToolbox, Analysis Tools, Extract toolset to clip the 303(d) 

listed impaired waters and TMDL datasets to the boundaries of the Analysis Areas data layer. The layers can be named 

Impaired_NWRS and TMDL_NWRS respectively and saved 

to the WaterQuality geodatabase. 

Reproject the NHD Flowlines and Water-Quality 

Datasets

The prepared NHD flowlines, 303(d) listed impaired 

waters, and TMDL datasets need to be converted to a projected coordinate system to calculate stream-segment length 

in meters. Use the Project or Batch Project tool from the Data 

Management Tools, Projections and Transformations toolbox (fig. 21) to convert the prepared datasets to a projected 

coordinate system. Select the North America Equidistant 

Conic projection file in the Projected Coordinate Systems, 

Continental, North America folder. Name the layers NHDflowline_NWRS_Join_Project, Impaired_NWRS_Project, and 

TMDL_NWRS_Project, respectively, and save to the WaterQuality geodatabase. 

Export Tables

The attribute table for each prepared data layer will need 

to be saved to a format that can be read by Microsoft Access. 

Open the attribute table for the prepared NHD flowlines 

(NHDflowlines_NWRS_Join_Project), 303(d) listed impaired 

waters (Impaired_NWRS_Project), and TMDL (TMDL_

NWRS_Project) datasets and choose Export under the Table 

Options tab (fig. 22). When saving the tables, be sure to select 

dBASE table as the file type. Save each table as a .dbf file 

using the following table names; NHD.dbf, Impaired.dbf, and 

TMDL.dbf (fig. 23). This naming convention must be followed for the WQIS database to function properly. 

Prepare the Parameter Attribute Tables

Parameter data related to 303(d) impaired waters and 

TMDL datasets are maintained in separate tables developed 

and maintained by EPA. These tables also will need to be 

Figure 21. Screen capture of the Project tool used to convert the prepared datasets to a projected 

coordinate system.
Spatial Overlay 17

Figure 22. Screen capture of Exporting the attribute table for the prepared files; NHDflowlines, Clean Water Act Section 303(d) 

listed impaired waters, and total maximum daily load data layer.

Figure 23. Screen capture of saving the data 

table exported from ArcGIS as a .dbf file.
18 User’s Manual to Update the National Wildlife Refuge System Water Quality Information System (WQIS)

prepared for import into the WQIS database. In ArcGIS, add 

the impaired waters parameter attribute table by navigating 

to the rad_303d geodatabase, then add the rad_303d_prgattr 

table (fig. 24). Next add the TMDL parameter attribute table 

by navigating to rad_impwtmdls geodatabase, then add the 

rad_impwtmdls_prgattr table. 

Save these two tables as .dbf files by choosing Export 

under the Table Options tab. Name the tables impatt.dbf and 

tmdlatt.dbf, respectively. This naming convention must be 

followed for the WQIS database to function properly. 

Refreshing the WQIS Database

Create a backup copy of the WQIS database before making any changes. This step is critical especially if any problems are encountered refreshing the WQIS database. Open the 

WQIS database in Microsoft Access and open the All Access 

Objects table of contents. Import each of the five newly 

created tables (Impaired.dbf, impatt.dbf, NHD.dbf, TMDL.

dbf, and tmdlatt.dbf) by clicking on the External Data Tab, 

click More, then click dBASE File, then selecting the table 

to import. A message box should be displayed stating that 

“all new objects were imported successfully.” The new table 

will be given the table name, with a 1 added (for example, 

Impaired1). After importing all the new tables, compare both 

the new and old versions of each table (for example, Impaired

and Impaired1) by opening both tables in Design View and 

positioning them side by side (fig. 25). 

Overwrite the old version of the table with the new 

version by renaming the tables. Rename the new version of 

the table and remove the 1 from the name of each of the new 

tables (for example, rename Impaired1 to Impaired, overwriting the old version). A warning message will popup stating, 

“The name you entered already exists for another object of the 

same type in this database. Do you want to replace the existing 

table?” Click yes. Another warning message will popup stating, “You can’t delete the table until its relationships to other 

tables have been deleted. Do you want Microsoft Access to 

delete the relationships now?” Click yes.

The Dates table contains the publication dates of the 

FWS cadastral dataset and the EPA water-quality dataset 

(fig. 26). The dates in this table need to be manually updated 

so that the dates displayed in the reports accessed using the 

WQIS database will be correct. Open the Dates table and input 

the dates previously recorded for each dataset.

Delete the RankImp and RankTMDL tables. The WQIS 

database cannot be properly optimized if these two tables are 

present. These tables will be recreated by the database when 

they are needed. 

Figure 24. Screen capture of the parameter attribute table for Clean Water Act Section 303(d) 

impaired waters within the U.S. Environmental Protection Agency RAD_303(d) geodatabase.
Refreshing the WQIS Database 19

Figure 25. Screen capture showing the side-by-side comparison of fields contained in the old Impaired and new Impaired1 

versions of the table.

Figure 26. Screen capture showing the Dates table within the WQIS database.
20 User’s Manual to Update the National Wildlife Refuge System Water Quality Information System (WQIS)

Optimize the Database 

To optimize the performance of the WQIS database, click 

the Database Tools tab, then Analyze Performance button. 

Click the Queries tab in the Performance Analyzer, then click 

the Select All button, and click OK (fig. 27). 

The Performance Analyzer returns a list of results, click 

select all, and then click Optimize (fig. 28). The database cannot be further optimized if the Optimize button is greyed out, 

click Close instead. The WQIS is now available to query.

Troubleshooting 

The WQIS database was developed using a 32-bit 

Windows 7 operating system and Microsoft Access 2010. 

The WQIS may run on other Access versions and operating 

systems, but was not designed to do so. Upgrades of Windows 

and Microsoft Access in the future may require additional 

manipulations to ensure database functions properly. If you 

are running Microsoft Access 2010 on Windows 7 operating 

system and experience errors (for example, “An error occurred 

while loading... .”, “Invalid procedure call or argument”, 

or “The database cannot be opened because the VBA project 

contained in it cannot be read... .”), upon opening the WQIS 

database, first ensure that all Windows Updates have been 

installed and the system has been rebooted. 

If all Windows Updates have been installed and the 

system has been rebooted and the database does not open 

properly, adjust the Trust Center settings. Open Microsoft 

Access, not the WQIS database, under the File tab, click 

Options (fig. 29). 

Click on Trust Center in the table of contents in the 

Access Options box. Then click on the Trust Center Settings 

button (fig. 30). 

Click on Macro Settings in the table of contents in the 

Trust Center box, ensure that the Enable all macros is enabled 

(fig. 31). 

Click on DEP Settings in the table of contents in the Trust 

Center box. Uncheck the Enable Data Execution Prevention 

mode option (fig. 32). 

Close Microsoft Access and reopen the WQIS database 

after making these changes. 

Figure 27. Screen capture of the Performance Analyzer tools in Microsoft Access. The Analyze Performance button (top) and 

Queries tab (bottom) are circled in red. 
Troubleshooting 21

Figure 28. Screen capture of the Performance Analyzer results. The Optimize button is circled in red. 

Figure 29. Screen capture of the Access Options to configure Microsoft Access to successfully run the WQIS 

database. The Options button is circled in red. 
22 User’s Manual to Update the National Wildlife Refuge System Water Quality Information System (WQIS)

Figure 30. Screen capture of the Access Options box in Microsoft Access. The Trust Center Settings button is circled in red.

Figure 31. Screen capture of the Macro Settings within the Microsoft Access Trust Center. 
References Cited 23

Figure 32. Screen capture of the Enable Data Execution Prevention setting in the Microsoft Access Trust Center.

References Cited

Code of Federal Regulations, 2012a, Title 50—Wildlife 

and fisheries, PART 16, Injurious wildlife: accessed on 

November 1, 2012, at http://www.gpo.gov/fdsys/browse/

collectionCfr.action?collectionCode=CFR&searchPath=Tit

le+50%2FChapter+I&oldPath=Title+50&isCollapsed=tru

e&selectedYearFrom=2012&ycord=1475.

Code of Federal Regulations, 2012b, Title 40—Protection of 

environment, PART 130, water quality planning and management 130.7, Total maximum daily loads (TMDL) and 

individual water quality–based effluent limitations: accessed 

on September 1, 2012, at http://edocket.access.gpo.gov/

cfr_2005/julqtr/pdf/40cfr130.7.pdf.

Code of Federal Regulations, 2008, Title 40—Protection of 

environment, PART 112, Oil Pollution Prevention; Spill 

Prevention, Control, and Countermeasure Rule; Revisions to the Regulatory Definition of “Navigable Waters”: 

accessed on September 1, 2012, at http://www.epa.gov/EPAWATER/2008/November/Day-26/w28123.htm. 

Hinck, J.E., K. Chojnacki, S. Finger, G. Linder, and K. 

Kilbride, 2011, A geospatial approach to identify water 

quality issues for National Wildlife Refuges in Oregon and 

Washington: Journal of Fish and Wildlife Management, v. 2, 

issue 1, p. 12–21.

Horizon Systems Corporation, 2012, National Hydrography 

Dataset (NHD) Plus: U.S. Environmental Protection Agency 

and U.S. Geological Survey database, accessed on September 1, 2012 at http://www.horizon-systems.com/NHDPlus/.

NHDPlus Team, 2010, NHDPlus Version 1 (NHDPlusV1) 

User Guide: U.S. Environmental Protection Agency and 

U.S. Geological Survey, accessed on September 1, 2012, at 

http://www.horizon-systems.com/NHDPlus/NHDPlusV1_

documentation.php.

U.S. Environmental Protection Agency, 2003, Guidance for 

2004 assessment, listing, and reporting requirements pursuant to Sections 303(d) and 305(b) of the Clean Water Act: 

accessed on September 1, 2012, at http://www.epa.gov/

owow/tmdl/tmdl0103/2004rpt_guidance.pdf.
24 User’s Manual to Update the National Wildlife Refuge System Water Quality Information System (WQIS)

U.S. Environmental Protection Agency, 2012, Reach Address 

Database (RAD): U.S. Environmental Protection Agency 

database, accessed on September 1, 2012, at http://

epamap32.epa.gov/radims/.

U.S. Fish and Wildlife Service, 2011, Conserving the Future, 

Wildlife Refuges and the Next Generation: accessed on 

September 1, 2012, at http://www.fws.gov/refuges/index.

html.

U.S. Fish and Wildlife Service, 2012a, Service Manual Chapters: U.S. Fish and Wildlife Service, accessed on November 

1, 2012, at http://www.fws.gov/policy/manuals/.

U.S. Fish and Wildlife Service, 2012b, U.S. Fish and Wildlife 

Service National Cadastral Geodatabase: U.S. Fish and 

Wildlife Service database, accessed on September 1, 2012, 

at http://www.fws.gov/GIS/data/CadastralDB/index.htm.

Publishing support provided by: 

Rolla Publishing Service Center 

For more information concerning this publication, contact:

Director, USGS Columbia Environmental Research Center

4200 New Haven Road

Columbia, MO 65201

(573) 875–5399

Or visit the Columbia Environmental Research Center Web site at:

http://www.cerc.usgs.gov/

Chojnacki and others—User’s Manual to Update the National Wildlife Refuge System Water Quality Information System (WQIS)—Techniques and Methods 11–C8