i

United States Environmental Protection Agency 

Office of Water 

Office of Wastewater Management 

EPA 832-R-06-003 

Final Guidance on Awards of Grants 

to Indian Tribes under Section 106 of 

the Clean Water Act 

For Fiscal Years 2007 and Beyond 
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Table of Contents

Abbreviations and Acronyms .............................................................................................................................. vii

Executive Summary .......................................................................................................................................... ES-1

Chapter 1: Introduction ...................................................................................................................................... 1-1

Purpose of this Guidance ........................................................................................................................................................... 1-1

Section 106 Tribal Program Background .................................................................................................................................... 1-2

Need for this Guidance .............................................................................................................................................................. 1-2

GPRA, PART, and Environmental Results .................................................................................................................................. 1-4

EPA’s Strategic Plan ................................................................................................................................................................... 1-4

Tribal Program Options and Structure of the Guidance ............................................................................................................. 1-5

Structure of the Guidance’s Chapters ........................................................................................................................................ 1-6

Other EPAActivities Related to Tribes ...................................................................................................................................... 1-6

Chapter 2: Three Approaches to Implementing Tribal Water Quality Programs ..................................... 2-1

Nonregulatory Approach ........................................................................................................................................................... 2-2

Tribal Law Water Quality Protection Approach ......................................................................................................................... 2-2

EPA-Approved Water Quality Protection Approach ................................................................................................................. 2-3

Chapter 3: Program Initiation, Planning, and Administration Activities .................................................... 3-1

Introduction ............................................................................................................................................................................... 3-1

I. Fundamental Program Activities ............................................................................................................................................. 3-3

1. Applying for TAS Eligibility for the Section 106 Program ............................................................................................... 3-3

2. Implementing Financial Management Systems ............................................................................................................... 3-4

3. Applying for Section 106 Grants ..................................................................................................................................... 3-5

4. Identifying Basic Tribal Water Resources ....................................................................................................................... 3-9

5. Identifying Tribal Needs ............................................................................................................................................... 3-11

6. Identifying Program Objectives and Goals .................................................................................................................... 3-12

7. Hiring Staff .................................................................................................................................................................... 3-13

8. Training Staff ................................................................................................................................................................ 3-13

9. Using Contractors as Appropriate to Your Needs ......................................................................................................... 3-14

10. Developing Program Milestones ................................................................................................................................. 3-14

11. Submitting Work Plans to EPA .................................................................................................................................... 3-14

12. Conducting Community Education on Basic Program Establishment and Direction ................................................... 3-14

13. Financial and Performance Reporting .......................................................................................................................... 3-16

14. Conducting Program Evaluations ................................................................................................................................ 3-16

15. Developing a Multi-year Plan ...................................................................................................................................... 3-17

II. Intermediate Program Activities ........................................................................................................................................... 3-17

1. Seeking Other EPA Funding Opportunities ................................................................................................................... 3-17

2. Providing Enhanced Training to Staff ........................................................................................................................... 3-18

3. Using Contractors as Appropriate to Your Needs ......................................................................................................... 3-19

4. Reassessing Program Objectives and Goals ................................................................................................................. 3-19

5. Enhancing and Focusing Tribal Community Education ................................................................................................ 3-19

6. Conducting Program Evaluations ................................................................................................................................. 3-20

III. Mature Program Activities .................................................................................................................................................. 3-20

1. Seeking Additional Federal Funding Opportunities ...................................................................................................... 3-20

2. Using Contractors as Appropriate to Your Needs ......................................................................................................... 3-21

3. Conducting Comprehensive Community Outreach and Public Awareness Programs ................................................... 3-21

4. Conducting Program Evaluations ................................................................................................................................. 3-21

5. Mentoring Other Tribes and Local Governments ......................................................................................................... 3-21

6. Partnering with Other Organizations ............................................................................................................................. 3-21

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Chapter 4: Monitoring, Data Management, and Data Assessment and Analysis ..................................... 4-1

Introduction ............................................................................................................................................................................... 4-1

I. Fundamental Program Activities ............................................................................................................................................. 4-5

1. Monitoring ...................................................................................................................................................................... 4-5

2. Data Management ......................................................................................................................................................... 4-17

3. Data Assessment and Analysis .................................................................................................................................... 4-20

4. Initiating Mitigation Measures for Known Water Quality Problems ............................................................................. 4-25

II. Intermediate Program Activities ........................................................................................................................................... 4-26

1. Monitoring .................................................................................................................................................................... 4-26

2. Data Management ......................................................................................................................................................... 4-27

3. Data Assessment and Analysis .................................................................................................................................... 4-29

III. Mature Program Activities .................................................................................................................................................. 4-29

1. Understanding and Using EPA’s “Elements” Guidance ................................................................................................ 4-29

Chapter 5: Nonregulatory Approach ................................................................................................................ 5-1

Introduction ............................................................................................................................................................................... 5-1

I. Fundamental Program Activities ............................................................................................................................................. 5-2

1. Understanding Watershed-based Planning .................................................................................................................... 5-2

2. Understanding NPS Pollution ......................................................................................................................................... 5-5

3. Understanding Decentralized Wastewater Treatment Facilities ...................................................................................... 5-6

4. Understanding Source Water Protection ........................................................................................................................ 5-7

5. Choosing and Setting Water Quality Goals .................................................................................................................... 5-7

6. Determining Areas with Water Quality Problems ............................................................................................................ 5-8

7. Choosing and Setting Watershed-based Goals .............................................................................................................. 5-9

8. Developing Projects to Meet Water Quality Goals ......................................................................................................... 5-9

9. Conducting Public Outreach and Encouraging Public Involvement ............................................................................. 5-10

II. Intermediate Program Activities ........................................................................................................................................... 5-13

1. Understanding Section 319 Grants ................................................................................................................................ 5-13

2. Section 319 Eligibility .................................................................................................................................................... 5-13

3. Developing a Watershed-based Plan ............................................................................................................................ 5-15

4. Conducting a Source Water Assessment ...................................................................................................................... 5-17

5. Implementing Water Quality Protection and Restoration Activities.............................................................................. 5-18

6. Implementing Section 106 Grant Activities Related to Decentralized Systems .............................................................. 5-18

7. Analyzing Water Quality Data and Defining Performance Measures ........................................................................... 5-19

III. Mature Program Activities .................................................................................................................................................. 5-20

1. Evaluating Restoration Activities ................................................................................................................................. 5-20

2. Providing Updated Information to Your Partners and Community ................................................................................ 5-20

3. Refining Your Assessment Report, Management Program, Source Water Assessment, and Watershed-based Plan ... 5-21

4. Coordinating and Cooperating with Other Programs .................................................................................................... 5-21

5. Working in Partnership with Other Tribes and States ................................................................................................... 5-21

6. Other Voluntary Programs ............................................................................................................................................. 5-22

Chapter 6: Tribal Law Water Quality Protection Approach .......................................................................... 6-1

Introduction ............................................................................................................................................................................... 6-1

I. Fundamental Program Activities ............................................................................................................................................. 6-2

1. Understanding Water Quality Standards ........................................................................................................................ 6-2

2. Understanding What Tribal Standards Can Do .............................................................................................................. 6-2

3. Identifying Goals of Tribal Standards ............................................................................................................................. 6-2

4. Working in Partnership with EPA, Tribes, and States ..................................................................................................... 6-2

II. Intermediate Program Activities ............................................................................................................................................. 6-3

1. Developing Draft Standards ............................................................................................................................................ 6-3

2. Sharing Draft Standards with EPA, Tribes, and States for Review, as Appropriate ........................................................ 6-3

3. Conducting Public Outreach ........................................................................................................................................... 6-3

4. Drafting Tribal Code Based on Standards ....................................................................................................................... 6-3

5. Formally Adopting Standards through Tribal Council .................................................................................................... 6-3

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III. Mature Program Activities .................................................................................................................................................... 6-4

1. Implementing Standards .................................................................................................................................................. 6-4

2. Reviewing Standards ...................................................................................................................................................... 6-4

3. Developing MOAs with EPA for Permitting Purposes .................................................................................................... 6-4

Chapter 7: EPA-Approved Water Quality Protection Approach .................................................................. 7-1

Introduction ............................................................................................................................................................................... 7-1

I. Fundamental Program Activities ............................................................................................................................................. 7-4

1. Understanding Water Quality Standards ........................................................................................................................ 7-4

2. Understanding Section 401 Certification ......................................................................................................................... 7-5

3. Understanding Section 404 Permitting ............................................................................................................................ 7-5

4. Using EPA WQS Trainings and Educational Materials ................................................................................................... 7-5

5. Reviewing Existing Tribal and State Water Quality Standards ........................................................................................ 7-6

6. Identifying Goals of Tribal Regulatory Program .............................................................................................................. 7-6

7. Working in Partnership with EPA, Tribes, and States ..................................................................................................... 7-6

II. Intermediate Program Activities ............................................................................................................................................. 7-7

1. Applying for TAS Eligibility for a WQS Program and a Section 401 Certification Program ............................................. 7-7

2. EPA Review of Tribal Application for TAS Eligibility for WQS Program and Section 401 Certification Program ............ 7-8

3. Developing Standards ..................................................................................................................................................... 7-8

4. Submitting Draft WQS for Formal Public Hearing and Comment .................................................................................. 7-14

5. Formally Adopting WQS through Tribal Council ......................................................................................................... 7-15

6. Submitting Adopted WQS for EPAApproval ............................................................................................................... 7-15

7. Understanding EPA’s WQS Review Process ................................................................................................................ 7-16

8. Understanding EPA’s Dispute Resolution Mechanism ................................................................................................. 7-16

III. Mature Program Activities .................................................................................................................................................. 7-17

1. Implementing WQS ....................................................................................................................................................... 7-17

2. Conducting Triennial Reviews ...................................................................................................................................... 7-17

3. Implementing Section 401 Certifications ....................................................................................................................... 7-18

4. NPDES Program Overview ............................................................................................................................................ 7-19

5. Sources Regulated under the NPDES Program ............................................................................................................. 7-19

6. Understanding NPDES Permits ..................................................................................................................................... 7-20

7. Reviewing Permits ......................................................................................................................................................... 7-20

8. Considering NPDES Program Authorization ................................................................................................................. 7-21

9. Developing Capabilities for Permitting, Compliance, and Enforcement ........................................................................ 7-22

10. Preparing for NPDES Program Authorization .............................................................................................................. 7-22

11. Obtaining NPDES Program Authorization ................................................................................................................... 7-23

12. Assuming the Section 404 Program ............................................................................................................................. 7-24

13. Working with EPA to Transition from Federal to Tribal Implementation ..................................................................... 7-24

14. Conducting Public Outreach ....................................................................................................................................... 7-24

Chapter 8: Reporting .......................................................................................................................................... 8-1

Introduction ............................................................................................................................................................................... 8-1

Reporting Requirements ............................................................................................................................................................ 8-3

Fundamental Reporting Parameters .................................................................................................................................... 8-4

Intermediate Reporting Parameters ..................................................................................................................................... 8-4

Mature Reporting Parameters ............................................................................................................................................. 8-5

Data Formatting and STORET ................................................................................................................................................... 8-6

v 
Appendix A: Assessment Reports................................................................................................................... A-1

I. Monitoring Strategies ............................................................................................................................................................ A-1

1. Monitoring Strategies for Fundamental-Level Tribal Programs ..................................................................................... A-2

2. Monitoring Strategies for Intermediate-Level Programs ................................................................................................ A-3

3. Monitoring Strategies for Mature-Level Programs ........................................................................................................ A-4

II. Water Quality Assessment Report ........................................................................................................................................ A-4

1. Fundamental Water Quality Program ............................................................................................................................. A-4

2. Intermediate and Mature Water Quality Program ........................................................................................................... A-5

III. Monitoring Data, Submitted Electronically, for Each Assessed Water Body ...................................................................... A-7

Appendix B: Requirements for Authorization of Tribal Administration of the WQS Program .............. B-1

Appendix C: Letter to Tribal Leaders on Information Access ................................................................... C-1

Appendix D: Bibliography ................................................................................................................................. D-1

vi 
Abbreviations and Acronyms

AIEO: American Indian Environmental Office 

ANA: Administration for Native Americans 

ARARs: Applicable or Relevant and Appropriate 

Requirements 

BIA: Bureau of Indian Affairs 

BOR: Bureau of Reclamation 

CALM: Consolidated Assessment Listing Methodology 

CFR: Code of Federal Regulations 

CSO: Combined Sewer Overflow 

CWA: Clean Water Act 

CWA Section 106: Grants for Pollution Control 

Programs 

CWA Section 303: Water Quality Standards and 

Implementation Plan 

CWA Section 305: Water Quality Inventory 

CWA Section 319: Nonpoint Source Management 

Programs 

CWA Section 401: Certifications 

CWA Section 404: Permits for Dredged or Fill Material 

CWA Section 504: Emergency Powers 

CWA Section 518: Indian Tribes 

DO: Dissolved Oxygen 

DOC: Dissolved Organic Carbon 

DOI: United States Department of the Interior 

DQO: Data Quality Objective 

EDAS: Ecological Data Application System 

EPA: United States Environmental Protection Agency 

FERC: Federal Energy Regulatory Commuission 

FOIA: Freedom of Information Act 

FY: Fiscal Year 

GAP: General Assistance Program 

GASB: Governmental Accounting Standards Board 

GIS: Geographic Information System 

GPRA: Government Performance and Results Act 

IT: Information Technology 

ITEP: Institute for Tribal Environmental Professionals 

MOA: Memorandum of Agreement 

MOU: Memorandum of Understanding 

MS4: Municipal Separate Storm Sewer System 

MTBE: Methyl Tertiary Butyl Ether 

NEIEN: National Environmental Information Exchange 

Network 

NHD: National Hydrography Dataset 

NPS: Nonpoint Source 

NPDES: National Pollutant Discharge Elimination 

System 

NRCS: Natural Resources Conservation Service 

OEP: Office of Environmental Protection 

OMB: Office of Management and Budget 

ONRW: Outstanding National Resource Waters 

OST: Office of Science and Technology 

OWM: Office of Wastewater Management 

OWOW: Office of Wetlands, Oceans, and Watersheds 

PART: Program Assessment Rating Tool 

POTW: Publicly Owned Treatment Works 

PPG: Performance Partnership Grant 

QA: Quality Assurance 

QAPP: Quality Assurance Project Plan 

QC: Quality Control 

RA: Regional Administrator 

SOP: Standard Operating Procedure 

SS: Suspended Solids 

STORET: Storage and Retrieval 

TAS: Treatment in a Manner Similar to a State 

TEAs: Tribal Environmental Agreements 

TMDL: Total Maximum Daily Load 

TDS: Total Dissolved Solids 

TKN: Total Kjeldahl Nitrogen 

TSS: Total Suspended Solids 

USDA: United States Department of Agriculture 

USGS: United States Geological Survey 

WAM: Watershed Analysis and Management 

WATERS: Watershed Assessment, Tracking, and 

Environmental Results 

WPDGs: Wetland Program Development Grants 

WQI: Water Quality Indicators 

WQS: Water Quality Standards 

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Notice 

This document discusses requirements contained in the Clean Water Act and its implementing regulations. 

The reader is directed to the statute and the regulations for a full and complete statement of those 

requirements. Tribes are encouraged to consult with their tribal attorney general or equivalent regarding the 

application of these requirements to tribal activities. 

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Executive Summary

The Guidance on Awards of Grants to Indian Tribes under Section 106 of the Clean Water Act is intended 

to help tribal water quality program managers, staff, and other tribal environmental decision makers design and 

implement effective and successful water quality programs. The guidance also provides United States 

Environmental Protection Agency (EPA) regions with a framework of procedures and guidelines for awarding 

and administering grants to federally recognized tribes under the authority of Section 106 of the Clean Water Act 

(CWA) for fiscal year (FY) 2007 and subsequent years. The guidance is effective for grants issued in FY 2007 

and beyond. 

The guidance seeks to help tribal water quality programs at various levels of sophistication and development. For 

new programs, it provides models for successfully initiating and developing a water quality program. For tribes 

with well-established programs, it contains additional water quality protection activities to consider. To meet the 

needs of tribes at all levels of development, the guidance presents basic steps a tribe can take to collect the 

information it will need to make effective decisions about its water quality program. 

In addition, the guidance outlines new reporting requirements and data expectations for all tribal programs 

receiving Section 106 funds. The new reporting requirements will help tribes to collect critical data and 

information for effective management of their water quality programs. The requirements will also help EPA 

measure environmental results of the Section 106 Tribal Program and comply with the Government Performance 

and Results Act (GPRA) and other federal requirements. In the reports that tribes are required to submit as set 

forth in their CWA Section 106 work plan, tribes will be required to include: a description of identified needs, goals, 

and objectives of their monitoring programs; a description of sampling methodology and parameters sampled; and 

a narrative account detailing the types of water sampled, sampling procedures, data summaries, and the tribe’s 

interpretation of both the data and the assessment methodology used. Based on their capabilities, tribes are also 

required to include water quality data for up to nine parameters: dissolved oxygen, pH, water temperature, total 

phosphorus, total nitrogen, turbidity, E. coli or enterococci, macroinvertebrates, and basic habitat information. 

The guidance presents three approaches to implementing tribal water quality programs. Recognizing that tribal 

water quality programs have different program goals, EPA has designed flexible approaches that can 

accommodate these differences. A tribe may adopt any of these approaches or a combination of them. The three 

approaches are: 

Nonregulatory Approach. This approach is appropriate for tribes that can most successfully achieve their 

environmental goals through nonregulatory approaches for controlling, preventing, and eliminating water pollution, 

and does not require the development of enforceable standards. It provides a framework for achieving results 

through voluntary and collaborative activities, with an emphasis on nonpoint source (NPS) control, non-structural 

management measures, and source water protection. The approach focuses on nonregulatory aspects and does 

not address other enforceable components that may also be part of implementing a voluntary or collaborative 

program. The programs supported under this approach will provide the data, tools, and management infrastructure 

necessary to make informed decisions about the best ways of improving tribal water quality (see chapter 5). 

Tribal Law Water Quality Protection Approach. This approach for environmental decision making is based on 

a tribally defined environmental regulatory program. It is intended for tribes that are not interested in pursuing 

federally approved water quality standards (WQS) authority, but that would nonetheless like to develop 

mechanisms under tribal law to protect water quality. This approach gives tribes the option of pursuing standards 

and goals that can be adopted under tribal law; these standards may differ from the standards adopted by a 

surrounding state. The standards may also help tribes identify impaired water bodies, propose solutions, and 

develop water quality reports that meet EPA’s reporting requirements. Under this option, tribes will use tribal law 

to protect water quality. Because the approach relies on tribal law, the guidance does not address it in detail (see 

chapter 6). ES-1 
EPA-Approved Water Quality Protection Approach. This approach is designed for tribes that want to pursue 

eligibility for establishing EPA-approved WQS, which will serve as the regulatory basis for water quality pollution 

controls, including CWA Section 401 certifications and National Pollutant Discharge Elimination System (NPDES) 

permits. It requires tribes to apply to EPA for program authorization for WQS. This approach will lead to the 

development of tribal WQS programs with authority and functions similar to state programs. EPA will continue to 

have responsibility for administering and enforcing other provisions of the CWA. If a tribe elects not to pursue 

authorization for the NPDES program, EPA will continue to administer and enforce it (see chapter 7). 

ES-2
Chapter 1: Introduction

Purpose of this Guidance 

The Clean Water Act (CWA) of 1972 was developed to address growing environmental and public health 

concerns related to water pollution. The Act created mechanisms to regulate the discharge of pollutants and to 

ensure continuing water quality. The United States Environmental Protection Agency (EPA) is the primary federal 

agency responsible for administering the CWA. States also may apply to EPA to administer some of the activities 

of the CWA. Section 518(e) of the CWA authorizes EPA to treat federally recognized tribes in the same manner 

as states (TAS). This allows eligible federally recognized tribes to address water quality issues, including the 

development of their own water quality programs and standards. Funding for these activities is available through 

grants authorized by Section 106 of the CWA. 

The Guidance on Awards of Grants to Indian Tribes under Section 106 of the Clean Water Act is intended to 

help tribal water quality program managers, staff, and other tribal environmental decision makers design and 

implement effective and successful water quality programs. The guidance also provides EPA regional offices with 

guidelines for awarding and administering grants to federally recognized tribes under the authority of Section 106 

of the CWA for fiscal year (FY) 2007 and subsequent years. In FY 2007 and beyond, EPA regional offices will 

use this guidance in the award and administration of tribal 106 grants. Annual regional CWA Section 106 funding 

opportunity announcements will contain specific information on how each regional office will use the guidance to 

make grant determinations. 

The guidance seeks to help tribal water quality programs at various levels of sophistication and development. For 

new programs, it provides models for successfully initiating and developing a water quality program. For tribes 

with well-established programs, it contains additional water quality protection activities to consider. To meet the 

needs of tribes at all levels of development, the guidance presents basic steps a tribe can take to collect the 

information it will need to make effective decisions about its water quality program. 

In addition, the guidance outlines new reporting requirements and data expectations for all tribal programs 

receiving Section 106 funds. The new reporting requirements will help tribes collect critical data and information 

for effective management of their water quality programs. They also will help EPA measure environmental results 

of the Section 106 Tribal Program and comply with the Government Performance and Results Act (GPRA) and 

other federal requirements. 

This document discusses the process of developing a water quality program. You should refer to this document as 

you develop or refine your water quality program and as you revise or incorporate new types of projects into your 

program. As your program develops, you can also use the guidance to help make sure that your program continues 

to meet applicable requirements. 

1-1 
Section 106 Tribal Program Background 

Many tribal environmental programs receive some or all of their funding to implement and maintain water quality 

protection activities through Section 106 grants. Section 106 authorizes EPA to award federal grants to assist 

tribes, states, and interstate agencies in administering programs for the prevention, reduction, and elimination of 

water pollution, “water quality programs.” EPA sets aside a portion of the total Section 106 funds appropriated by 

Congress to fund tribal water quality programs. 

The Section 106 set-aside funds for tribes are allocated to the EPA regions based on the Section 106 tribal 

allotment formula adopted by EPA for FY 1998 and beyond. Each region then makes Section 106 grant awards to 

eligible tribes consistent with statutory limitations, EPA regulations, and EPA guidance. Since 1995, Section 106 

funding for tribes has increased from $3 million to $25 million a year. 

Section 106 tribal grants are used to fund a wide range of water pollution control activities, including: 

z Water quality planning, assessments, and studies 

z Ambient monitoring 

z Community outreach and education activities 

z Source water, surface water, ground water, and wetland protection 

z Nonpoint source (NPS) control activities (including NPS assessment and management programs) 

z Development of water quality standards (WQS) 

z Development of watershed-based plans 

z Development of total maximum daily loads (TMDLs) 

z Data management and reporting 

Need for this Guidance 

This guidance has been developed in response to the need for a unified guidance that helps tribes develop and 

implement water quality programs and defines what EPA expects from tribal water quality protection programs. 

EPA recognizes the importance of strong tribal water quality protection programs and the EPA-tribal government 

relationship that supports tribes in implementing their water quality protection programs. To help strengthen tribal 

water quality protection programs, this guidance provides an overview of programmatic and technical 

requirements, discusses some common considerations across programs, and provides links to technical resources 

available to develop tribal programs. To help strengthen EPA-tribal government relationships, the guidance defines 

expectations for tribes receiving Section 106 grants and explains how these expectations align with EPA’s national 

goals and objectives. The guidance also provides EPA regional offices with a vehicle to use in evaluating work 

plans and budgets. 

1-2 
Although many tribes are implementing successful water quality programs using Section 106 grants, it has been 

difficult for EPA to report national results for the Section 106 Tribal Program. Because of a lack of national tribal 

guidance on data collection and data reporting, EPA lacks comparable data across tribal programs that can be 

used to show national improvement in water pollution control on Indian reservations. This has become an 

increasingly critical problem as the emphasis on demonstrating results for all governmental agency programs has 

increased. One of the goals of this guidance is to make it possible to aggregate data in a way that allows EPA to 

assess national results associated with the Section 106 Tribal Program. 

The guidance provides a framework for evaluating program results and more clearly defines expectations and 

requirements for tribal Section 106 grant recipients. In addition to information on strategies for collecting and 

managing data, working with your regional EPA office, and specific reporting requirements, this guidance also 

contains numerous links to other resources that may be useful as you establish or develop your program. The 

framework of the guidance is based on three approaches that tribes can use to develop their water quality 

programs and includes programmatic and reporting requirements. (Chapter 2 provides more information on each 

approach to developing a water quality program.) 

EPA recognizes the diversity of tribal water quality programs. By describing three approaches to water quality 

program development in this guidance, EPA has attempted to accommodate this diversity and offer a framework 

that tribes can use to develop and implement a water quality program. The guidance explains how results from 

each type of program will connect to EPA’s strategic plan and will give EPA an overall picture of how the Section 

106 Tribal Program is improving water quality on Indian reservations. 

St. John River Headwaters. Photograph courtesy of Fred Corey, Micmac Tribe. 

1-3 
GPRA, PART, and Environmental Results 

The Government Performance and Results Act (GPRA), Public Law 103-62, requires federal agencies to set 

strategic goals, measure performance, and report on the degree to which they met their goals. GPRA requires 

each federal agency to develop strategic plans to cover a period of at least 5 years and to include the agency’s 

mission statement, the agency’s long-term strategic goals, and information on how the agency intends to achieve 

those goals. Activities conducted by individual programs within agencies must correspond to agency priorities 

described in the strategic plans. Under GPRA, strategic plans are the starting point for agencies to set annual 

goals for programs and to measure their performance in achieving those goals. 

The Office of Management and Budget (OMB) reviews programs within agencies to evaluate performance using 

the Program Assessment Rating Tool (PART). During PART reviews, OMB evaluates the measurement and 

reporting of program results, outcomes, and performance to determine whether a program is achieving its 

strategic and annual goals. EPA relies on program evaluations and analyses, including PART, to inform decisions, 

design effective strategies, and adjust approaches to improve results. EPA senior managers use the results of 

PART during the budget process to identify needs for program improvement, justify resource requests, and guide 

decisions. 

Objectives and Sub-Objectives of EPA’s Goal 2 – 

EPA’s Strategic Plan Clean and Safe Water 

EPA’s 2006-2011 Strategic Plan describes the Objective 2.1: Protect Human Health 

programmatic and quantitative measures for Sub-objective 2.1.1: Water Safe to Drink 

improving water quality nationwide and sets Sub-objective 2.1.2: Fish and Shellfish Safe to Eat 

five long-term goals for the next 5 years. The Sub-objective 2.1.3: Water Safe for Swimming 

focus of the strategic plan is to achieve 

measurable environmental results. The plan Objective 2.2: Protect Water Quality 

includes strategic targets that EPA uses to Sub-objective 2.2.1: Improve Water Quality on a 

track progress quantitatively. The strategic Watershed Basis 

plan is available online at www.epa.gov/ocfo/ Sub-objective 2.2.2: Improve Coastal and Ocean Waters 

plan/plan.htm The objectives and subobjectives associated with Goal 2, Clean and Objective 2.3: Enhance Research to Support Clean 

Safe Water, address issues that apply to state and Safe Water 

and tribal water quality programs. Objective 

4.3, associated with Goal 4, also contains 

elements that apply to water quality 

programs. Means and Strategies for Achieving Goal 4, 

Objective 4.3 – Restore and Protect Critical 

Tribes and intertribal consortia, as recipients Ecosystems 

of EPA grant funds, play an integral part in 

achieving EPA’s objectives and sub- z Increase wetlands 

objectives and in demonstrating z Facilitate the ecosystem-scale restoration of estuaries environmental results. EPA uses the of national significance information that tribes and intertribal z Improve the health of the Great Lakes consortia provide as a basis for linking the z Improve the health of the Chesapeake Bay ecosystem

Agency’s actual expenditures with EPA’s z Improve the health of the Gulf of Mexico ecosystem results-based accomplishments or outcomes. z Restore and protect Long Island Sound 

z Restore and protect the South Florida ecosystem 

z Restore and protect the Puget Sound Basin 

z Restore and protect the Columbia River Basin 

1-4 
Tribal Program Options and Structure of the 

Guidance 

This guidance discusses the development and implementation of successful tribal water quality programs using 

Section 106 funding. An effective tribal water quality program should include common activities in three areas. 

These areas are: 

z Program initiation, planning, and administration 

z Monitoring, data management, and data assessment and analysis 

z Reporting 

Program initiation, planning, and administration are discussed in chapter 3. Chapter 4 addresses monitoring, data 

management, and data analysis and assessment. Chapter 8 lays out reporting and data requirements associated 

with Section 106 tribal grants. The chapter covers basic data requirements for water quality reporting and 

expectations and options for developing and submitting reports. 

EPA recognizes that tribal programs may have different levels of sophistication and different water quality 

protection goals. To address these differences, EPA has suggested three options or approaches to developing 

water quality programs that can accommodate different types of tribal goals: 

1. A nonregulatory approach, which uses voluntary and collaborative activities such as community education 

and outreach to achieve environmental results. This approach can focus on the nonregulatory components 

of NPS control, watershed-based plans, water quality protection, and restoration projects. 

2. An approach that relies on tribal ordinances, codes, water quality standards, or other standards recognized 

by a tribe to protect water quality on Indian reservations. 

3. An EPA-approved water quality protection approach designed for tribes that want to pursue eligibility for 

the purpose of implementing EPA-approved WQS and Section 401 certification. Tribal WQS approved by 

EPA would provide a basis for NPDES permit and enforcement action to protect water quality. Tribes also 

may apply to implement the NPDES permit and enforcement program. 

All three approaches rely on the development of tribal water quality protection goals specific to tribal water 

bodies. 

All three approaches will allow tribes to advance the objectives and sub-objectives of EPA’s strategic plan and 

will lead to improved environmental results; the Agency does not endorse any one approach above the others. The 

approaches are not discrete and may overlap as tribal programs develop. Chapter 2 offers more information on 

each approach. Chapters 5, 6, and 7 discuss each approach in detail. 

1-5 
Structure of the Guidance’s Chapters 

Chapters 3 through 8 are divided into three program activity subsections: 

z Fundamental program activities establish the foundation for a successful program. These program 

activities will help you identify water quality goals and objectives for your program. 

z Intermediate program activities build the tribal water quality program and advance it towards its water 

quality goals and objectives. 

z Mature program activities enable tribes to achieve the goals and objectives of their programs as well as 

develop new water quality goals and objectives. 

Figure 1 shows the structure of the guidance’s chapters. 

EPA anticipates that tribes will move from fundamental to intermediate and mature program activities over 

several years and recognizes that some activities will occur many years in the future. In addition, all activities will 

not progress at the same pace, and a tribe may not implement all activities at once, so different program areas 

may be at various levels of maturity. Because program capabilities, program priorities, and levels of experience 

differ among tribes, EPA does not expect that mature activities will occur at the same rate for all tribes. For 

example, a tribe might have a mature monitoring program while only utilizing fundamental and intermediate 

nonregulatory watershed-based protection activities. EPA does expect that all tribes will develop more 

sophisticated programs over time and will make progress toward mature program activities, but the rate of 

progress may vary from tribe to tribe and will be determined through negotiations between tribes and the 

appropriate EPA regional office on a case-by-case basis. Funding decisions will also be negotiated between tribes 

and the appropriate EPA regional office on a case-by-case basis and may or may not be tied to a program’s rate 

or level of progress. 

Other EPA Activities Related to Tribes 

In addition to the specific tribal program activities listed in this guidance, EPA is implementing other national 

activities related to environmental issues on Indian reservations. The scope of this document, however, is limited 

to issues and activities that are related to Section 106 grants to tribes and the development of tribal water quality 

protection programs, although some other EPA funding programs are discussed generally on pages 3-17 and 3-18. 

Focusing on this particular set of issues and activities avoids duplication with strategies or plans prepared for other 

EPA media programs, or resources and activities administered by the American Indian Environmental Office 

(AIEO). Consequently, discussions of several major EPA-wide tribal activities are omitted. 

A number of these EPA-wide activities provide additional foundation for building a strong water quality program 

and may be appropriate to specific tribal programs. Additional information on these or any other EPA-wide tribal 

programs can be obtained from your EPA regional tribal coordinator. 

1-6 
1-7

Figure 1: EPA Clean Water Act Section 106 Tribal Guidance Summary

Chapter 3: Program

Initiation, Planning,

and Administration

Activities

Chapter 4:

Monitoring, Data

Management, and

Data Assessment

and Analysis

Chapter 5:

Nonregulatory

Approach

Chapter 6: Tribal

Law Water Quality

Protection

Approach

Chapter 7: EPAApproved Water

Quality Protection

Approach

Chapter 8:

Reporting

F

u

n

d

a

m

e

n

t

a

l

Applying for TAS Eligibility for

the Section 106 Program

Monitoring

Data Management

Data Assessment and

Analysis

Initiating Mitigation

Measures for Known Water

Quality Problems

Understanding Watershedbased Planning

Understanding NPS Pollution

Understanding Decentralized

Wastewater Treatment

Facilities

Understanding Source Water

Protection

Choosing and Setting Water

Quality Goals

Determining Areas with Water

Quality Problems

Choosing and Setting

Watershed-based Goals

Developing Projects to Meet

Water Quality Goals

Conducting Public Outreach

and Encouraging Public

Involvement

Understanding Water Quality

Standards

Understanding What Tribal

Standards Can Do

Identifying Goals of Tribal

Standards

Working in Partnership with

EPA, Tribes, and States

Understanding Water Quality

Standards

Understanding Section 401

Certification

Understanding Section 404

Permitting

Using EPA WQS Trainings

and Educational Materials

Reviewing Existing Tribal and

State Water Quality

Standards

Identifying Goals of Tribal

Regulatory Program

Working in Partnership with

EPA, Tribes, and States

Your Assessment Report

must include the following

elements: Implementing Financial

Management Systems

Applying for Section 106

Grants

1.

2.

3.

�

�

�

�

Description of your

monitoring strategy

Water quality assessment

Electronic data on the

following parameters:

Dissolved oxygen

pH

Water temperature

Turbidity

Identifying Basic Tribal Water

Resources

Identifying Tribal Needs

Identifying Program

Objectives and Goals

Hiring Staff

Training Staff

Using Contractors as

Appropriate to Your Needs

Developing Program

Milestones

Submitting Work Plans to

EPA

Conducting Community

Education on Basic Program

Establishment and Direction

Financial and Performance

Reporting

Conducting Program

Evaluations

Developing a Multi-year Plan

I

n

t

e

r

m

e

d

i

a

t

e

Seeking Other EPA Funding

Opportunities

Providing Enhanced Training

to Staff

Using Contractors as

Appropriate to Your Needs

Reassessing Program

Objectives and Goals

Enhancing and Focusing

Tribal Community Education

Conducting Program

Evaluations

Monitoring

Data Management

Data Assessment and

Analysis

Understanding Section 319

Grants

Section 319 Eligibility

Developing a Watershedbased Plan

Conducting a Source Water

Assessment

Implementing Water Quality

Protection and Restoration

Activities

Implementing Section 106

Grant Activities Related to

Decentralized Systems

Analyzing Water Quality Data

and Defining Performance

Measures

Developing Draft Standards

Sharing Draft Standards with

EPA, Tribes, and States for

Review, as Appropriate

Conducting Public Outreach

Drafting Tribal Code Based

on Standards

Formally Adopting Standards

through Tribal Council

Applying for Program

Authorization for

Administering a WQS

Program and a Section 401

Certification Program

Your Assessment Report

must include the following

elements:

EPA Review of Tribal

Application for TAS Eligibility

for WQS Program and

Section 401 Certification

Program

1.

2.

3.

�

�

Description of your

monitoring strategy

Water quality assessment

Electronic data on the

following additional

parameters:

Phosphorus

Total nitrogen

Developing Standards

Submitting Draft WQS for

Formal Public Hearing and

Comment

Formally Adopting WQS

through Tribal Council

Submitting Adopted WQS for

EPA Approval

Understanding EPA's WQS

Review Process

Understanding EPA's

Dispute Resolution

Mechanism

M

a

t

u

r

e

Seeking Additional Federal

Funding Opportunities

Using Contractors as

Appropriate to Your Needs

Conducting Comprehensive

Community Outreach and

Public Awareness Programs

Conducting Program

Evaluations

Mentoring Other Tribes and

Local Governments

Partnering with Other

Organizations

Understanding and Using

EPA's "Elements" Guidance

Evaluating Restoration

Activities

Providing Updated Information

to Your Partners and

Community

Refining Your Assessment

Report, Management

Program, Source Water

Assessment, and Watershedbased Plan

Coordinating and

Cooperating with Other

Programs

Working in Partnership with

Other Tribes and States

Other Voluntary Programs

Implementing Standards

Reviewing Standards

Developing MOAs with EPA

for Permitting Purposes

Implementing WQS Your Assessment Report

must include the following

elements: Conducting Triennial

Reviews

Implementing Section 401

Certifications

1.

2.

3.

�

�

�

Description of your

monitoring strategy

Water quality assessment

Electronic data on the

following additional

parameters:

Macroinvertebrates

E. coli or enterococci

Basic habitat information

NPDES Program Overview

Sources Regulated under the

NPDES Program

Understanding NPDES

Permits

Reviewing Permits

Considering NPDES

Program Authorization

Developing Capabilities for

Permitting, Compliance, and

Enforcement

Preparing for NPDES

Program Authorization

Obtaining NPDES Program

Authorization

Assuming the Section 404

Program

Working with EPA to

Transition from Federal to

Tribal Implementation

Conducting Public Outreach
This page intentionally left blank 

1-8 
Chapter 2: Three Approaches

to Implementing Tribal

Water Quality Programs

This guidance presents three approaches to implementing tribal water quality programs. Recognizing that tribal 

water quality programs have different levels of experience and program goals and face different types of 

jurisdictional issues, EPA has developed three flexible approaches that can accommodate these differences. The 

approaches also enable tribes to collect and provide to EPA water quality data and information that will help EPA 

assess improvement in water quality nationwide. 

As noted in chapter 1, all three approaches can help tribes successfully manage water resources, and no one 

approach is better than the others. A tribe may adopt any of these approaches or a combination of these 

approaches. The approaches are designed as sets of activities based on different options for achieving 

environmental results. The three approaches are: 

z A nonregulatory approach focusing on voluntary programs such as NPS pollution prevention and 

watershed-based approaches to water quality management. This approach identifies nonregulatory means 

for protecting and improving water quality. 

z An approach that uses tribal standards, ordinances, or codes recognized by a tribal government that can be 

tribally enforced to protect water quality on Indian reservations. 

z An approach that follows the Clean Water Act (CWA) approach to protecting water quality. This 

approach includes development of EPA-approved WQS and Section 401 certification authority to protect 

water quality on Indian reservations. Tribal WQS approved by EPA can be used by EPA or tribes with 

authorized NPDES programs to achieve water quality protection through limits on point source 

dischargers. 

Not every approach is appropriate for every tribe. If you are just beginning to implement a water quality program, 

you should review the information provided below to decide which approach best suits your tribe’s needs. If you 

are already implementing a water quality program, you should use the guidance to help you identify activities that 

could enhance it. You also should assess whether you should modify or adapt your approach based on information 

in the guidance. The guidance is meant to help you decide which approach fits best with your tribe’s water quality 

needs. All tribal programs should use the guidance to evaluate program objectives, future program direction, and 

all applicable requirements. 

Program Links 

Review chapters in this guidance that apply to the approach you choose to implement, remembering that the 

most successful programs will incorporate activities across program areas. To help you identify links across 

different program areas, in many sections you will find links directing you to related sections of the 

guidance. Refer to these related sections for information from other program areas that may apply to your 

program. 

2-1 
EPA recognizes that there are overlaps among these approaches. The most successful tribal programs will 

incorporate elements from all approaches to meet their water quality objectives. For example, tribes with 

EPA-approved WQS may also incorporate voluntary approaches into their programs; if appropriate, tribes 

following the nonregulatory approach can provide information about tribal water quality to EPA and/or a 

neighboring state for their use in developing point source limitations. 

Nonregulatory Approach 

This approach is appropriate for tribes that can most successfully achieve their environmental goals through 

nonregulatory activities. This approach does not require the development of WQS. It provides a framework for 

achieving results through voluntary and collaborative activities, with a strong emphasis on NPS control, nonstructural management measures, source water protection, and watershed-based planning. The programs 

supported under this approach will provide the data, tools, and management infrastructure necessary to make 

informed decisions about the best ways of improving tribal water quality. 

If tribes using only this approach identify point source problems, they will not have the regulatory authority in 

place to require an entity to meet an EPA-approved WQS. If enforcement became necessary (e.g., against a 

point source discharger operating without a permit), the tribe would have to rely on enforcement by the federal 

government. For this reason, the approach is most appropriate for tribes that are not interested in directly pursuing 

enforcement activities or do not view enforcement as their best means of controlling water pollution. 

Allowable NPS Control Activities 

NPS management measures requiring construction are implemented under Section 319 of the CWA and are 

thus ineligible for Section 106 funding. Section 106 funding can be used to develop NPS assessment reports 

and management programs, which are required elements when applying for Section 319 program 

authorization. Section 106 grants can also be used to develop watershed-based plans, but cannot be used to 

implement watershed-based plans. See chapter 5 for more information on NPS activities eligible for Section 

106 funding. 

Tribal Law Water Quality Protection Approach 

This approach for environmental decision making is based on a tribally defined environmental regulatory program. 

It is intended for tribes that are not interested in pursuing federally approved WQS authority but that would 

nonetheless like to protect water quality. This approach gives tribes the option of pursuing standards and goals that 

can be adopted under tribal law. The standards could help the tribe identify impaired water bodies, propose 

solutions, and develop water quality reports that meet EPA’s reporting requirements. (More information on 

reporting requirements is included in chapter 8.) 

This approach gives tribes a mechanism for setting standards under tribal law without obtaining EPA approval for 

establishing WQS under the CWA. It allows tribes to define their own regulatory priorities. EPA may look to tribal 

standards for guidance for CWA permitting purposes based on the circumstances. Tribes may also use tribal 

standards as a guideline when reviewing and providing comments to EPA on proposed permits. 

2-2 
EPA will retain the responsibility for issuing federal permits and establishing federally enforceable permit limits. 

This approach is most appropriate for tribes that are not interested in establishing federally approved and 

enforceable WQS as their best means of controlling water pollution. 

EPA-Approved Water Quality Protection Approach 

This approach to water quality management uses a regulatory framework based on the CWA structure to control 

water quality. This is an approach that some tribes have followed already to develop their tribal water quality 

programs. Tribes that use this approach develop and establish EPA-approved WQS, which serve the dual 

purposes of establishing the water quality goals for a specific water body and serving as the basis for 

establishment of water quality-based controls. This path requires tribes to obtain a TAS eligibility determination 

from EPA and to obtain approval from EPA of the water quality standards that have been adopted by the tribe. 

Tribes that want to implement the NPDES program will also need to obtain separate authorization for the NPDES 

program. This approach could lead to the development of tribal WQS programs with authority and functions 

similar to state programs. EPA would continue to have responsibility for administering other provisions of the 

CWA. If a tribe elects not to pursue authorization for the NPDES program, EPA would continue to administer the 

NPDES program on reservation waters. 

This approach is most appropriate for tribes with mature water quality programs. Tribes that pursue this path to its 

completion will be able to have their EPA-approved standards incorporated into enforceable CWA NPDES 

permits to regulate point source dischargers. This will ensure that tribal waters are protected pursuant to the 

tribe’s EPA-approved WQS. Obtaining WQS eligibility is the first step in this approach. A tribe must be 

determined eligible before EPA can approve its water quality standards. The tribe’s EPA-approved standards may 

allow the tribe to more effectively protect cultural or traditional uses of water bodies. 

Other Approaches to Water Quality Protection 

This guidance establishes minimum reporting requirements. EPA regional offices have the flexibility to work 

with tribes to ensure that their water quality programs meet both tribal and EPA needs. Many tribes are 

already implementing well-established water quality programs that are tailored to their individual 

circumstances. EPA recognizes the diversity of tribal water quality programs and has attempted to 

accommodate this diversity in this guidance. 

2-3 
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2-4 
Chapter 3: Program

Initiation, Planning, and

Administration Activities

Introduction 

This chapter discusses the administrative activities associated with implementing a tribal water quality program. 

Regardless of which approach to water quality program development you choose to pursue, your program should 

include these activities. In this chapter, you will find specific regulatory requirements associated with certain 

activities, such as required information that you must include in grant applications. It also discusses general 

concepts to consider for activities that you can implement in a number of ways, such as developing a community 

outreach plan. 

The frequency with which you carry out each activity varies. In some cases (e.g., identifying your tribe’s basic 

water resources), an activity will be conducted only once. In other cases (e.g., conducting a program evaluation), 

an activity will be conducted periodically. 

Tule River. Photo Courtesy of Tule River Indian Tribe. 

3-1 
1

2

3

4

5

6

Activities Included in Chapter 3 

Fundamental Program Activities

1. Applying for TAS Eligibility for the Section 106 Program

2. Implementing Financial Management Systems

3. Applying for Section 106 Grants.......................................... Understanding Grant Application Package Requirements

Understanding 40 CFR Part 35 Work Plan Requirements

Establishing Output- and Outcome-based Activities: Environmental Results

4. Identifying Basic Tribal Water Resources

5. Identifying Tribal Needs......................................................... Identifying Water Quality Needs

Identifying Resource Needs

6. Identifying Program Objectives and Goals

7. Hiring Staff............................................................................... Identifying Skills Needed to Develop a Water Quality Progam

Identifying Available Resources

8. Training Staff

9. Using Contractors as Appropriate to Your Needs

10. Developing Program Milestones

11. Submitting Work Plans to EPA

12. Conducting Community Education on Basic Program Establishment and Direction

13. Financial and Performance Reporting

14. Conducting Program Evaluations...................................... Conducting a Joint Evaluation

Conducting a Self-evaluation

15. Developing a Multi-year Plan

Intermediate Program Activities

Tribes should begin these activities after having completed the relevant fundamental program activities.

1. Seeking Other EPA Funding Opportunities

2. Providing Enhanced Training to Staff

3. Using Contractors as Appropriate to Your Needs

4. Reassessing Program Objectives and Goals

5. Enhancing and Focusing Tribal Community Education

6. Conducting Program Evaluations

Mature Program Activities

Tribes should begin these activities after having completed the relevant fundamental and intermediate program activities.

. Seeking Additional Federal Funding Opportunities

. Using Contractors as Appropriate to Your Needs

. Conducting Comprehensive Community Outreach and Public Awareness Programs

. Conducting Program Evaluations

. Mentoring Other Tribes and Local Governments

. Partnering with Other Organizations

3-2 
I. Fundamental Program Activities 

1. Applying for TAS Eligibility for the Section 106 Program 

The general requirements for TAS are set forth in CWA Section 518 and for the 106 program in particular at 40 

CFR 130.6(d) and 40 CFR 35.583. Some of the CWA Section 518 statutory requirements are summarized below, 

but the tribe should refer to the statute and regulations for a complete statement of the TAS requirements. 

1. The tribe must be recognized by the Secretary of the Interior and exercise governmental authority over a 

federal Indian reservation; 

2. The tribe must have a governing body carrying out substantial governmental duties and powers; 

3. The functions to be exercised by the tribe must pertain to the management and protection of water 

resources that are held by an Indian tribe, held by the United States in trust for Indians, held by a member 

of an Indian tribe if such property interest is subject to a trust restriction on alienation, or otherwise within 

the borders of an Indian reservation; and, 

4. The tribe is reasonably expected to be capable, in EPA’s judgment, of carrying out the functions to be 

exercised in a manner consistent with the terms and purposes of the CWA and all applicable regulations. 

Clean Water Act Citations 

Throughout this guidance, you will see CWA citations. You can view full CWA text online at http:// 

www.epa.gov/region5/water/cwa.htm. 

As authorized under 40 CFR 35.583, intertribal consortia are eligible to receive grants under Section 106 if they 

can show that each of the member tribes authorizing the consortium to act on its behalf is federally recognized 

and has met the requirements for Section 106 TAS eligibility. A consortium must have adequate documentation of 

the existence of the partnership and the authorization to apply for and receive assistance. Tribes may receive 

grants both as a tribe and as a part of an intertribal consortium as long as the grants do not fund the same 

projects. 

You must submit a TAS eligibility application to your EPA region, and the region must approve it in order for your 

tribe to become eligible to receive Section 106 grants. Therefore, you cannot fund your Section 106 TAS eligibility 

application with Section 106 funds. Tribes have used General Assistance Program (GAP) grants to fund their 

application process. See section II.1 of this chapter for more information on GAP grants. Your TAS eligibility 

application can be included with an application for a Section 106 grant. Check your region’s annual Section 106 

funding opportunity announcement for more information on submission of TAS eligibility applications. 

Code of Federal Regulations Citations 

Throughout this guidance, you will see Code of Federal Regulations (CFR) citations. You can view full CFR 

text at the Government Printing Office’s Electronic CFR (eCFR) Web site, http://www.gpoaccess.gov/ecfr/. 

3-3 
The TAS eligibility process ensures that tribes have the legal, technical, and managerial resources to successfully 

use a water quality grant. Contact your EPA regional office to begin the application process. Updated contact 

information is available online at http://www.epa.gov/owm/mab/indian/106coord.htm. 

Over 200 tribes in the country already have received eligibility for Section 106 grants. The experiences of these 

tribes may be valuable to tribes that are considering applying for Section 106 eligibility. Your EPA regional office 

may be able to provide you with contact information for other tribal water quality programs in your region if you 

need it. 

Obtaining Hard Copies of Electronic Resources 

Throughout this guidance you will find links to online technical documents, policies, and other guidances. If you 

wish to obtain a hard copy of any of these documents, you should contact your EPA regional office or the 

EPA Water Resource Center using the contact information provided below: 

United States EPA 

Water Resource Center (PC-4100) Phone: (202) 566-1729 

1200 Pennsylvania Ave., NW Fax: (202) 566-1736 

Washington, D.C. 20460 

2. Implementing Financial Management Systems 

You must be able to adequately track your grant expenditures and establish effective accounting procedures to 

comply with grant requirements. OMB requires that all grantees report their financial status to the agency that 

issued their grant. At all times, you should ensure that you keep adequate books and records, use appropriate 

budgeting, accounting, and financial planning methods, and manage financial resources effectively, in accordance 

with OMB Circular A-87, available online at http://www.whitehouse.gov/omb/circulars/a087/a087-all.html. 

The Governmental Accounting Standards Board (GASB) establishes standards of financial accounting and 

reporting for governmental entities. You may want to review information available on its Web site (http:// 

www.gasb.org/) and use this information to evaluate your financial management systems. 

OMB has issued a number of publications related to financial management systems and requirements for grant 

recipients. Visit http://www.whitehouse.gov/omb/financial/fin_grants_expanded.html#admin for more information 

on financial management systems. 

Office of Grants and Debarment 

EPA’s Office of Grants and Debarment Web site (http://www.epa.gov/ogd/index.htm) contains tutorials, 

forms, policies and regulations, and other resources that may help you navigate the grant application 

process. Visit the Web site for more information. 

3-4 
3. Applying for Section 106 Grants 

a. Understanding Grant Application Package Requirements 

You may submit applications to receive Section 106 grant awards if your tribe has been found eligible for TAS for 

Section 106 grants. You may also submit your TAS eligibility application in conjunction with your application to 

receive a Section 106 grant award or in accordance with your region’s annual tribal Section 106 funding 

opportunity announcement. In accordance with OMB Circular A-87, your grant application must: 

z Include EPA grant application form SF 424, Revision 9, and all required forms and certifications, 

which can be obtained from your EPA regional office or from the following EPA Web site: http:// 

www.epa.gov/ogd/AppKit/index.htm. 

z Include a proposed work plan. More information on developing a work plan is provided in section I.3.b 

of this chapter; you should also refer to your region’s annual tribal Section 106 funding opportunity 

announcement. 

z Specify the amount of funds requested. EPA may provide up to 95 percent of your eligible costs for a 

Section 106 grant award. Your tribe must provide 5 percent of the work plan costs. Work plan costs 

include costs of planning, developing, establishing, improving, or maintaining a water pollution control 

program. The match requirement also may be met by tribal in-kind contributions (e.g., volunteer services, 

property, supplies, equipment). See the Interim Guidance for Cost Sharing/Match Requirement on the 

Award of Grants to Indian Tribes, January 30, 1998 (available online at http://www.epa.gov/owm/rmes/ 

tribalcwas106_app-d.pdf) for more information. Your Regional Administrator (RA) may increase the 

maximum federal share if you can show that fulfilling the match requirement through either matching 

funds or in-kind contributions would impose undue hardship (40 CFR 35.585). Your tribe can also 

contribute more than the 5 percent match if funds are available. A tribe would have to contribute more if 

there were no more federal funds available to carry out the grant. 

z Demonstrate that the tribe meets the requirements of CWA Section 106(e) for water quality 

monitoring and emergency authority. This emergency authority, described in CWA Section 504, is to 

respond to a discharge of pollutants that is presenting an imminent and substantial endangerment to the 

health or livelihood of any person by bringing suit in a court to immediately enjoin the discharge or to “take 

such other action as may be necessary.” 

z Meet the requirements of 40 CFR Part 31, Subpart B. These requirements may include special 

conditions that may apply to specific situations (e.g., grants to “high-risk” grantees). Ask your EPA 

regional office for more information. 

z Meet the requirements of 40 CFR Part 35. These requirements specify what you need to include in 

your work plan and are discussed in section I.3.b of this chapter. 

You must submit a complete application to your EPA regional office in accordance with your EPA region’s annual 

tribal Section 106 funding opportunity announcement. You may negotiate the length of the budget period. If you 

have questions regarding the grant application process, you should consult your regional grant project officer. 

Additionally, consult your EPA regional office on due dates for work plans and proposals, as these dates vary 

from region to region. 

3-5 
b. Understanding 40 CFR Part 35 Work Plan Requirements 

The work plan is the basis for managing, planning, and evaluating performance under the Section 106 grant 

agreement. Work plans are the result of negotiations with your EPA regional office and reflect consideration of 

national, regional, and tribal environmental and programmatic needs and priorities. You should make sure that your 

work plan is consistent with the goals and objectives, priorities, and performance measures in EPA’s strategic plan 

(see chapter 1 for more information on EPA’s strategic plan) and the activities included are eligible under Section 

106 (see figure 2 for more information on eligible activities). Close interaction with your grant project officer 

throughout the work plan development process can help you develop an effective work plan. In regions where the 

Section 106 grant process is competitive, however, grant project officers will be limited in their ability to provide 

assistance. When assistance agreements are awarded competitively, EPA policy requires that the competitive 

process be fair and impartial, that all applicants be evaluated only on the criteria stated in the announcement, and 

that no applicant receive an unfair competitive advantage. You can find information on EPA’s competitive process, 

including EPA Order 5700.5A1, “Policy for Competition of Assistance Agreements,” on EPA’s Office of Grants 

and Debarment Web site, http://www.epa.gov/ogd/. 

Your work plan must comply with applicable federal statutes, regulations, circulars, executive orders, and 

delegation or authorization agreements, and at a minimum must specify: 

z The work plan components to be funded under the grant 

z The estimated work years and estimated funding amount for each work plan component 

z The work plan commitments for each work plan component and a time frame for their accomplishment 

z A performance evaluation process and reporting schedule 

z The roles and responsibilities of the recipient and EPA in carrying out the work plan commitments 

z Environmental outcomes, the results, effects, or consequences that will occur from carrying out the 

environmental program or activity that is related to a work plan’s environmental or programmatic goal or 

objective 

z Environmental outputs, environmental activities or efforts, and associated work products related to an 

environmental goal or objective that will be produced or provided 

z A budget (see section I.5.b of this chapter for more information on budgets) 

Lake Havasu. Photo courtesy of Chemehuevi Indian Tribe. 3-6 
Section 106 grants are intended to support the prevention and reduction of surface and ground water pollution 

from point and nonpoint sources. As noted in the introduction, you may use Section 106 grants to fund a wide 

range of water pollution control activities, including: 

z Water quality planning, assessments, and studies 

z Ambient monitoring 

z Community outreach and education activities 

z Source water, surface water, ground water, and wetland protection activities 

z Development and update of NPS control planning activities (including NPS assessments and management 

plans) 

z Development of WQS 

z Development of total maximum daily loads (TMDLs) 

Funds cannot be used for construction, operation, or maintenance of wastewater treatment plants or drinking 

water systems, nor can they be used for costs that are already financed by other federal grants. Tribes receiving 

GAP grants may not duplicate their capacity building efforts with Section 106 grants. Your region’s annual tribal 

Section 106 funding opportunity announcement may include other requirements for the use of Section 106 funds. 

Review your regional announcement for more information. 

Figure 2 lists examples of eligible and ineligible Section 106 activities. 

Sections I.4 through I.11 of this chapter will help you develop work plan components, commitments, and goals 

based on your tribe’s water resources, needs, and program goals and objectives. 

c. Establishing Output- and Outcome-based Activities: Environmental Results 

EPA Order Number 5700.7 (Environmental Results under EPA Assistance Agreements) went into effect in 

January 2005. The order requires EPA to link all grant activities to its strategic plan and to consider how the 

environmental results of completed activities will further EPA’s goals and objectives when making decisions on 

grant applications. EPA also must ensure that grant activities address outputs and outcomes. Your grant 

application should contain a description of the link between activities you propose and EPA’s strategic plan and a 

discussion of any expected outputs or outcomes. You can view the order and guidance on complying with the 

order at http://www.epa.gov/ogd/grants/award/5700.7.pdf. 

For the purposes of EPA work plans, outputs reflect the products or services a program will provide. They do 

not by themselves measure or quantify the environmental results of a work plan. Examples of outputs include 

training, the number of permits issued, and the number of samples collected. 

Environmental outcomes are actual changes or benefits resulting from the activities or outputs of the program 

and must be quantifiable. Examples of outcomes are measurable improvements in water quality and increases in 

the number of facilities that meet effluent limits. 

3-7 
Figure 2: Allowable and Ineligible Section 106 Activities 

Classification Category Activity

Capacity building

Compliance and enforcement

Finance, budgeting, and record-keeping

Networking and cross-boundary coordination

Program

Non-structural source water, surface water, ground water, and wetland

protection

Management Personnel costs, including contractor costs

Planning, developing, improving, or maintaining a water pollution control

program

Program initiation and administration

Training

Water quality planning, assessments, and studies

Quality Assurance Project Plan (QAPP) development

Data analysis and assessment

Data management

Experiments

Monitoring Investigations, surveys, and special studies

Allowable Data collection and related quality assurance

Activities Laboratory costs

Research and development

Source water, surface water, ground water, and wetlands monitoring activities

Developing water quality standards (WQS)

Permit issuance, including National Pollutant Discharge Elimination System

(NPDES) permits to control point sources

Standardsbased

Violation enforcement activities aimed at correcting violations, deterring future

violations, and promoting equal treatment of the regulated community Activities

Developing a 401 Certification Program

Developing total maximum daily loads (TMDLs)

Attending NPS meetings and trainings

Nonpoint Developing non-structural controls to reduce NPS pollution

Sources Forming partnerships to address NPS issues

(NPS) NPS inventories, assessments, and management plans

Watershed-based planning

Community Community/tribal outreach, education, and public awareness

Related Involving the public in program development

Activities Establishing voluntary programs

Construction, operation, or maintenance of wastewater treatment plants or

drinking water systems

Ineligible Costs that are already financed by other grants (e.g., Section 319 grants)

Activities NPS management measures requiring construction (i.e., "on the ground"

management measures)

Public Water System Supervision (PWSS) compliance monitoring

3-8 
Although your program should strive to produce outcomes, in some cases outputs will be the most appropriate 

goals for your work plan, especially early in your program’s development. Outcomes may take many years to 

achieve or occur after a grant period ends. In addition, even if a desired environmental outcome occurs, it may be 

difficult to link the outcome to the activities you performed. 

Examples of Outputs and Outcomes for Environmental Activities 

Monitoring 

z Outputs: Number of samples collected

z Outcomes: Improved understanding of water body condition

Research and development, studies, surveys, investigations, and experiments 

z Outputs: Number of experiments or samples, number of reports or publications

z Outcomes: Advancement in knowledge on the effects of pollution as reflected in a peer-reviewed

scientific journal article

Training and outreach 

z Outputs: Number of training sessions, number of persons trained

z Outcomes: Increase in knowledge as demonstrated by pre- and post-training surveys

Compliance and enforcement 

z Outputs: Number of inspections or enforcement actions

z Outcomes: Increase in number of facilities that reduce emissions or other pollutants, quantity of

emissions or pollutants reduced

4. Identifying Basic Tribal Water Resources 

The first step in creating a water quality program is assessing the water resources located on your reservation or 

that pertain to reservation water resources. The most effective water quality programs will incorporate all types 

of water bodies located on your tribe’s reservation. Although initially your program might not be able to address 

every type of water body, you should make sure that you are aware of all of your tribe’s water resources when 

assessing your needs. Types of water resources include: 

z Streams and Rivers: A stream is a natural body of flowing water; a river is a large stream. 

z Oceans, Coasts, and Coastal Waters: Coastal waters include shore miles, near coastal waters, and 

estuaries. 

z Lakes: Lakes are inland bodies of salt water or fresh water. 

z Wetlands: Wetlands include swamps, marshes, bogs, and similar areas. Wetlands serve many important 

functions including flood mitigation, water storage, habitat, and natural water filtration. 

z Ground Water: Ground water occurs as part of the hydrologic cycle. As rain and snow fall to the earth, 

some water soaks into the ground and flows downward. Ground water refers to water in the “saturated 

zone” — the area in which the spaces between rocks, gravel, sand, or soil are filled with water. Areas 

where ground water exists in sufficient quantities to supply wells or springs are called aquifers. 

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Incorporating Section 106 Funds into Performance Partnership Grants 

Section 106 grants are eligible for inclusion in Performance Partnership Grants (PPGs). PPGs combine funds 

from two or more environmental program grants into a single grant with a single budget. PPGs enable you to 

better direct funding toward the most critical environmental problems while continuing to address core program 

requirements; better address cross-program strategies such as community-based environmental protection, 

pollution prevention, and environmental justice; and reduce administrative burdens and costs by reducing the 

numbers of grant applications, budgets, work plans, and reports. If you are interested in pursuing PPGs, you 

should work in partnership with your EPA regional office to develop a PPG that meets EPA statutory and 

program requirements. An application for a PPG must contain: 

z A list of the environmental programs and the amount of funds from each program to be combined in the 

PPG 

z A consolidated budget 

z A consolidated work plan that addresses each program being combined in the grant and that meets the 

Section 106 work plan requirements 

You can find more information on PPGs at http://www.epa.gov/water/PPG/ppgguide.html. PPG requirements 

are also listed in 40 CFR 35.530 et. seq. 

Your tribe may already be familiar with all the water resources located on your land. If you do not know all of 

your water resources, the following organizations may be able to help you identify them: 

z Your EPA regional office, http://www.epa.gov/ow/region.html. 

z EPA’s Watershed Assessment, Tracking, and Environmental Results (WATERS) Reach files, a series of 

national hydrologic databases that identify and interconnect the stream segments or “reaches” that 

compose the country’s surface water drainage system. WATERS Reach data and tools are available 

online at http://www.epa.gov/waters/doc/rfindex.html. 

z The United States Geological Survey (USGS), http://www.usgs.gov/, in particular the National 

Hydrography Dataset (NHD), available online at http://nhd.usgs.gov/. NHD is a comprehensive set of 

digital spatial data that contains information about surface water features such as lakes, ponds, streams, 

rivers, springs, and wells. 

z The United States Department of Agriculture’s (USDA’s) Natural Resources Conservation Service 

(NRCS), http://www.nrcs.usda.gov/. 

z Regulatory agencies for neighboring states or tribes (e.g., departments of health, environment, parks and 

recreation, natural resources, forestry, fish and wildlife). 

z Local colleges or universities. 

z Perhaps most important, members of your tribe. 

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5. Identifying Tribal Needs 

a. Identifying Water Quality Needs 

Identifying your tribe’s environmental and water quality protection needs is the most essential part of developing a 

water quality program. A tribe’s environmental and water quality protection needs will define the approach you 

take to building your program, its direction, and the projects you choose to implement. Your needs can be related 

to any type of water pollution control activity eligible for funding with Section 106 grants. (See section I.3.b of this 

chapter for more information on eligible activities.) You might need to assess the environmental condition of your 

water bodies (e.g., develop a baseline assessment of the quality of your rivers). If you have access to 

assessments conducted by other parties (e.g., state environmental offices), review the assessment in the context 

of your tribal goals to determine whether it sufficiently captures the quality and condition of your water bodies or 

whether you should conduct a new or supplementary assessment. Your needs might be related to a known or 

potential environmental problem or threat to public health, the environment, or your tribe’s quality of life (e.g., a 

polluted river). If your tribe relies on septic systems, you might consider identifying system malfunctions and 

health and water risks and setting up a management program to reduce the threats to water quality a major need. 

After you have identified your environmental and water quality needs, you should rank them to identify the most 

critical ones. There is no one correct way to prioritize your needs, but some factors that you might want to take 

into consideration are: 

z What needs are most important to your tribe 

z How the needs relate to one another (i.e., will your tribe have to address one need before it can address 

another need?) 

z Whether the needs pose a threat to public health, safety, or the environment 

z The expected benefits of addressing the need 

z How much it will cost to address the need 

Prioritizing your needs will help you decide which activities require urgent attention and which cannot or do not 

need to be addressed immediately. They will also shape your program goals. 

b. Identifying Resource Needs 

In accordance with 40 CFR 35.507(b)(2)(ii), your work plan must include a budget, or the cost associated with 

completing the activities in the work plan. After you have identified your water quality needs, think about the 

financial resources you will require to address those needs. Financial needs include personnel costs, consultant 

costs, travel, equipment, supplies and materials, laboratory services, and overhead costs (e.g., office space, 

supplies, computer equipment). Although your application budget can include those costs that may not be funded 

by EPA, the approved budget and work plan in a grant must reflect only the federal and tribal dollars which are 

included within the scope of the grant and are carried out with grant funding. Your EPA regional office may be 

able to help you develop a budget. 

Remember that your tribe must provide 5 percent of the work plan costs. Your Regional Administrator may 

increase the maximum federal share if you can show that fulfilling the match requirement through either matching 

funds or in-kind contributions would impose undue hardship. 

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6. Identifying Program Objectives and Goals 

Goals are the desired outcomes for your program, based on the water quality needs you identified in section I.5.a. 

For example, if you identified the lack of a baseline assessment of the quality of tribal waters as a significant 

need, one of your program goals should be to develop a baseline assessment. 

Your objectives are the activities you take to achieve your goals. For example, if your goal is to develop a 

baseline assessment of water quality condition of your water bodies, you should include monitoring water bodies 

on your reservation as an objective. 

The objectives and goals you identify in this section will shape the rest of your program. You should structure your 

work plan activities so that you will meet your goals and objectives. Your goals and objectives will also determine 

which approach to water quality program development you select. 

In cases where your waters are unimpaired, the maintenance and documentation of continued water quality 

should be considered to be a worthy goal. Other goals and objectives, such as the completion of a baseline 

monitoring assessment, may be necessary to support this goal. 

Figure 3 illustrates the relationship among needs, goals, and objectives. 

Figure 3: Needs, Goals, and Objectives 

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Indirect Costs 

Indirect costs are expenses that do not result from the cost of direct labor. Such costs include Overhead, 

costs ancillary to direct labor, General and Administrative (G&A), which are the costs of running an 

organization as a whole, and Materials Handling, the costs of administering contractors and consultants. 

Some tribes have a standard rate that they use to calculate indirect costs for their budgets. Contact your tribal 

officers or EPA regional office for more information. 

7. Hiring Staff 

a. Identifying Skills Needed to Develop a Water Quality Program 

You will need personnel with specific skills to help you implement your water quality program. Depending on your 

program’s size and goals, you may need the skills of environmental specialists, water quality specialists, biologists, 

lab technicians, engineers, and administrative assistants, among others. When developing your work plan, you 

should consider what kinds of personnel you will need to achieve your water quality program goals. See section 

I.6 of this chapter for more information on developing water quality program goals. 

For more information on identifying key program personnel, see page 48 of Listening to Watersheds: A 

Community-based Approach to Watershed Protection (Angie Reed and Geoff Dates; River Network National 

Office; Portland, OR; 2003). This guidebook was written specifically for tribes. It is available online at http:// 

www.rivernetwork.org/ltw/. 

b. Identifying Available Resources 

Consider any resources that are available to your program. Can staff from neighboring tribal programs provide 

you with technical assistance? Some tribes that have advanced water quality programs have mentored tribes with 

less advanced programs to help develop their programs. Can volunteers help carry out any of the activities in your 

work plan? Several tribal programs have used volunteers from the community, local high schools, tribally 

sponsored internship programs, community colleges, or university programs. Some tribes use seasonal or part-time 

hires to help collect samples during busy summer months. You may be able to incorporate volunteer recruitment 

into your community outreach efforts and count activities carried out by volunteers towards your 5 percent match 

requirements according to the provisions in 40 CFR 31.24(c). See section II.5 of this chapter for more information 

on recruiting volunteers. 

8. Training Staff 

Regardless of the expertise of your program’s staff members, you will probably need to provide some training for 

them. Training topics will vary depending on your program needs and staff qualifications but could include sample 

collection, quality assurance (QA) procedures for samples, computers, and data management. Identify elements 

on which your staff will need training to achieve your program goals. If anticipated training is included in your 

work plan and is related to CWA Section 106 issues, it is an allowable expense. Check with your grant project 

officer to ensure that the training cost is allowable. 

Tribes, states, EPA Headquarters, EPA regions, technical assistance providers, colleges and universities, and 

stakeholder groups are some of the organizations that offer training, workshops, and symposia to help you and 

your staff acquire necessary knowledge. EPA’s Office of Wastewater Management (OWM) maintains a list of 

some training opportunities online at http://www.epa.gov/owm/mab/indian/training.htm. The American Indian 

Environmental Office (AIEO) lists a number of educational opportunities at http://www.epa.gov/indian/ 

training.htm. EPA’s Office of Wetlands, Oceans, and Watersheds (OWOW) also offers distance learning courses 

on its Web site (http://epa.gov/watertrain/). EPA’s Office of Science and Technology offers training on the Water 

3-13 
Quality Standards Program at http://www.epa.gov/waterscience/standards. Contact neighboring tribes and states 

as well as your EPA regional office to see if they offer training that might be of use to your tribe. 

Keep future availability of training in mind when deciding whether to attend training; if you have access to a 

unique training opportunity that does not meet immediate program needs but might benefit future activities, you 

may want to consider attending. 

9. Using Contractors as Appropriate to Your Needs 

Tribes can use their Section 106 funds to support water program activities through contractor support. Contractors 

can supplement the technical capacity of your program if your in-house staff lacks technical expertise in some 

areas and even help you to develop your program and perform some basic program functions, such as sample 

collection. You may find contractor support for complex activities, such as sample analysis, information technology 

(IT) support, training, and legal analysis, among others, especially helpful in the early stages of program 

development. Procurement for contractor services must be consistent with 40 CFR 31.36. 

10. Developing Program Milestones 

It may take several years to achieve your program goals and objectives. Milestones, or significant 

accomplishments towards achieving your goals and objectives, will enable you to track progress. For example, 

completing a baseline assessment for a specified percentage of the water bodies on your reservation could be a 

milestone in completing a baseline assessment for all water bodies on your reservation. 

Your work plan should include milestones, especially if you anticipate that you will need more than one grant cycle 

to achieve your goals and objectives. Milestones will help you and EPA track performance even if you do not 

achieve your long-term goals and objectives in one grant cycle. 

11. Submitting Work Plans to EPA 

After you have considered the information in sections I.3-I.10 of this chapter, you should draft a work plan and 

submit it to your EPA regional office for approval. In all cases, the work plan will reflect the result of negotiations 

between the tribe and its grant project officer. In non-competitive situations, the best proposals are developed 

through close interaction with your grant project officer throughout the work plan development process. 

Remember that in cases where Section 106 grants are awarded through a competitive process, grant project 

officers may be limited in their ability to assist you in work plan development. See section I.3.b of this chapter for 

more information. 

When evaluating your work plan, your grant project officer will consider how your work plan fits in with EPA’s 

strategic plan, including this national guidance, and any additional regional goals and programs. If applicable, your 

grant project officer will also consider previous work plans and other jointly identified needs and priorities. If your 

proposed work plan goals differ significantly from these, your grant project officer may ask for a modified work 

plan. 

12. Conducting Community Education on Basic Program Establishment and

Direction

For many tribes, water resources are a vital part of tribal culture. Tribal communities have sustained watersheds 

and waterways for centuries. The knowledge your tribe has accumulated through its history of environmental 

stewardship is an invaluable resource to your water quality program. A successful tribal water quality program 

depends on community involvement and participation. In addition, informed members of the community are more 

likely to support your program’s efforts to protect the environment. As mentioned in section I.7.b of this chapter, 

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EPA New England Regional Laboratory Ecology Monitoring Team 

It may be infeasible or impracticable to develop some expertise in-house. In these cases, EPA may be able 

to provide technical assistance to fill these needs through in-kind assistance. The EPA New England 

Regional Laboratory Ecology Monitoring Team, for instance, provides a wide array of services to states and 

tribes in Region 1. Specific capabilities include: 

Field Studies 

• Baseline or Ambient Water Quality Monitoring (e.g., nutrient-flux studies used to develop TMDLs) 

• Biomonitoring (i.e., biological assessment of macroinvertebrate and fish communities) 

• Time-of-travel and Dispersion Studies 

• Global Positioning System 

• Sediment Sampling 

• Ecological Risk Assessment 

• Wetland Assessments (e.g., delineation, botanical studies) 

• NPS Monitoring 

• Point Source Monitoring 

• Emergency Response (e.g., accidental release assessments) 

Biology Laboratory 

• Toxicity Testing 

• Microbiology 

• Polymerase Chain Reaction (PCR) 

• Other Capabilities (e.g., algae identification, statistical analysis, research grant application 

development) 

Contacts

Connecticut: Maureen Hilton (617) 918-8608

Maine: Tim Bridges (617) 918-8603

Massachusetts: Tom Faber (617) 918-8672

New Hampshire: Jack Paar (617) 918-8604

Rhode Island: Maureen Hilton (617) 918-8608

Vermont: Tom Faber (617) 918-8672

Tribes: Tim Bridges (617) 918-8603

volunteers from the community might be able to help you implement the program, allowing you to devote funding 

to other areas. Community members might have ideas that help you define your program’s needs and priorities. 

And if you need financial assistance from your community, a more informed population is more likely to help. 

In the early stages of your program’s development, you probably will not have a great deal of information to pass 

along to your community, but it is still a good idea to let your community know that you have started to develop a 

water quality program. You can tell the community members about the needs, goals, and objectives you have 

identified and explain how you will address them. Let them know that as the program develops, you will provide 

information on its progress. 

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13. Financial and Performance Reporting 

In addition to any work plan requirements, there are financial and performance reporting requirements associated 

with Section 106 grants. Your region may require additional elements, but at a minimum, all progress reports must 

contain the required elements listed in 40 CFR 31.40(b): 

z A comparison of actual accomplishments to the objectives established for the period 

z An explanation of why you failed to meet any objectives (if applicable) 

z Any additional pertinent information, such as analyses or explanations of cost overruns 

In addition, your report must discuss how activities performed under the Section 106 work plan addressed water 

quality problems on your reservation. Regional grant offices may choose not to grant a new proposal until the old 

grant is properly closed out and you have met all reporting requirements. Your region may grant you an extension 

if you need one. 

Your region may have additional reporting requirements, and your work plan may establish additional 

commitments and deliverables based on negotiations with your EPA region. Check with your EPA regional office 

for more information on reporting requirements and schedules in your region. 

Note that in addition to performance reporting requirements, you must submit an Assessment Report to EPA. The 

Assessment Report must include certain data collected using Section 106 funding. This reporting is discussed 

more extensively in chapter 8. 

14. Conducting Program Evaluations 

a. Conducting a Joint Evaluation 

As required by 40 CFR 35.515, you and your EPA regional office must develop a joint process for evaluating 

work plan progress and accomplishments. During the evaluation process, you must discuss: 

z Accomplishments against work plan commitments 

z Cumulative effectiveness of the work performed under each of the work plan components 

z Existing and potential problem areas 

z Suggestions for improvement, including, where feasible, schedules for making improvements 

z Water quality problems specific to your tribe 

Your regional grant project officer will compile an end-of-year evaluation report and provide it to you. 

b. Conducting a Self-evaluation 

In addition to the joint evaluation you conduct with EPA, you should consider taking stock of your program 

through a program-wide self-evaluation not limited to your current work plan. A program-wide evaluation can help 

you make sure that besides meeting all regulatory requirements, you are making the best decisions for your 

program and its priorities. Some of the questions you may want to ask during your self-evaluation are: 

3-16 
z How do you establish program goals and objectives? Is this process efficient? How should you establish 

goals in the future? 

z Are you making progress toward achieving your program’s goals? Are you on schedule to meet your 

program goals? Why or why not? 

z Do you have enough resources (e.g., money, equipment, facilities, training) to achieve the goals? 

z How efficiently are you achieving your goals? Can you think of ways to complete tasks more efficiently? 

During your self-evaluation, you can request feedback from other members of your tribe, the tribal government, 

your regional EPA coordinator, and other appropriate individuals who have worked with your program. 

15. Developing a Multi-year Plan 

After you have completed a program evaluation, the last fundamental activity that you should consider 

accomplishing before moving forward with your program is to develop a multi-year plan for your own records. 

Reassess your tribal needs and your program objectives and goals when you develop your multi-year plan. You 

may find that new circumstances or the results of your activities have given you insight into other needs or 

problem areas. Begin to think about more complex projects that build on the results of your previous work plans. 

For instance, if you have found that a water body on your reservation has high levels of nutrients, set out to 

identify the causes behind those levels. 

Developing a multi-year plan will help you make sure that your program evolves in the right direction as it matures 

and develops, and it will help you stay focused on achieving your goals. Your plan does not have to be set in stone 

or contain detailed information about specific activities, but it should describe the goals your program intends to 

achieve, why you intend to achieve them, and how you will achieve them. 

II. Intermediate Program Activities 

1. Seeking Other EPA Funding Opportunities 

As your program matures, you may want to implement activities that require additional funding from non-Section 

106 funds. EPA makes available several other grant opportunities to tribes: 

z General Assistance Program (GAP) Grants: GAP grants are authorized through the Indian 

Environmental General Assistance Program Act of 1992. The GAP program is administered by AIEO. 

The program provides tribes and intertribal consortia with general assistance for planning, developing, and 

establishing the capability to implement environmental protection programs in Indian Country. Activities 

covered by GAP grants include development of legal and administrative structures, development of 

technical capability, and establishment of a management program for project and program-specific 

assistance (e.g., Section 106 grants). 

z Wetland Program Development Grants (WPDGs): Tribal governments and intertribal consortia are 

eligible to apply for WPDGs. EPA awards wetlands development grants to assist in the development of 

new, or the refinement of existing, wetlands protection and management programs. Grants can be used for 

research, investigations, experiments, training, demonstrations, surveys, and studies relating to the causes, 

effects, extent, prevention, reduction, and elimination of water pollution. 

3-17 
z Section 319 Grants: Congress has authorized EPA to award NPS pollution control grants to tribes under 

Sections 319 and 518 of the CWA. NPS pollution occurs when rainfall, snowmelt, or irrigation runs over 

land or through the ground, picks up pollutants, and deposits them into water 

bodies. Tribes must have approved NPS assessments and management 

programs as well as TAS status to receive Section 319 funding. An NPS 

assessment report describes existing and potential NPS-related water quality 

problems as well as existing methods used to control NPS pollution. An NPS 

management program describes how you intend to correct or prevent existing 

and potential NPS pollution. NPS assessments and management plans can be 

developed using Section 106 funds. More information on Section 319 grants and NPS activities is in 

chapter 5. 

z National Environmental Information Exchange Network (NEIEN) Grants: EPA and states, 

territories, and tribes are working together to develop the NEIEN, an Internet- and standards-based, 

secure information network that will allow electronic reporting, sharing, integration, analysis, and use of 

environmental data from many different sources. The NEIEN Grant Program provides funding to tribes 

and intertribal consortia to help them develop the information management and technology capabilities they 

need to participate in the exchange network. This grant program supports: the acquisition and development 

of computer hardware and software; the development of common data standards, formats, and trading 

partner agreements for sharing data over the exchange network; and, the planning, development, and 

implementation of collaborative, innovative uses of the exchange network. 

You can find more information on GAP and Section 319 grants at http://www.epa.gov/indian/tgrant.htm. You can 

find more information about WPDGs at http://www.epa.gov/owow/wetlands/grantguidelines/. More information 

on NEIEN grants is available at http://www.epa.gov/neengprg/. 

These are not the only EPA funding opportunities available to tribes. EPA Region 8 has developed Water 

Management Solutions: A Guide for Indian Tribes (EPA 908-K-93-001), available online at http://epa.gov/ 

waterscience/tribes/files/wms.pdf. This guide contains detailed information about EPA water quality programs 

available to tribes, including requirements, sources of technical assistance, and regulations related to each 

program. You can also find additional sources of funding at EPA’s Catalog of Federal Funding Sources for Water 

Protection Web site, http://cfpub.epa.gov/fedfund/, a searchable database of grant, loans, and cost-sharing 

programs available to fund a variety of watershed protection projects. 

2. Providing Enhanced Training to Staff 

The capabilities of your staff should mature as your program grows and matures to ensure that you can continue 

to meet your program’s needs. As your program develops, and as funding allows, identify training opportunities 

that would benefit your staff. Keep tabs on your staffing needs and think of ways to address them as necessary. 

(See section I.7.a of this chapter for more information on identifying staffing needs.) 

Retaining qualified program staff is one of the greatest challenges facing many tribal programs. If your program 

relies exclusively on one person for expertise in any given area, it stands to lose that expertise if that person 

leaves. To the extent possible, train other staff members in program areas for which you rely on one person for 

expertise. This way, your program’s performance will be less severely affected if a member of your team 

becomes unavailable. 

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3. Using Contractors as Appropriate to Your Needs 

Generally, intermediate programs should have the capacity to perform all of their fundamental activities across all 

program areas with in-house staff, although they may use contractors to supplement the program staff in 

performing fundamental program activities. (See the following chapters for information on fundamental program 

activities within other program areas.) You may still need contractor assistance for more complex activities, such 

as analyzing samples or providing training. 

4. Reassessing Program Objectives and Goals 

As you complete work plan activities and reach milestones identified under section I.10 of this chapter, you will 

learn more about your tribe’s water resources. Reassess your tribal needs and your program objectives and goals 

using this information, as you did when developing a multi-year plan. (See section I.15 of this chapter.) To 

maximize the success of your water quality program, you must keep your goals and objectives up to date. 

Incorporate your environmental results and goals into all aspects of program planning. 

5. Enhancing and Focusing Tribal Community Education 

As your program matures, you should continue to provide information about it to your community. In addition to 

following up on the information you have already provided (e.g., updating program goals and objectives, 

highlighting new community needs, reporting achievements), you can also develop focused community outreach 

plans to meet specific needs. For example, you could distribute fliers requesting participants for a volunteer 

monitoring program or hold a public meeting to discuss the importance of properly disposing of motor vehicle 

fluids. The excerpt from the Mississippi Band of Choctaw Indians’ 2002-2003 work plan, below, describes a 

program to educate the tribe’s youth about water quality issues. 

OWM’s What You Can Do Web site (http://www.epa.gov/water/citizen.html) lists a number of publications and 

Web sites with information on raising public awareness. EPA’s Office of Wetlands, Oceans, and Watersheds 

(OWOW) Web site (http://www.epa.gov/owow/volunteer.html) has information on volunteer activities. EPA’s 

Environmental Education Web site (http://www.epa.gov/enviroed/index.html) also has links to a number of 

resources you can use. 

From the Mississippi Band of Choctaw Indians’ 2002-2003 work plan: 

The Choctaw Tribe realizes that education is the best tool for conserving the natural resources.... The 

Choctaw Tribe realizes that the future is in the hands of today’s youth. In collaboration with the Youth 

Opportunity Program, the Choctaw Environmental Program Office will introduce training sessions and 

various laboratory procedures for the analysis of water samples.... Educational outreach activities will also 

be conducted at the tribal schools to promote public awareness of the CWA and its goal to protect and 

enhance water quality. 

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6. Conducting Program Evaluations 

In accordance with 40 CFR 35.515, you must continue to conduct joint program evaluations (described in section 

I.14.a) with your EPA regional office. In addition, you should continue to conduct program self-evaluations 

regularly. As your program matures and you incorporate more sophisticated activities into your work plan, you 

may find that answering the questions presented in section I.14.b has become more challenging. You may identify 

additional goals and objectives that strain your resources and make you prioritize your activities. The approaches 

you adopted earlier may not work in all circumstances. Your experience may change your perspective on a 

project you considered unfeasible earlier, or you may be able to expand on the results of past projects. But unless 

you make a point of holding periodic program self-evaluations, you may not realize how your program has 

changed and the steps you should take to continue to improve and protect water quality on your reservation. 

At this point, you may want to consider an independent third-party program review. EPA’s Program Evaluation 

Information Resources Web site, http://www.epa.gov/evaluate/links.htm, lists a number of organizations that can 

assist in conducting program evaluations. 

III. Mature Program Activities 

1. Seeking Additional Federal Funding Opportunities 

As your program matures, you may want to investigate grant opportunities outside of EPA. There are a number 

of governmental agencies that provide grants to tribes. For example: 

z USDA’s NRCS offers grants to tribes through its Conservation Partnership Initiative. NRCS staff have 

worked closely with a number of tribes and have helped them identify additional funding opportunities. 

Information on the Conservation Partnership Initiative is available online at http://www.nrcs.usda.gov/ 

programs/cpi/index.html. 

z AIEO maintains a list of federal agencies and other organizations that may provide grants at http:// 

www.epa.gov/indian/links.htm. 

z The Administration for Native Americans (ANA), within the Administration for Children and Families in 

the Department of Health and Human Services, provides Environmental Regulatory Enhancement grants 

to tribes to develop tribal environmental projects that are responsive to tribal needs. Information on 

Environmental Regulatory Enhancement Grants is available online at http://www.acf.dhhs.gov/grants/ 

grants_ana.html. 

z The Bureau of Indian Affairs (BIA), within the DOI, provides Water Resources on Indian Lands Grants to 

tribes to assist in the management, planning, and development of their water and related land resources. 

Federal Search Engines 

Grant opportunities available across the federal government are posted on http://www.grants.gov. This Web 

site allows users to sign up to receive e-mail alerts about new grant opportunities in relevant areas. 

The General Services Administration also maintains a catalog of federal grant opportunities at http://

12.46.245.173/cfda/cfda.html. You can use these Web sites to help identify a number of grants related to

tribes and environmental programs.

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Previously funded projects have included geographic and hydrologic quantitative and qualitative analysis of 

water, ground water and surface water quality and quantity monitoring, aquifer classification, and stream 

gauging. The BIA Web site is temporarily unavailable, but you may obtain more information about this 

opportunity by calling 202-208-3710. In addition, you may visit the catalog of federal grant opportunities 

online at http://12.46.245.173/cfda/cfda.html and search for the Water Resources on Indian Lands grant 

opportunity. 

2. Using Contractors as Appropriate to Your Needs 

Mature programs should be able to manage all of their programs (including technical programs) using in-house 

staff. You may use contractors to provide specific or specialized technical expertise, training, or laboratory 

analyses, but for the most part you should now be able to independently manage all aspects of your program and 

conduct the majority of the work associated with the program. 

3. Conducting Comprehensive Community Outreach and Public Awareness

Programs

Your community outreach and awareness program should no longer be limited to informing your community about 

the results of your program or providing specific targeted information on selected topics. Instead, it should cover a 

number of topics related to your program, including information on water bodies on your reservation, volunteer 

activities, human health concerns, management measures, pollution prevention, education, and general information. 

You can also encourage the formation of volunteer groups that independently conduct activities that support your 

program’s goals. Remember that no matter how comprehensive your program is, you will still rely on community 

involvement and participation to achieve the best results. 

4. Conducting Program Evaluations 

At this point, you should have a good understanding of the environmental conditions on your reservation, and you 

should be able to connect your program needs to EPA’s goals and objectives. Your program evaluations should 

help you ensure that your program is aligned with EPA’s national water quality objectives. 

5. Mentoring Other Tribes and Local Governments 

As your program matures, consider mentoring other tribes and local governments. Your experience could be 

invaluable to less-experienced tribal water quality programs that may lack the technical expertise, financial 

resources, and general program background you have. In some cases, adjacent local governments welcome tribal 

expertise. 

Tribal pesticide programs are an example of an area in which coordination between tribes can yield positive 

results. Because pesticides may leach into ground water or be carried into streams and lakes, establishing 

relationships with neighboring jurisdictions is essential for promoting general water quality and establishing an 

adequate information base about threats to waters on your reservation. In addition, mentoring other tribes with 

fledgling programs may foster positive relationships and instill goodwill in neighboring communities. If you need 

contact information for other tribes in your region, your EPA regional office can provide it. 

6. Partnering with Other Organizations 

Partering with other organizations such as neighboring tribes and states, universities, private groups, local 

governments, watershed-based organizations, and others can help you implement your water quality protection 

program and achieve your program goals. In addition, you may find it useful to engage other programs within your 

tribe (e.g., fish and game programs, tribal planning offices) to alleviate duplication of effort, maximize resources, 

and expedite your program development. Sections III.4 and III.5 of chapter 5 contain more information on 

forming partnerships with other organizations. 3-21 
Providing Mentoring to Tribes: Region 8 Water Quality Training 

Fort Peck Assiniboine & Sioux Tribes, Northeast Montana 

The Water Quality Training Program Project for Region 8 tribes actively began in 2002, using monies from 

the Section 106 Special Project Monies, with matching funds from the Fort Peck Assiniboine & Sioux 

Tribes’ Office of Environmental Protection (OEP). The project implements a multi-phased approach to 

meeting the requests from the tribes within Region 8 for a water quality training curriculum taught primarily 

by tribal water quality professionals within the region and specifically tailored to meet tribal personnel needs. 

Fort Peck Assiniboine & Sioux Tribes, working in conjunction with the Institute for Tribal Environmental 

Professionals (ITEP) at Northern Arizona University (NAU) and EPA Region 8 personnel, have developed 

and begun to implement a regional tribal water quality certification program offering professional 

certification on increasingly technical levels. 

The certification program is loosely built around the college curriculum format based on classroom 

interaction time, whereby 8 hours of training leads to one credit. To progress from one level to the next, 

program participants are required to complete specific core classes, as well as a specific number of elective 

credit hours. A standardized protocol and a review board consisting of EPA personnel, tribal professionals, 

and educational representatives approve core and elective course curriculums. All courses implement and 

enforce a stringent attendance policy, pre- and post- course testing, and completion of out of class 

assignments. 

The certification program currently offers certification to water quality staff on three separate levels: Water 

Quality Technician (Level I Certification); Water Quality Specialist (Level II Certification); and 

Environmental Specialist (Level III Certification). Core requirements for certification on these levels include 

classes such as the basic monitoring course, data entry/introduction to data analysis, monitoring design, 

advanced data analysis, and 305(b) report writing. 

To date, curricula for data entry/introductory data analysis, monitoring design, basic water quality 

monitoring, advanced data analysis, and biological monitoring have been developed and training has been 

held at different locations around the region. Additional training courses and repeat training courses are 

planned. 

3-22 
Chapter 4: Monitoring, Data

Management, and Data

Assessment and Analysis

Introduction 

This chapter will help you develop a water quality monitoring program that will enable you to achieve your 

program goals. An effective water quality program includes monitoring, data management, and data assessment 

and analysis. These activities are closely related. Once you have collected monitoring data, you will need to 

manage and analyze the information. You should consider all three activities when working through this chapter. 

As your water quality program moves from fundamental to mature activities, you should ensure that your 

capabilities in monitoring, data management, and data assessment and analysis advance at the same pace. 

To highlight the activities required to monitor, manage data, and conduct assessment and analysis, sections I and II 

of this chapter address each of these program areas in separate subsections. Once you understand and implement 

each of these program areas, however, you should think of them as one tightly integrated part of your program. 

For this reason, section III of this chapter includes an integrated discussion of these topics. 

A water quality monitoring program is perhaps the most important component of a water quality management 

program. The initial results of your water quality monitoring program will help you identify water quality problems 

and set program goals and objectives to address those problems. As your program grows, your monitoring 

program will help you measure the effectiveness of your efforts to improve water quality. You cannot make 

informed decisions about your water quality program without monitoring, managing, and assessing and analyzing 

water quality data. 

EPA expects that all monitoring programs will include some basic components. Every monitoring program should 

have as its foundation a long-term strategy that addresses how it will meet water management needs. Your 

program should be driven by clear monitoring objectives, and it should be designed to allow you to meet those 

objectives. You should establish quality assurance (QA) and quality control (QC) procedures that are documented 

in a Quality Assurance Project Plan (QAPP). Your program should use a core set of water quality indicators 

(WQI) — measurements that you can use to assess the quality of a water body — that you can compare over 

time. The indicators you use can measure the physical (e.g., temperature), chemical (e.g., phosphorus, nitrogen), 

or biological (e.g., macroinvertebrates, bacteria) characteristics of your waters. The program eventually should 

grow to address all water body types (e.g., streams, lakes, wetlands, estuaries, rivers, ground water). This chapter 

will help you to establish a monitoring program that meets all of these requirements. 

4-1 
Activities Included in Chapter 4 

Fundamental Program Activities

1. Monitoring................................................................................ Developing Monitoring Goals and Strategies

Establishing a Baseline Monitoring Program

Developing Standard Operating Procedures

Developing QAPPs

Analyzing Monitoring Samples Using Outside Laboratories

Submitting Your QAPP for EPA Reviewand Approval

Incorporating Your Monitoring Results into Your Community Outreach Program

2. Data Management.................................................................. Understanding Metadata and Compiling Useful Data Sets

Developing Electronic Data Storage Capacity

Managing Electronic Data

Performing Data Validation as Part of Your QA/QC Plan

Reporting Data to EPA

3. Data Assessment and Analysis............................................ Developing Data Assessment and Analysis Capabilities

Developing Data Display Capabilities

Using Data to Understand Problem Areas and Trends

4. Initiating Mitigation Measures for Known Water Quality Problems

Intermediate Program Activities

Tribes should begin these activities after having completed the relevant fundamental program activities.

1. Monitoring................................................................................ Updating Monitoring Goals, Strategies, and Objectives

Expanding and Refining the Baseline Monitoring Program

2. Data Management.................................................................. Updating and Upgrading Electronic Data Systems

Incorporating Additional Monitoring Parameters

Using STORET or Electronically Compatible Formats

Maintaining a Database with Graphing Capabilities

3. Data Assessment and Analysis............................................ Evaluating Monitoring Program Effectiveness

Measuring Water Quality Improvement

Mature Program Activities

Tribes should begin this activity after having completed the relevant fundamental and intermediate program activities.

1. Understanding and Using EPA's "Elements" Guidance

4-2 
In addition to the information provided in this chapter, use the resources that EPA and other organizations have 

produced to develop your monitoring program. In particular: 

z Tribes implementing fundamental and intermediate water quality monitoring programs should refer to 

Listening to Watersheds: A Community-based Approach to Watershed Protection (Angie Reed and 

Geoff Dates; River Network National Office; Portland, OR; 2003). This guidebook describes a 

community-based approach to protecting water resources and was written specifically for tribes. It is 

available online at http://www.rivernetwork.org/ltw/. In addition, tribes implementing a fundamental 

program should refer to EPA’s volunteer monitoring guidances, available online at http://www.epa.gov/ 

owow/monitoring/vol.html. These guidances will help tribes understand some of the terminology and 

concepts used in this guidance. 

z Tribes implementing mature water quality programs should refer to EPA’s Elements of a State Water 

Monitoring and Assessment Program (EPA 841-B-03-003), available online at http://www.epa.gov/ 

owow/monitoring/repguid.html. It recommends 10 basic elements of a state water monitoring program. 

Mature water quality programs should fully incorporate all of these elements: 

1. Monitoring program strategy 

2. Monitoring objectives 

3. Monitoring design 

4. Core and supplemental WQI 

5. Quality assurance 

6. Data management 

7. Data analysis and assessment 

8. Reporting 

9. Programmatic evaluation 

10. General support and infrastructure planning 

EPA encourages all tribal water quality programs, regardless of their level of sophistication, to use the Elements 

of a State Water Monitoring and Assessment Program where appropriate. 

Water sampling. Photograph courtesy of Gila River Indian Community. 

4-3 
In addition, EPA has published a compendium of best practices for developing water quality monitoring programs, 

referred to as the Consolidated Assessment Listing Methodology (CALM). You may find the best practices listed 

in CALM a useful reference tool, particularly when developing the Assessment Reports described in chapter 8. 

The CALM Guidance Document is available online at http://www.epa.gov/owow/monitoring/calm.html. 

QAPPs and Monitoring 

EPA has established quality control (QC) mechanisms to make sure that environmental data collected under 

programs the Agency supports are of sufficient quantity and quality to support the data’s intended use. You 

must meet the applicable QA and QC requirements listed in 40 CFR 31.45 to use Section 106 funds for 

environmental data collection through monitoring. You must develop and implement QA practices consisting of 

policies, procedures, specifications, standards, and documentation sufficient to produce data of adequate 

quality to meet project objectives and to minimize loss of data due to out-of-control conditions or malfunctions. 

One of the control mechanisms EPA has developed is the Quality Assurance Project Plan (QAPP). You are 

required to develop a QAPP if you are conducting any data collection, including monitoring under a Section 

106 grant. You must submit your completed QAPP before you begin any monitoring. A QAPP is a written 

document that outlines procedures that a monitoring project will use to ensure that the samples it collects and 

analyzes, the data it stores and manages, and the reports it produces are of sufficient quality to meet project 

needs. The QAPP should also outline the assessment or decision criteria that you will use to address your 

monioring objectives. The QAPP unites all the technical and quality aspects of a project (e.g., monitoring, 

detection limits, analytical methods, data management, data analysis, reporting) and provides a blueprint for 

obtaining the type and quality of environmental data and information needed. 

EPA has developed guidances for developing QAPPs for all types of monitoring programs, from a simple 

volunteer monitoring initiative to established state programs. In particular, some tools to which you should refer 

include: 

z EPA guidances on developing QAPPs, available at http://www.epa.gov/quality/qapps.html. Specifically, 

refer to EPA Requirements for Quality Assurance Project Plans (QA/R-5) and Guidance for 

Quality Assurance Project Plans (QA/G-5). 

z EPA’s Elements of a State Water Monitoring and Assessment Program contains information on

developing QAPPs specific to monitoring programs.

z For basic information on QAPPs, consult EPA’s Volunteer Monitor’s Guide to Quality Assurance

Plans (EPA 841-B-96-003), available online at http://www.epa.gov/owow/monitoring/volunteer/.

z Listening to Watersheds, pages 65-69, also contain information on developing QAPPs. 

z Regions 1 and 9, with support from Regions 3 and 10, as well as the Tribal Air Monitoring Support

Center at Northern Arizona University, have developed the Quality Assurance Project Plan

Development Tool. This CD-ROM tool may be obtained by contacting your regional QAPP

coordinator.

z Lastly, see the “Building Credibility” Factsheet, available at http://www.usawaterquality.org/volunteer/ 

outreach/BuildingCredibilityVI.pdf. 

4-4 
QAPPs for Ground Water Monitoring 

Due to regional variations in geology and hydrology, there is no one method for ground water monitoring. By 

establishing a comprehensive ground water QAPP with field, sampling, lab, and assessment protocols, tribes 

can effectively sample wells for contaminants such as metals, volatile organic compounds, and nutrients. 

Research into past land use as well as hydrogeological surveys of the area will supply knowledge regarding 

the characteristics of aquifers as well as potential sources of contamination. Sound data collection will help 

tribes develop the foundation they need to determine their ground water protection needs. 

I. Fundamental Program Activities 

1. Monitoring 

a. Developing Monitoring Goals and Strategies 

The primary purposes of a monitoring program are to determine the physical, chemical, and biological conditions 

of a water body and evaluate them against WQI. Within that context, you may conduct water quality monitoring 

to meet any of the program needs, goals, and objectives you have identified. (See sections I.5 and I.6 of chapter 3 

for more information on identifying needs, goals, and objectives.) For example, you may conduct water quality 

monitoring to collect baseline data on water quality throughout your reservation or to measure the effects of a 

specific activity, such as construction, agricultural activities, or mining. The needs you want to address will 

determine your monitoring goals and strategies. 

Your program may lack the time and resources to effectively monitor all water bodies on your tribe’s reservation. 

Take this fact into account when establishing monitoring goals and strategies. Time and resource considerations 

may also affect the monitoring approach you take. Consider the water use habits of your tribe and your special 

circumstances when developing monitoring goals. If you obtain much of your water from ground water wells but 

have never tested your ground water for contaminants, conducting this testing might be a priority. If you know 

that there are wetlands on your reservation but have never catalogued them, you might want to begin initial 

monitoring to assess their health. 

i. Developing Monitoring Objectives 

A. Collecting Existing Information 

Before you can make informed decisions about your monitoring program, make sure you collect as much existing 

information as possible about all the water bodies on your reservation. Remember to include all the water bodies 

you identified in section I.4 of chapter 3. Do not focus on collecting only high-level quantitative data; qualitative 

information from maps, aerial photos, and reports can also provide information about water quality. Identify any 

gaps in information. Based on your goals, you may not need to address the gaps now, but it is important that you 

are aware of them. In addition, it is probably a good idea to address them in your monitoring program now or in 

the future. 

Remember that even if you have not conducted any water quality monitoring in the past, other organizations may 

be able to provide you with some monitoring data for your water resources. Section I.4 of chapter 3 lists some 

organizations you should consult. Remember to talk to your community and collect any information its members 

can provide. Page 5 of Listening to Watersheds lists additional resources you can use. Existing state or tribal 

303(d), 305(b), or integrated water quality reports may contain information on water quality on your reservation. 

You can view 305(b) reports online at http://www.epa.gov/305b/. In addition, EPA’s Surf Your Watershed Web 

site (http://www.epa.gov/surf/) can help you locate and use environmental information about your watershed. 

While you may ultimately decide that you need to collect additional supplementary data, existing data can provide 

a valuable starting point from which to begin to determine the quality of your water bodies. 4-5 
Environmental Monitoring and Assessment Program 

In developing a monitoring design, you may find it helpful to consult EPA’s Environmental Monitoring and 

Assessment Program (EMAP). EMAP is a research program to develop the tools necessary to monitor and 

assess the status and trends of national ecological resources. EMAP’s goal is to develop the scientific 

understanding for translating environmental monitoring data from multiple spatial and temporal scales into 

assessments of current ecological conditions and forecasts of future risks to our natural resources. EMAP 

develops indicators to monitor the condition of ecological resources. EMAP also investigates designs that 

address the acquisition, aggregation, and analysis of multiscale and multitier data. The Regional EMAP 

(REMAP) was initiated to test the applicability of the EMAP approach to answer questions about ecological 

conditions at regional and local scales. Using EMAP’s statistical design and indicator concepts, REMAP 

conducts projects at smaller geographic scales and in shorter time frames than the national EMAP program. 

Tribes may find useful resources, such as information on water quality data sets, assessment methodologies, 

and regional information, on EMAP’s Web site, http://www.epa.gov/emap/. Information on REMAP is 

available online at http://www.epa.gov/emap/remap/index.html. 

B. Using Existing Information to Define Monitoring Objectives 

Monitoring objectives drive how you implement your monitoring program. Monitoring should help you gather data 

that will help you achieve your goals and strategies. For example, if your goal is to determine whether specific 

pollution control activities are effectively protecting water quality, your objectives should include monitoring water 

quality in water bodies where control activities for that pollutant are in place. Using the information on your 

reservation’s water bodies that you have collected, and considering your goals, define the objectives for your 

monitoring program. For each objective you identify, describe why it is important to meet the objective, what data 

you expect to produce to meet the objective, and who will use the monitoring data. 

You should consider your overall program goals when developing your monitoring objectives. EPA’s Elements of 

a State Water Monitoring and Assessment Program identifies five basic questions for a monitoring program to 

address. Although you may not be able to answer all these questions immediately, you should keep them in mind 

when developing your objectives and use them to guide the direction of your monitoring program. As your 

program develops, you will be able to answer more of these questions in greater detail. 

1. What is the overall water quality of water bodies? You should determine the extent to which your 

waters meet your program objectives. These may include the objectives of the CWA; attainment of 

applicable WQS and designated uses; protection and propagation of balanced populations of fish, shellfish, 

and wildlife; water quality; protection of ecosystem health; maintenance of pristine waters; or protection of 

public health. 

2. To what extent is water quality changing over time? You should assess the extent to which water 

quality has changed over time. Understanding if and how water quality has changed over time may help 

you identify areas of concern and determine whether protection or restoration activities your program has 

initiated are working. 

3. What are the problem areas, and what areas need protection? You should identify high-quality, 

pristine waters that should be protected from degradation. You should also identify areas that have water 

quality problems that need to be addressed. If your tribe has EPA-approved WQS or tribal code in place, 

you can use your standards or code to identify impaired or problem areas. If your tribe does not have 

EPA-approved WQS or tribal code in place, you can use WQS from neighboring tribes or states as proxies 

to determine impairment. 

4-6 
4. What level of protection do these areas need? Over time, as you develop an understanding of the 

quality of your waters, you should establish a level of protection for each of the water bodies that you 

monitor so that you have a benchmark against which to evaluate monitoring results. For example, a tribe 

that has established water quality goals could use monitoring results to determine which water bodies are 

not meeting those goals and assess which management strategies for NPS are most appropriate. 

5. How effective are clean water projects and programs? You should monitor the effectiveness of 

specific projects and overall programs. You may find it difficult, especially early in your program 

development, to evaluate whether a specific program is helping to reduce water pollution or protect pristine 

water bodies. You should keep this question in mind, however, and try to establish monitoring objectives to 

help you answer this question. 

b. Establishing a Baseline Monitoring Program 

i. Developing a Monitoring Design 

Once you have established objectives, the next step in developing a baseline monitoring program is to develop a 

monitoring design. A monitoring design establishes the frequency of monitoring, the water bodies that will be 

monitored, the locations that will be monitored within the water body, the parameters (e.g., pH, temperature, 

macroinvertebrates) that will be sampled, and how the information will be used or displayed to answer your 

monitoring objective. You should use a monitoring design that meets your monitoring objectives. For example, if 

you are concerned with the health of your fish community, you should consider developing a biological monitoring 

program. If you are concerned with the health risks associated with consuming fish, you should consider taking 

fish tissue samples. Note that fish community and tissue analyses may be more appropriate for more established 

monitoring programs. 

Monitoring Plan Support 

Before developing a monitoring plan, be sure to contact your EPA regional monitoring coordinator, who can 

provide assistance, suggestions, and support to ensure its success. 

Region 1 Region 6 

Diane Switzer (617) 918-8377 Charlie Howell (214) 665-8354 

Region 2 Region 7 

Darvene Adams (732) 321-6700 Lyle Cowles (913) 551-7081 

Region 3 Region 8 

Eva Ammentorp (215) 814-5265 Tina Laidlaw (406) 457-5016

Kris Jensen (303) 312-6237

Region 4

Jim Harrison (404) 562-9271 Region 9

Janet Hashimoto (415) 972-3452

Region 5 Terry Fleming (415) 972-3462

Sarah Lehman (312) 353-4328

Region 10 

Gretchen Hayslip (206) 553-1685 

4-7 
Gila River Indian Community 

The Gila River Indian Community (GRIC) encompasses approximately 580 square miles in central Arizona, 

adjacent to the metropolitan Phoenix area. There are approximately 20,000 Pima and Maricopa tribal 

members living in the Community. The Community’s water resources are influenced by seven major 

watersheds. Within the Community, there are approximately 20 million acre-feet of ground water, which is 

used industrially and commercially, and is the sole source of the Community’s drinking water. The 

Community has more than 8 miles of perennially flowing riverine habitat, including the Salt River and the 

Lower Gila River, and 116 miles of ephemeral surface waters, including the Upper Gila River, the Santa 

Cruz River, and the Santa Rosa, Vekol, and McClellan Washes that only flow in response to precipitation. It 

also has more than 1,500 acres of wetlands, including the Lower Gila River Wetlands and the Pee Posh 

Wetlands, more than 80 miles of canals, and 20 miles of spillage and riparian areas. The current uses of the 

Community’s surface water resources include recreation, wildlife habitat, fisheries, livestock watering, and 

agriculture irrigation. 

GRIC’s ongoing water quality investigations include surface water and ground water sampling and 

continuous monitoring and streambed sediment sampling. Data from these investigations undergo an 

extensive in-house data validation and verification review using GRIC’s integrated water quality database 

(19,000 separate water quality analyses), and is used to advance water quality assessments, promote the 

development and implementation of Tribal WQS, help develop NPS management programs with data to 

support management decisions, and to evaluate water quality trends. 

In addition, the GRIC has developed WQI to evaluate (1) support of Community Water Quality Goals and 

(2) effectiveness of GRIC Department of Environmental Quality (DEQ) water quality programs, as 

depicted in the table on the following page. 

Gila River Indian Community YSI Sonde installation for continuous water quality 

monitoring at the Pee Posh Wetlands. Photo courtesy of Gila River Indian Community. 

4-8 
-

Gila River Indian Community (GRIC)

Water Quality Indicators and Relationship to GRIC Goals

GRIC Goal GRIC Sub Goal Water Quality Indicator How Results are Tracked

Clean

Surface

Water

Protect Aquatic

Ecosystems

Stream channel

stability

Gila/Santa Cruz Rivers and Gila River Wetlands:

measure stream channel cross-sections; enter

entrenchment & width/depth ratio data into

database; monitor for trends.

Change in

macroinvertebrate

richness

Gila River Wetlands: macroinvertebrate samples

collected in 2000-2001 established baseline;

future samples to be collected biannually, as

funds are available; entered into database to

track species composition, abundance, richness,

and health against baseline.

Changes in ambient

stream chemistry (e.g.,

nutrients, pH, DO)

Natural perennial waters: with fixed monitoring

stations, monitor field (e.g., DO, pH, TDS, SS,

etc.) & laboratory (e.g., E. coli, nutrients, metals,

etc.) parameters and enter into database;

evaluate data against GRIC pathogen criteria.

Support

Designated

Uses

Miles of water bodies

that support primary

contact recreation

Surface waters designated for swimming:

quarterly and after storm events, collect E. coli

samples, enter into database; evaluate data

against GRIC pathogen criteria.

Number of nutrient

criteria exceedances

in ambient surface

water

Gila River Wetlands and other important surface

waters: quarterly, collect nitrate + nitrite & total

Kjeldahl nitrogen data (the sum of these two

parameters provides a total nitrogen

concentration result); enter results into database;

graph number of exceedances.

Number of metals

criteria exceedences

in ambient surface

water

Natural perennial waters, e.g., Gila River

Wetlands and created aquatic habitats other than

canals: regular monitoring for arsenic, cadmium,

copper, lead, mercury, nickel, selenium, and zinc;

enter results into database; measure against

criteria for protection of aquatic life; identify

trends.

Clean

Ground

Water

Protect Human

Health

Trends in nitrate and

total dissolved solids

concentration in

drinking water wells

At drinking water wells representative of drinking

water supply: annually, sample for nitrate and

TDS; every 5 years, sample full suite of

inorganics; enter into database; identify trends.

Trends in nitrate and

total dissolved solids

concentration in

monitoring wells

At monitoring wells representative of land use

activities: annually, sample for nitrate and TDS;

every 5 years, sample full suite of inorganics;

enter into database; identify trends.

Quality of

Life

Conserve,

Restore, and

Enhance

Aquatic

Ecosystems

Acres of native

riparian vegetation

Gila River aquatic system: periodically, e.g.,

every 5 years or after habitat restoration

activities, map vegetation using aerial

photography and ground-truthing and compare

against recent wetlands survey to evaluate the

status of remaining vegetation and identify new

native vegetation.

4-9 
A. Selecting WQI/Parameters to be Monitored 

You should define a set of indicators that you can use to assess water quality. The indicators should give you the 

data you need to meet your monitoring objectives. 

EPA requires that you monitor and report results for basic water quality parameters depending on your tribal 

program’s capacity. You must consider the required parameters that apply to your tribe when developing your 

monitoring design. The next section in this chapter provides information on those parameters. In addition, if your 

tribe has WQI or tribal codes in place, you can use your WQI or codes to identify impaired or problem areas. The 

WQI table below provides recommended core and supplemental WQI, including required monitoring parameters. 

In addition, the case study and chart from the Gila River Indian Community (GRIC) on pages 4-8 and 4-9 

provides an example of the use of WQI in a monitoring design. 

Water Quality Indicators 

The chart below is taken from EPA’s Elements of a State Water Monitoring and Assessment Program, 

which discusses recommended core and supplemental WQI. Core indicators provide basic information 

about the aquatic environment. Supplemental indicators provide specific or additional information and can be 

used to support a special study or screen for a potential pollutant. You may find this distinction useful when 

selecting parameters to monitor. While not all of the core indicators must be included in a tribe’s monitoring 

program, items in bold are required monitoring elements depending on the level of your tribal monitoring 

program (i.e., fundamental, intermediate, mature). You do not need to address all parameters in your first 

year. 

Recommended Core and Supplemental Indicators

Aquatic Life and Wildlife Recreation Drinking Water Fish/Shellfish

Consumption

Recommended Core

Indicators

*Condition of biological

communities (EPA

recommends the use of at

least two assemblages)

*Dissolved oxygen

*Temperature

*Conductivity

*pH

*Habitat assessment

*Flow

*Nutrients

*Landscape conditions

(e.g., % cover of land uses)

Additional indicators for

lakes:

*Eutrophic condition

Additional indicators for

wetlands:

*Wetland hydrogeomorphic

settings and functions

*Pathogen indicators (E.

coli, enterococci)

*Nuisance plant growth

*Flow

*Nutrients

*Chlorophyll

*Landscape conditions

(e.g., % cover of land uses)

Additional indicators for

lakes:

*Secchi depth (part of

habitat assessment)

Additional indicators for

wetlands:

*Wetland hydrogeomorphic

settings and functions

*Trace metals

*Pathogens

*Nitrates

*Salinity

*Sediments/Total

Dissolved Solids (TDS)

*Flow

*Landscape conditions

(e.g., % cover of land uses)

*Pathogens

*Mercury

*Chlordane

*DDT

*PCBs

*Landscape conditions

(e.g., % cover of land uses)

Supplemental

Indicators

*Ambient toxicity

*Sediment toxicity

*Other chemicals of concern

in the water column or

sediment

*Health of organisms

*Other chemicals of concern

in water column or sediment

*Hazardous chemicals

*Aesthetics

*VOCs (in reservoirs)

*Hydrophyllic pesticides

*Nutrients

*Other chemicals of concern

in water column or sediment

*Algae

*Other chemicals of concern

in water column or sediment

4-10 
Pyramid Lake, Nevada. Photograph courtesy of the 

Pyramid Lake Paiute Tribe. 

B. Understanding EPA’s Reporting Requirements 

Although tribes are encouraged to report all data they collect, tribes are required to report only the nine basic 

parameters listed below. Although all tribes are encouraged to report all of the nine basic parameters, tribes’ 

abilities to monitor and report on some of the nine basic parameters may vary. Hence, EPA has classified each of 

the nine parameters as fundamental, intermediate, or mature based on the level of complexity required by the 

monitoring and reporting activities associated with that parameter. EPA regions will use these classifications as 

guidelines in determining reporting requirements for each tribe but ultimately will decide which parameters a tribe 

is required to report on a case-by-case basis. In situations where tribes cannot monitor for all nine parameters, 

EPA regional offices and tribes should negotiate ways to build tribal capacity (e.g., training, technical assistance, 

purchase of laboratory equipment) so that the tribe can ultimately collect information on all nine parameters. See 

chapter 8 for more information on reporting requirements. 

The nine parameters are: 

Fundamental Reporting Parameters 

1. Dissolved oxygen 

2. pH 

3. Water temperature 

4. Turbidity 

Intermediate Reporting Parameters 

1. Phosphorus 

2. Total nitrogen 

Mature Reporting Parameters 

1. Macroinvertebrates 

2. E. coli or enterococci 

3. Basic habitat information 

Information on these nine parameters is included below. The discussion is taken from EPA’s Volunteer Stream 

Monitoring: A Methods Manual (EPA 841-B-97-003), available online at http://www.epa.gov/owow/monitoring/ 

volunteer/stream/, and EPA Region 10’s Ecological Condition of Western Cascades Ecoregion Streams (EPA 

910-R-04-005), available online at http://www.epa.gov/emap/remap/html/docs/wcs.html. Please note that the 

Western Cascades reference is cited because it states clearly for the layman what each measurement parameter 

is for. Location of collection has no relevance in this case. The American Public Health Association (APHA) has 

developed a reference manual, Standard Methods for the Examination of Water and Wastewater, which can 

help you identify appropriate sampling methods for dissolved oxygen, pH, temperature, turbidity, total nitrogen, and 

total phosphorus or ortho-phosphorus. The methods manual is available online at http://www.apha.org/media/ 

science.htm. In addition, many Web sites of large national vendors of kits, meters, and probes provide instructions 

on how to measure dissolved oxygen, pH, temperature, turbidity, total nitrogen, and total phosphorus or orthophosphorus. The references listed above will explain methods and technical issues as well as describe required 

monitoring equipment. 

4-11 
Dissolved oxygen: Dissolved oxygen serves as an indicator of the biological health of the water body. Dissolved 

oxygen concentrations vary naturally with water temperature and altitude. If more oxygen is consumed than is 

produced, and oxygen levels drop below their natural levels, some sensitive animals may weaken, move away, or 

die. Dissolved oxygen levels are affected by changes in water temperature and levels of organic materials. 

Changes in water temperature can occur as a result of thermal discharges from manufacturing or power plants or 

reduction of riparian shade. Industrial and municipal wastes can raise levels of organic materials. Consult section 

5.2 of Volunteer Stream Monitoring for more information on dissolved oxygen. Because fluctuations in dissolved 

oxygen levels can occur over the course of a day, tribes must track metadata on where and when the samples 

were collected. Dissolved oxygen can be collected and analyzed using any of the kits readily available on the 

market. If your monitoring objectives require greater precision, the use of probes, meters, or contract laboratories 

may be necessary. 

pH: pH is a measurement of water acidity. pH affects many chemical and biological processes in the water. Most 

aquatic animals prefer a pH range of 6.5 - 8.0. pH outside of this range reduces the diversity in the stream 

because it stresses the physiological systems of most organisms and can reduce reproduction. Low pH can also 

cause conditions that are toxic to aquatic life by allowing toxic elements and compounds to become mobile. 

Changes in pH can be caused by acid rain, mining activities, and wastewater discharges. pH can be measured 

using any of the kits readily available on the market. If your monitoring objectives require greater precision, the 

use of probes, meters, or contract laboratories may be necessary. 

Water temperature: As noted above, temperature affects dissolved oxygen levels. It also influences the rate of 

photosynthesis by aquatic plants; the metabolic rates of aquatic organisms; and the sensitivity of aquatic 

organisms to toxic wastes, parasites, and diseases. Optimal temperature ranges depend on the species in the 

water body. If temperatures are outside the optimal range for the species in a water body for extended periods of 

time, organisms will be stressed and may die. For fish, there are two kinds of limiting temperatures — the 

maximum temperature for short exposures and a weekly average temperature that may vary by time of year and 

life cycle stage. Reproductive stages are the most sensitive to temperature changes. Causes of temperature 

change include weather, removal of riparian shade, dams and other barriers that confine water bodies, industrial 

discharges, and stormwater. See section 5.3 of Volunteer Stream Monitoring for more information. Temperature 

can be measured using thermometers available from laboratory supply stores. If your monitoring objectives 

require greater precision, the use of probes, meters, or contract laboratories may be necessary. 

Turbidity: Turbidity measures the clarity of a water body. It is closely related to erosion and sediment that carry 

nutrients and bacteria into streams and lakes. Suspended particles absorb more heat, raising water temperature, 

which in turn affects the oxygen content of the water. When they eventually settle at the bottom of water bodies, 

suspended materials can also clog fish gills and smother fish eggs and macroinvertebrates. Sediment can also 

change the physical structure of habitats. Causes of high turbidity include soil erosion, wastewater discharges, 

urban runoff, farming and forestry practices, eroding stream banks, and excessive algae growth. You can find 

more information on sediment at http://www.epa.gov/bioindicators/aquatic/sediment.html. Turbidity data should be 

collected in lakes and reservoirs using a Secchi disc method, kits, probes, or meters. In streams, turbidity data 

should be collected using a turbidity tube, kits, probes, or meters. 

Total phosphorus: Phosphorus is an essential nutrient for plants and animals, which is why it is often an 

ingredient in fertilizers. Because it is naturally in short supply (i.e., the “limiting nutrient”) in most fresh water 

bodies, even small increases in phosphorus can cause undesirable consequences such as algae blooms, 

accelerated plant growth, and low dissolved oxygen (decomposition of additional vegetation will consume more 

oxygen). Phosphorus is considered limiting in most fresh water systems because it is not as abundant as carbon 

and nitrogen, which are available in the atmosphere. Sources of phosphorus include soil and rocks, wastewater 

treatment plants, runoff from fertilized lawns and cropland, runoff from animal manure storage areas, disturbed 

land areas, drained wetlands, water treatment, decomposition of organic matter, and commercial cleaning 

preparations. Total phosphorus and ortho-phosphorus may be measured using kits, probes, or meters, or by using a 

contract laboratory. 

4-12 
Total nitrogen: Plants and animals need nitrogen, but excess nitrogen can cause low levels of dissolved oxygen 

and alter the types of plants and animals in the water body. The forms of nitrogen most commonly found in water 

are ammonia, nitrates, and nitrites. Sources include wastewater treatment plants, runoff from fertilized lawns and 

croplands, failing septic systems, runoff from animal manure and storage areas, and industrial discharges that 

contain corrosion inhibitors. Total nitrogen may be measured using kits, probes, or meters, or by using a contract 

laboratory. Total nitrogen is the sum of total kjeldahl nitrogen (TKN), ammonia, and nitrate-nitrite. It can be 

derived by monitoring for TKN, ammonia, and nitrate-nitrite individually and adding the components together, but 

you can also measure total nitrogen directly using kits readily available on the market. 

Macroinvertebrates: Macroinvertebrates are indicators 

of the biological integrity of a water body. The numbers of 

certain species in a water body can be compared to 

established indices to determine the health of a stream. 

Macroinvertebrates respond to different stressors in 

different ways, so it is often possible to use the 

macroinvertebrate population to determine what kinds of 

stressors are affecting the water body. Depending on your 

program’s characteristics and capabilities, you can use 

different methods to measure macroinvertebrates. Methods 

range in complexity from using a net and manually counting 

macroinvertebrates to using a laboratory to conduct 

population analyses. Work with your EPA regional office to 

establish which method you should use. EPA recommends 

a multihabitat approach using a D-frame net (500-micron 

opening mesh) collecting, counting, and identifying a 

minimum of 200 macroinvertebrates. Family-level ID (and 

in some cases species-level ID) is ultimately expected, but 

starting at the order level is acceptable for programs that 

have not previously collected macroinvertebrate data. 

Many local nonprofit or state agencies offer free training 

on macroinvertebrate identification, as well as QA/QC 

certification. EPA encourages tribes to target collecting 

data on at least two assemblages (e.g., macroinvertebrates 

and fish), and developing baseline condition information for 

their biological sampling programs. Several additional 

acceptable collection methods are described in EPA’s 

Rapid Bioassessment Protocols for Use in Wadeable 

Streams and Rivers: Periphython, Benthic, Macroinvertebrates, and Fish, Second Edition, available online at 

http://www.epa.gov/owow/monitoring/rbp/, and chapter 4 of EPA’s Volunteer Stream Monitoring: A Methods 

Manual, available online at http://www.epa.gov/owow/monitoring/volunteer/stream/. Other user-friendly 

macroinvertebrate identification guides include Aquatic Entomology: The Fishermen’s and Ecologists’ 

Illustrated Guide to Insects and their Relatives (McCafferty, W.P.; Boston, MA; Science Books International; 

1981) and A Guide to Common Freshwater Invertebrates in North America (Voshell, J.R.; Blackburg, VA; The 

McDonald & Woodward Publishing Company; 2002). 

Macroinvertebrate Sampling. Photograph courtesy of Gila 

River Indian Community. 

4-13 
E. coli or enterococci: E. coli and enterococci are used as indicators of the presence of pathogens in drinking 

and recreational waters. They indicate the possible presence of disease-causing bacteria, viruses, and protozoans. 

If pathogens are present, fishing and swimming in the water may cause health risks. These pathogens can also 

cause cloudy water, unpleasant odors, and increased oxygen demand (reducing levels of dissolved oxygen). 

Sources of bacteria include wastewater treatment plants, septic systems, stormwater runoff, animal carcasses, 

and runoff from animal manure and manure storage areas. You can find more information about pathogens at 

EPA’s Agriculture 101 Web site, http://www.epa.gov/agriculture/ag101/impactpathogens.html. Enterococci levels 

should be monitored in marine and fresh waters. E. coli levels should be monitored in fresh waters. E. coli and 

enterococci levels can be measured using any of the kits readily available on the market and an incubator. 

Samples can also be collected and sent to a laboratory for analysis. The APHA Standard Methods manual 

referenced above and EPA’s Microbiology Web site (http://www.epa.gov/nerlcwww/) provide EPA-approved 

standard methods and examples of test kit use. You can also review Web sites of major national vendors. 

Basic habitat information: Basic habitat information refers to physical attributes of a water body and its 

surrounding area that influence its condition. Physical habitat varies naturally, as do biological and chemical 

characteristics. Degradation of aquatic habitats by human activities, however, is recognized as one of the major 

causes of water pollution and water quality impairment. More information on basic habitat information measures 

can be found in chapter 4 of EPA’s Volunteer Stream Monitoring: A Methods Manual, available online at http:// 

www.epa.gov/owow/monitoring/volunteer/ 

stream/, and in EPA’s Rapid Bioassessment 

Protocols for Use in Wadeable Streams 

and Rivers: Periphython, Benthic, 

Macroinvertebrates, and Fish, Second 

Edition, available online at http:// 

www.epa.gov/owow/monitoring/rbp/. These 

manuals describe several habitat assessment 

methods. Any of the methods listed for 

habitat assessment are acceptable, but EPA 

expects that tribes will progress from 

simpler methods to more complete 

assessments as programs mature. State 

agencies may have modified EPA’s 

protocols to develop habitat assessment 

procedures on an ecoregion basis (or other 

scale). Many states have placed monitoring 

protocols and documents on their agency 

Web sites. These tools may be useful for 

tribal programs. 

C. Determine Monitoring Frequency of Each WQI/Parameter 

When determining the monitoring frequency for each WQI/parameter, certain factors should be considered, 

including cost, time, resources, accessibility of monitoring site(s), seasonal flows and conditions, and the 

significance of each WQI. Conditions in water bodies change over the course of a day, from season to season, 

and from year to year (page 19 of Listening to Watersheds has examples of how water quality conditions can 

vary based on when you collect your samples). These changes can be the result of natural variability (e.g., 

seasonal change, drought) or variability caused by human activity (e.g., construction, agriculture). Pages 41-44 of 

Listening to Watersheds contain some general information that will help you decide when and how often to 

collect your monitoring samples. Be sure to take into account index condition considerations as appropriate. For 

example, threshold values for trophic state indices and biological metrics can be calibrated to specific periods of 

time. 

Slump erosion, Nemadji River Basin Wisconsin, USDA Natural Resources 

Conservation Service. Photo courtesy of the EPA Great Lakes National 

Program Office. 

4-14 
D. Select Monitoring Sites 

The approach to selecting the water bodies that will be monitored and the monitoring locations within each water 

body should fall into one of the three categories described below. The census and probability-based approaches 

may be most appropriate for tribes with more mature water quality programs, but you should use whichever 

approach makes most sense for your program given its goals and the resources you have available. 

z Census: This approach means every water body on a reservation will be monitored. 

z Probability-based monitoring: In this approach, your survey design will be based on some form of 

random selection of sites or sampling location. This approach eliminates the potential for sampling bias 

towards waters with known problems. A probability-based design allows the extrapolation from a relatively 

small sample of monitored sites to the entire population of water body types covered by the design. 

z Judgmental or targeted assessment: In this approach, you will place monitoring sites at specific 

locations to meet a pre-determined purpose. Each site is selected on the basis of specific requirements that 

meet monitoring objectives. The selection process may consider environmental features (e.g., flow), 

human population densities, and ease of access to the site. 

Use the approach that most closely reflects your monitoring objectives, taking resource and time considerations 

into account. Pages 29-37 of Listening to Watersheds contain information on selecting monitoring sites. 

E. Determine How Monitoring Data Will Be Used and Displayed 

To determine how you will use and display your monitoring data, you should consider how it will help you measure 

your progress in meeting your monitoring objectives, identify trends, and address water quality concerns. You also 

may want to consider your target audience(s). See section I.3 of this chapter for more information on data use 

and data display. 

c. Developing Standard Operating Procedures 

Once you have decided what parameters you will monitor and where you will collect your monitoring data, you 

should decide when and how often you will collect your samples and develop proper procedures for sample 

collection, storage, preservation, tracking, chain of custody, QA, and analysis. You will also need to set procedures 

for sampling equipment maintenance, including calibration. These procedures are known as standard operating 

procedures (SOPs). SOPs are documents that describe 

activities that are of a routine and/or repetitive nature. 

Their objective is to achieve consistency and uniformity 

when performing tasks. They are also useful in training 

staff. Your SOPs should include procedures for every 

parameter you are monitoring, including parameters 

measured on-site using field instruments (e.g., water 

temperature, stream flow) and parameters measured in 

a tribal laboratory (e.g., total solids). Laboratories also 

use SOPs in their work, and in some cases it may be 

useful for the tribe to review commercial laboratories’ 

SOPs as they may contain quality control information 

not found in the laboratories’ QA plans. If you need to 

use an outside commercial laboratory, other tribes in 

your region can help you identify qualified labs in your 

area that may be able to provide sample analysis. 

Penobscot Indian Nation Department of Natural Resources 

staff cross-checking calibration of dissolved oxygen meters 

before sampling Penobscot River. Photo courtesy of the 

Penobscot Indian Nation. 

4-15 
EPA has developed methods manuals for many types of monitoring. The manuals include general information for 

monitoring all parameters as well as parameter-specific information on sampling and equipment considerations 

and proper collection and analysis procedures. You should use these methods manuals to help you develop your 

SOPs. These documents are available online at http://www.epa.gov/owow/monitoring/volunteer/. 

Wetlands Monitoring 

Because of their composition, wetlands are more complicated to monitor than most surface water bodies. 

Wetlands monitoring consists of several components: 

z Establishing baseline condition of wetlands, including their extent and condition 

z Measuring the physical and chemical properties of the wetland, including pH, color, turbidity, dissolved 

oxygen, total phosphorus, and sediment samples 

z Determining the hydrogeomorphic setting and function 

z Cataloguing biodiversity, the presence of rare or endangered species, and items of cultural significance 

z Inventorying local contamination sources, such as stormwater culverts and septic fields 

Tribes conducting wetlands monitoring should consult EPA Region 9’s Wetlands Quality Assurance Project 

Plan Guidance, available online at http://www.epa.gov/Region9/qa/pdfs/wetlandsqapp-04.pdf, which is 

designed to assist in documenting procedural and data requirements for projects involving environmental 

measurements and wetlands monitoring. For information on beginning a wetlands monitoring program, refer to 

Volunteer Wetland Monitoring: An Introduction and Resource Guide (EPA 843-B-00-001) at http:// 

www.epa.gov/owow/wetlands/monitor. 

d. Developing QAPPs 

All EPA-funded projects for the collection of data must have an EPA-approved QAPP before any monitoring 

activities may begin. As noted above, the QAPP is a written document that outlines the procedures that a 

monitoring project will use to ensure that the samples collected and analyzed, the data stored and managed, and 

the reports produced are of sufficient quality to meet project needs. QAPPs cover monitoring, data management, 

and data analysis and assessment activities. 

Your QAPP must include data quality objectives (DQOs). DQOs are the qualitative and quantitative statements 

that clarify study objectives, define the appropriate type of data to meet the objectives, and specify tolerable levels 

of potential decision errors that will be used as the basis for establishing the quality and quantity of data needed to 

support decisions. DQOs define the performance criteria that limit the probabilities of making decision errors by 

considering the purpose of collecting data, defining the appropriate type of data needed, and specifying tolerable 

probabilities of making decision errors. 

Use the Web sites listed on page 4-4 and contact your EPA regional office and quality assurance manager for 

more information on developing your QAPP. EPA’s Guidance for the Data Quality Objectives Process (EPA 

600/R-96/055), available online at http://www.epa.gov/quality/qs-docs/g4-final.pdf, contains more information on 

DQOs. 

e. Analyzing Monitoring Samples Using Outside Laboratories 

In some cases, you may lack the in-house expertise or equipment to analyze some water quality samples or 

perform taxonomic identification and enumeration of biological samples. In these cases, you will have to send your 

samples to an outside laboratory for analysis. You should develop SOPs to document how you will track samples 

that you ship to laboratories, including chain-of-custody procedures and procedures for field crews to follow when 

collecting, transferring, storing, and shipping samples. These SOPs should be included with the tribe’s QAPP. If 

SOPs are not developed, the tribe should document how these activities will be carried out in its QAPP. 

4-16 
From Integrating Quality Assurance into Tribal Water Programs, EPA Region 8 Water 

Management Division, Water Quality Branch, page 8: 

When choosing a laboratory for analyzing your water quality samples, it is best to conduct interviews. 

Provide the laboratory with a list of questions regarding the analyses you anticipate you will need and talk 

directly with the laboratory manager. When you develop a contract, include a specific period of time that the 

contract will cover, the scope of work (including materials the laboratory will furnish), terms for payment, a 

provision for giving both the tribe and EPA the right to audit the laboratory, and other terms and conditions 

as required or recommended by the tribal program. Make sure to agree on turnaround time in advance. 

When contracting with a laboratory, make sure you get a copy of its QA/QC plan and include it as an 

appendix to your QAPP. 

You should also discuss the format in which your laboratory will provide your monitoring results. Discuss if 

the lab can supply the data in a format compatible with your data management system or STORET. You will 

need to report certain data elements in a STORET-compatible format; receiving results from your lab in this 

format will reduce your data management burden. See chapter 8 for more information on data reporting 

requirements. 

f. Submitting your QAPP for EPA Review and Approval 

Once you have established what parameters you will monitor, how and when you will collect samples, and what 

procedures you will use to handle your samples, and have incorporated them into your QAPP, you should submit 

your QAPP to your EPA grant project officer, who will forward it to the appropriate regional staff for review and 

approval (EPA Order 5360.1 A2). Upon EPA approval, you should begin implementing your monitoring program. 

To the extent possible, you should utilize the design, implementation plan, and sample collection procedures you 

have developed. If you do not follow your procedures, you may find that the quality of your data does not meet 

your expectations or that you do not have enough data for your analysis and assessment activities. 

Over time, you may find that you need to modify or refine your monitoring program to address new water quality 

issues or concerns. For example, you may need to update your sample collection procedures to include new 

parameters. Section II.1 of this chapter contains more information on considerations for updating your monitoring 

procedures. 

g. Incorporating Your Monitoring Results into Your Community Outreach 

Program 

If you are conducting any public outreach activities (discussed in section I.12 of chapter 3), use monitoring data to 

reinforce your message. You should use the data analysis tools discussed in section 3, below, to summarize and 

report data in a way that makes sense to your community. Your community is more likely to share your concerns 

or understand your accomplishments if you can provide quantitative data that support your claims. If you have not 

yet begun to conduct public outreach, consider reporting your monitoring results to your community. 

2. Data Management 

Monitoring data will not be especially useful to your program unless you are able to store your results (and 

information about your results) in a format that allows you to manipulate, summarize, and analyze them. The 

process of converting your monitoring results into a useful set of data that you can use to make decisions about 

your program is known as data management. This section provides information on managing your data, including 

how to compile useful data sets, store and manage your data in an electronic format, validate your data, and 

report your results. Pages 71-73 of Listening to Watersheds also contain information on data management. 

4-17 
a. Understanding Metadata and Compiling Useful Data Sets 

Metadata are “data about data,” that is, information about a specific water quality sample that helps to provide 

context for the sampling activity. Metadata contain information about when, where, why, and how a water quality 

sample was collected. Recording metadata is important for a number of reasons: 

z Metadata help you improve your analysis of water quality conditions. As noted in section I.1.b of this 

chapter, conditions in water bodies change over the course of a day, from season to season, and from year 

to year. If you do not have information that helps you identify the context for your samples, you will not be 

able to make comparisons among water bodies or across time. 

z Metadata increase the validity of your results. The more information you can provide about the 

circumstances surrounding a water quality result, the more weight your reports will carry. 

z Metadata can help you understand unexplained or unusual results. For example, if you knew when a 

sample was collected, you could tie an unexpectedly high result to a reported spill. 

z Although you collect water quality samples to help meet your current goals and objectives, you may want 

to use the data for different purposes in the future. To decide whether you can use the data for other 

purposes, you will need to understand the context in which the sample was originally collected. 

z The technician who collects a water sample and the staff of your program at the time of sample collection 

know when, where, how, and why they are monitoring, but as time passes and staff change, that 

information will be lost unless you track it. Collecting metadata will help future program staff members 

better understand past data. 

z If you share your data with any other tribal entity, EPA regional offices, or states, metadata will make the 

sample results more useful to them. 

When monitoring, you should record metadata such as the location where you collected each sample (e.g., 

longitude and latitude, water body), the conditions at the time of collection (e.g., water temperature, flow, 

atmospheric conditions), units for each parameter, replicate information, and the date and time. Also record 

information such as the reason you collected the sample (e.g., to determine if phosphorus poses a threat to a 

particular water body), what method you used to analyze the sample, and the method’s detection limit. EPA 

Headquarters will work with tribes and EPA regional offices to develop a standard format for data reporting, 

including metadata. Standard templates will be available through EPA regional offices before tribes begin to 

implement the reporting requirements outlined in this document. 

What is Georeferencing? 

Georeferencing describes the process of locating an event according to its latitude and longitude. 

Georeferencing has become more prominent in recent years due to the increasing availability of Global 

Positioning Systems (GPS) and Geographic Information System (GIS) tools designed to facilitate this process. 

GPS units allow technicians in the field to determine the latitude and longitude of a position. Once a water 

body has been georeferenced using a GPS unit, the data can be entered into the GIS, which is a computer 

system for capturing, storing, manipulating, analyzing, and displaying data related to positions on the Earth’s 

surface. Once a water body has been georeferenced, the relationship between it and its location can be used 

to map and display information about it. Using GIS tools to analyze data can help you spot and track 

information related to a water body’s location. Visit http://www.epa.gov/owow/monitoring/georef/ for more 

information on georeferencing. 

4-18 
b. Developing Electronic Data Storage Capacity 

To use and analyze your data effectively, you should store data in a way that allows them to be easily organized, 

summarized, and manipulated. Electronic spreadsheets will allow you to easily store data. Many spreadsheetbased software programs you can use for this purpose are commercially available. Some of these programs also 

include tools (e.g., graph-building, calculator, and modeling functions) that will help you analyze, manipulate, and 

report your data. Pages 71-90 of Listening to Watersheds provide more information on electronic data storage. 

Depending on your familiarity with computers, you may want to take a basic spreadsheet or database training 

course. You can find courses through local community colleges, night classes at high schools, or commercial 

computer training centers. 

EPA expects that all required tribal data ultimately will be submitted to its water quality data warehouse but 

recognizes that in many cases tribes lack the financial and technical resources to upload their data. In these cases, 

EPA will assist tribes with the process. 

c. Managing Electronic Data 

Once you can store your data electronically, you should develop procedures to manage your electronic data. 

Procedures should include information on: 

z Checking field and lab forms for accuracy and completeness 

z Entering the information into your electronic software program 

z Evaluating data and producing reports 

z Reviewing data after entry 

z Backing up electronic data 

Backing Up Electronic Data 

You need to back up your data regularly to make sure that you do not lose information if your electronic files 

are lost or destroyed because of a computer failure, software problem, or user error. You can back up data in 

a number of ways, such as copying the information to a CD, external hard drive, or flash drive or by 

electronically transmitting your data to another computer. You should store a backup copy of your data offsite 

to prevent loss in case your office is damaged. Some computer systems include built-in backup tools. Consult 

the user manual for your computer to see if your system includes this capability. 

EPA’s STORET water quality data warehouse can also serve as an off-site data repository. Tribes should

consider reporting as much data as possible to make sure that the data are not lost if their internal data

management system fails.

4-19 
d. Performing Data Validation as Part of Your QA/QC Plan 

You should establish a procedure for reviewing your data and making decisions about accepting, rejecting, or 

qualifying them. Procedures can include: 

z Comparing entries from field data sheets to information entered into your electronic spreadsheets 

z Looking for data gaps 

z Examining results for unexpectedly high or low results 

z Checking calculations 

z Correcting errors 

z Comparing project data to specified QA/QC criteria 

z Calculating precision and accuracy of instruments, placing this information in your metadata file, and 

submitting this data to EPA 

z Reviewing field data sheets for completeness and accuracy before leaving the field 

z Reviewing QC sample results to ensure acceptance criteria (either established by the tribe or defined in 

the laboratory’s QA plan and SOPs) were met 

You should include this information in your QAPP. Chapter 4 of EPA’s The Volunteer Monitor’s Guide to QAPP 

contains more information on data validation and QAPPs. Your data should be validated according to your 

procedures before you submit it to EPA. 

e. Reporting Data to EPA 

Your region will require you to submit certain data elements to EPA based on the agreed upon schedule and 

format in your work plan. In addition, you will be required to submit your data in an electronic format agreed upon 

with your EPA regional office. Standard templates for data reporting will be available through EPA regional 

offices. You will also be required to submit an Assessment Report to EPA to demonstrate how you have 

interpreted your data to meet your objectives. See chapter 8 for more information on these reporting 

requirements. 

3. Data Assessment and Analysis 

a. Developing Data Assessment and Analysis Capabilities 

Monitoring results cannot be used with confidence unless you assess your data. Data assessment is the process 

in which you evaluate field, lab, and data management activities, organizations (e.g., labs), and personnel. The 

assessment can include evaluations of performance (e.g., sample collection techniques), systems (e.g., equipment 

and analytical procedures), and data quality (e.g., comparisons of actual data results with project quality 

objectives). You should decide ahead of time how your program will correct any problems that you identify during 

your assessments. Corrective actions could include calibrating equipment more frequently or providing more 

training to your staff. 

Data analysis is the process through which monitoring results are evaluated to determine what they reveal about 

the condition of a water body. You will need to summarize your data and put them into a manageable form to 

prepare it for analysis. 

4-20 
Data analysis should provide answers that address monitoring objectives and goals. During data analysis, you 

should also evaluate whether you need more or different kinds of data. Listening to Watersheds lists some 

typical ways in which data are analyzed, including: 

z Status: comparing indicators against WQS or water quality goals you have established for a water body 

z Trends: comparing an indicator or indicators at one site over time 

z Site comparison: comparing an indicator or indicators at different sites at the same time 

Pages 75-90 of Listening to Watersheds have more information on data assessment and data analysis. 

b. Developing Data Display Capabilities 

You may find visual displays of the results of your analysis useful in understanding your data and presenting it to 

your community. As noted above, many software packages used to store data can quickly and easily produce 

graphic displays such as bar graphs, line graphs, and pie charts. Pages 78-80 of Listening to Watersheds have 

more information on developing charts and graphs. 

c. Using Data to Understand Problem Areas and Trends 

i. Using Data from Additional Sources 

Your monitoring data are not the only data you can use to evaluate the condition of your water bodies. If available, 

incorporate other data such as the water body’s geological characteristics, beach closures, fish consumption 

advisories, fish kills, and data from upstream and downstream states or tribes into your analysis. You can consult 

the organizations listed in section I.4 of chapter 3 or other environmental programs within your tribe to obtain this 

information. If your tribe has completed a source water assessment for its public water supplies, you can also use 

it as a resource. In addition, EPA maintains a number of databases containing data related to water quality online. 

You can access these databases at http://www.epa.gov/owow/data.html. EPA’s Surf Your Watershed Web site 

(http://www.epa.gov/surf/) also can help you locate and use environmental information about your watershed. 

Note that if data from secondary sources are used in decision making, then the tribe’s QAPP must include a 

discussion of how the data from the secondary source will be reviewed and determined suitable for the purpose 

for which the tribe intends to use it. 

Once you have reviewed all of the available data, including your monitoring results, you should understand some 

of the problems facing your water resources. The next sections will help you identify possible causes of problems 

and sources of pollution. 

ii. Understanding Common Causes of Water Quality Problems 

A number of factors can contribute to water quality problems in surface water and ground water. In addition to 

the parameters listed in section I.1.b of this chapter, some additional common pollutants and stressors include: 

Metals: Metals can reduce reproductive success, prevent proper growth and development, and even kill fish and 

shellfish. In addition, some metals accumulate in fish and shellfish, affecting humans, animals, and birds that eat 

them. More information on metals is available online at http://www.epa.gov/bioindicators/aquatic/pollution.html. 

4-21 
Monitoring Activities on the Southern Ute Indian Reservation 

The southwestern region of the United States has been experiencing extreme drought and fire conditions 

and as such, the Missionary Ridge Fire Complex affected La Plata County, Colorado, where the Southern 

Ute Indian Reservation is located, during summer 2002. 

An initial Burn Area Emergency Rehabilitation (BAER) report was completed and at that time a total of 

$39.8 million was expended for fire suppression and air support (USFS BAER Report, July 2002). At that 

time mitigation measures were initiated by the BAER Mitigation Team to minimize the impact to the Animas, 

Florida, and Pine Rivers when the monsoon pattern began. Unfortunately, all three rivers were impacted 

with heavy sediment loading as a result of numerous mudslides that occurred and are still occurring within 

the burn area. Current water uses on these streams include Tribal and non-member agricultural and 

domestic uses. The State of Colorado has designated the Pine, Florida, and Animas Rivers as agriculture 

and drinking water supply, Aquatic Cold I, and Recreation I. 

Along with the sediment and organic matter being washed into the streams from the burned areas, the 

drought has resulted in low flows, and thus indications of nutrient enrichment on the Pine and Animas 

Rivers. WQ staff have witnessed water quality impacts such as ash and debris material within the Pine, 

Florida, and Animas Rivers and have been monitoring for macroinvertebrates, dissolved oxygen, turbidity, 

pH, conductivity, temperature, pebble counts, and measures of embeddedness since the fire was officially 

contained in July 2002. 

For the long-term monitoring program, it is important 

that the effects of the fire and drought be distinguished 

from anthropogenic effects. Monitoring for the effects 

of the fire is conducted in parallel with monitoring for 

the effects of nutrient enrichment. Tribal WQ staff are 

participating with other entities such as EPA Regions 6 

and 8, Bureau of Reclamation (BOR), Ute Mountain 

Ute Tribe, New Mexico’s Surface Water Quality 

Bureau (SWQB), Colorado Department of Public 

Health and Environment (CDPH&E), Colorado 

Department of Wildlife (CDOW), and several special 

interest groups to address this issue on the Animas 

River. 

To complete a comprehensive study of the long-term 

impact of fire and anthropogenic effects, monitoring 

has been conducted and will continue for a number of 

years. Based on document searches and long-term 

research of the effects of fires on un-dammed streams conducted in Idaho and Yellowstone National Park, 

the effects of Missionary Ridge fires may be observed for approximately 8 to 10 years. 

The successful development of the EPA-funded Southern Ute Tribal Water Quality Program laid the 

foundation for participation in this project. The Tribe provided valuable insight, access, and water quality 

data that would not have been available to this emergency response team without years of sustained water 

quality data collection and management by the Southern Utes. The Southern Utes have proven themselves as 

leaders in tribal water quality data collection and assessment, and their expertise have been invaluable in the 

Missionary Ridge Fire Complex BAER Team post-fire assessment. 

Ashy sediment clogged irrigation diversions and 

embedded aquatic habitat. Photograph courtesy of EPA 

Region 8. 

4-22 
Pesticides: Pesticides are organic compounds that are used in agriculture, animal feeding operations, and other 

activities. Pesticides are toxic to many animals and may bioaccumulate in the environment. Any use of pesticides 

in or near surface water bodies or aquifer recharge areas may lead to residues in water, fish, and shellfish. 

Sources of pesticides include crop and urban runoff. You can find more information about pesticides at EPA’s 

Office of Prevention, Pesticides, and Toxic Substances Web site, http://www.epa.gov/oppts/ and EPA’s Office of 

Pesticide Programs Web site, http://www.epa.gov/pesticides/. 

Salinity: Salinity is a measure of the total salt content in water. Excess salinity can affect wildlife and the 

suitability of water for drinking. Agricultural irrigation can cause excess salinity. Urban and industrial uses can 

also cause salinity problems. Salt water intrusion into fresh water sources is a related problem. Salinity 

measurements are often included in measurements of Total Dissolved Solids (TDS). For more information on 

salinity, see http://www.epa.gov/watrhome/you/salty.html. 

Flow Alterations: Activities such as dam construction and water withdrawals can alter the natural water flow. 

Flow alteration threatens water bodies in different ways. Reduced flows impair the ability of water bodies to flush 

out nutrients and organic matter, thereby increasing contaminant concentrations. In addition, lower water levels 

can also affect aquatic species that require specific water levels to survive. Problems such as degradation of river 

and stream bottoms may also occur when water flow increases. Impervious surfaces can limit ground water 

recharge, diminishing the quantity of ground water available for use and/or increasing the cost of obtaining ground 

water. More information on flow alterations is available online at http://www.epa.gov/bioindicators/aquatic/ 

hydrology.html. 

iii. Understanding Common Sources of Impairment 

EPA’s guidance for tribal water quality reporting, Knowing Our Waters: Tribal Reporting under Section 

305(b), identifies the most common sources of water quality impairments. These activities (listed below) can 

potentially cause the impairments listed in the previous section: 

Channelization: Changes created by channelization and channel modification can be problematic if they alter 

environmental conditions. Channel modification can change the natural flow of water as well as water 

temperature and sediment characteristics, which in turn can affect water quality and the wildlife in the water 

body. More information on channelization is available online at http://www.epa.gov/owow/nps/MMGI/Chapter6/ 

ch6-2a.html. 

Feedlots: Animal wastes from large, industrial feedlot operations are among the greatest threats to our nation’s 

waters. Oxygen-demanding substances, ammonia, nutrients (including nitrogen and phosphorus), solids, pathogens, 

and odorous compounds are the pollutants most commonly associated with animal waste. Manure is also a 

potential source of salts, trace metals, and, to a lesser extent, antibiotics, pesticides, and hormones. Animal waste 

and wastewater can enter water bodies from spills or breaks of waste storage structures (due to accidents or 

excessive rain). More information is available online at http://cfpub1.epa.gov/npdes/home.cfm?program_id=7. 

Irrigated Cropland: Irrigation waters transported in open, unlined canals can seep into adjacent soils, eventually 

carrying soluble pollutants into ground or surface waters. Too much irrigation results in a portion of applied waters 

running off the land into surface waters or seeping through the soil and eventually ending up in surface or ground 

waters. Pollutants carried by irrigation waters can include sediment and organic solids, nutrients (including 

nitrogen and phosphorus), chemicals, metals, a portion of the applied pesticides, salts, bacteria, viruses, and other 

microorganisms. You can find more information on irrigated croplands online at http://www.epa.gov/ow/you/ 

chap2.html. 

4-23 
Land Disposal of Hazardous Waste: Currently, about 23 million tons of hazardous waste are disposed of on 

land each year. Land disposal can be either in or on the ground — in a landfill, injection well, or other land-based 

unit. Even though landfill units are equipped with safeguards, when hazardous waste is not properly treated before 

land disposal, it can contaminate ground water. Rain can penetrate and pass through hazardous waste and can 

leach out and carry hazardous chemicals into the ground water. For more information, see EPA’s Web site on land 

disposal, http://www.epa.gov/epaoswer/hazwaste/ldr/snapshot.htm. 

Municipal Discharges: Wastewater is considered a potential source of pollution because it may — especially if 

it is untreated or only partially treated — contain organic and inorganic materials that can be hazardous to humans 

and other life forms. Treated, untreated, or partially treated wastewater may also contain small amounts of 

radiation or toxics that increase the temperature of waters, affecting aquatic wildlife and habitat. Discharged 

wastewater, especially if it is untreated or partially treated, may reduce the amount of dissolved oxygen in the 

receiving stream and can be a source of E. coli, enterococci, and other pathogens. For more information on 

wastewater management and municipal discharges, visit EPA’s Office of Wastewater Management (OWM) Web 

site, http://www.epa.gov/owm/. 

Pastureland: Overgrazing exposes soils, increases erosion, encourages invasion by undesirable plants, and 

reduces the filtration of sediment necessary for building streambanks, wet meadows, and floodplains. This may 

result in nutrient runoff and sediment deposition in nearby waterways. You can find more information on 

pastureland and other potential sources of agricultural pollution at http://www.epa.gov/region08/water/nps/ 

npsag.html. 

Forestry: Studies show that a timber harvest 

disturbs 8-10 percent of the total area in road 

construction and landing sites. These areas can 

contribute to erosion, soil loss, and sedimentation. 

Forestry can also increase water flow through 

cleared sites and cause erosion along 

streambanks. EPA’s NPS Web site (http:// 

www.epa.gov/owow/nps/forestry.html) contains 

more information on forestry. 

Streambank Modification: Shoreline and 

streambank erosion can result in excessively high 

sediment loads and increased turbidity and 

nutrient levels that can adversely affect aquatic 

vegetation, shellfish beds, and tidal flats. More 

information on streambank modification is 

available online at http://www.epa.gov/ 

bioindicators/aquatic/hydrology.html. 

Surface Mining: Mining creates acid mine drainage, a metal-rich water formed from the chemical reaction 

between water and rocks containing sulfur-bearing minerals. The runoff formed is usually acidic and frequently 

comes from areas where ore or coal mining activities have exposed rocks containing pyrite, a sulfur-bearing 

mineral. Metal-rich drainage can also occur in mineralized areas that have not been mined. Mine drainage can 

contaminate drinking water and disrupt the growth and reproduction of aquatic plants and animals. For more 

information on mining, see EPA’s NPS Web site, http://www.epa.gov/region3/acidification/what_is_amd.htm. 

Loading logs on truck for transport to milling plant, Superior National Forest 

Minnesota USDA Forest Service, Superior National Forest. Photo courtesy 

of the EPA Great Lakes National Program Office. 

4-24 
4. Initiating Mitigation Measures for Known Water Quality Problems 

Once you have a grasp of possible causes and sources of water quality problems in your water bodies, you can 

begin to address them. If the problems stem from point source dischargers (e.g., industrial facilities or publicly 

owned treatment works), the discharges can be regulated through National Pollutant Discharge Elimination 

System (NPDES) permits. See section III.5 of chapter 7 for more information about the NPDES program. If a 

variety of sources are causing the problem, NPS pollution can be controlled through management measures. NPS 

and management measures are discussed in chapter 5. Remember that structural management measures and 

management measures requiring construction are not allowable activities under Section 106 grants. 

In many cases, (e.g., if facilities or events occurring upstream and/or on private property over which the tribe has 

no control are contributing to a water quality problem), the causes and sources of impairment may be difficult for 

tribes to address. In these cases, tribes may wish to cooperate with other local governments and consider 

implementing a watershed-based plan or other NPS control activities. 

Mitigation Measures for Ground Water 

Many tribes obtain much of their drinking water from ground water wells and therefore monitor and sample 

their ground water to determine its quality. Samples from these wells can help tribes that rely on ground 

water to understand its characteristics and quality. Several tribes whose monitoring results revealed ground 

water contamination have developed wellhead protection programs. Wellhead protection programs are 

programs designed to protect the “wellhead”—the surface and sub-surface area surrounding a ground 

water well—from contaminants. Wellhead contamination comes from a variety of sources, including septic 

tanks, landfills, animal waste lagoons, and agricultural runoff. Identifying wellhead areas and developing 

management strategies to protect them are critical activities for tribes that rely on ground water. 

Source Water Assessment Programs (SWAP) are another effective component of ground water protection. 

Source water assessments consist of delineating a source water protection area, conducting a contaminant 

source inventory, determining the susceptibility of the public water supply to contamination from the 

inventoried sources, and releasing the results of the assessment to the public. For more information on these 

programs, go to http://www.epa.gov/safewater/protect/swap.html. Chapter 5 contains more information on 

source water assessments. 

Even if monitoring reveals that your ground water has no substantial contamination, it is important to be 

proactive to ensure that your ground water remains pristine. 

4-25 
II. Intermediate Program Activities 

1. Monitoring 

a. Updating Monitoring Goals, Strategies, and Objectives 

As your program goals change, you should modify your monitoring goals and objectives. You should review your 

monitoring goals, strategies, and objectives during your program self-evaluation. See section I.14.b of chapter 3 

for more information on conducting a program evaluation. Use the questions presented in section I.1 of this 

chapter to determine whether you should update monitoring goals, strategies, and objectives. Remember that as 

your program matures, your goals and objectives should tie to CWA goals and objectives. See EPA’s Elements of 

a State Water Monitoring and Assessment Program for more information on CWA goals and objectives. In 

addition, consult EPA’s Guidance for the Data Quality Objectives Process (EPA QA/G-4 available online at 

http://www.epa.gov/quality/qs-docs/g4-final.pdf) for more information on defining objectives. 

b. Expanding and Refining the Baseline Monitoring Program 

As your monitoring program expands and your goals and objectives change, remember to evaluate your 

monitoring program to ensure that it is still providing the information you need. Remember that if you change any 

aspect of your monitoring program, you will need to update your QAPP and SOP documents and submit them to 

your EPA regional office for approval. 

i. Updating Monitoring Design 

As your understanding of your tribe’s water quality and the sophistication of your program increases, you may 

want to consider whether a probability-based monitoring design is applicable to your tribe (probability-based 

monitoring may not be necessary for many small tribes with few water bodies). This type of monitoring design 

relies on samples taken at a randomly selected sample of the target water bodies. The results of these samples 

are used to make statistical inferences about the distribution of values for the entire population of water bodies. 

Chapter 11 of EPA’s Consolidated Assessment and Listing Methodology (CALM) (available online at http:// 

www.epa.gov/owow/monitoring/calm/calm_ch11.pdf) contains more information on probability-based monitoring. 

You may need to alter your monitoring design if your program priorities change. For example, if you were using 

probability-based monitoring to provide a broad overview of the water quality of water bodies on your reservation 

and in the process identified a water body with pollution problems that you want to study more closely, you may 

need to incorporate targeted monitoring into your design. In addition, you may want to consider including 

effectiveness monitoring in your design. Effectiveness monitoring helps you collect water quality information to 

see if your projects resulted in improved water quality. Effectiveness monitoring will help you understand how 

well your efforts worked, whether you should continue implementing them, whether you should redesign them to 

work better, or whether you should try other measures. 

Even if your program goals have not changed, you should review your monitoring design to make sure that it 

allows you to collect the data you need. For example, if you are using targeted or probability-based monitoring, 

evaluate your monitoring data to ensure that the monitoring locations you selected best represent water resources. 

You also should begin to monitor for additional WQI to complement the priority indicators for which you already 

monitor. Additional parameters will help give you a more complete picture of water quality. They can include 

water-body-specific pollutants, ambient and sediment toxicity, health of organisms, and nutrients. Analyze your 

monitoring data and work with your EPA regional office, neighboring tribes, neighboring states, and appropriate 

federal agencies to help you identify any supplemental indicators for which you should monitor. Section I.1.b of 

this chapter provides more information on supplemental WQI. In some cases, you may also want to consider 

reducing or eliminating monitoring for some parameters at sites where your baseline data indicate that there is not 

a water pollution problem. 

4-26 
Only tribes with mature programs are required to report macroinvertebrate data to EPA. Depending on the needs 

of your program, however, you may want to begin collecting data on aquatic life earlier in program development. 

Biological assessment is an evaluation of the condition of a water body using biological surveys and other direct 

measurements of the resident biota in surface waters. In addition to helping you determine if the water body is 

supporting aquatic life, collecting biological data can help you: 

z Characterize the existence and severity of impairment to the water resource 

z Evaluate the effectiveness of control actions and restoration activities 

z Support use attainability studies and cumulative impact assessments 

z Characterize regional biotic attributes of reference conditions 

Check EPA’s Rapid Bioassessment Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic 

Macroinvertebrates, and Fish, Second Edition (Barbour, M.T., J. Gerritsen, B.D. Snyder, and J.B. Stribling; 

EPA 841-B-99-002; 1999, available online at http://www.epa.gov/owow/monitoring/rbp/) for more information on 

bioassessments. 

ii. Implementing Multiple Monitoring Designs 

As your monitoring program matures, its sophistication should increase. You should be collecting more samples, 

but you probably will not measure the same parameters for every sample. Your monitoring objectives and 

monitoring designs may vary by water body or type of water body. To address this increased complexity, you can 

organize your monitoring designs by water body type (e.g., ground water, lake, river), by watershed, by timing 

(e.g., seasonal, year-round, special study), by issue of concern (e.g., NPS pollution, point dischargers, specific 

pollutants), or by any other categorization that makes sense for your tribe. Developing multiple monitoring designs 

will give you the flexibility to shape monitoring for different water bodies in the way best suited to the objectives 

related to each water body. 

iii. Conducting Special Studies 

In collecting and analyzing monitoring data for your waters, you may identify areas of particular concern or 

interest. You may want to monitor the effects of an activity (e.g., a new construction project) on a specific water 

body. Or you may find that your monitoring program does not fully address a new program need. In situations like 

these, you should consider conducting a special study. Special studies supplement your baseline monitoring 

program and will provide you with monitoring data to answer specific questions. To carry out a successful special 

study, you should follow the procedure outlined in EPA’s Guidance for the Data Quality Objectives Process 

(EPA QA/G-4), available online at http://www.epa.gov/quality/qs-docs/g4-final.pdf. 

2. Data Management 

a. Updating and Upgrading Electronic Data Systems 

Hardware (e.g., computers, monitors) and software (e.g., spreadsheet programs, database programs) 

manufacturers often develop new and improved products that, over time, may make your existing system 

obsolete. At some point, you may need to invest in new hardware and software products. 

In addition, you should regularly check the Web sites or product centers of your hardware and software 

manufacturers to see if any upgrades are available. Many times, software manufacturers will issue product 

upgrades or modifications free of charge. 

4-27 
As the amount of data you store increases, you may find that the hardware and software tools no longer address 

all of your data management needs. If this is the case, consider upgrading to a more powerful computer with 

greater storage space or processing capacity or a more powerful software package. You may need to upgrade 

from a spreadsheet-based program to a database management system. When investing in new software, 

remember to consider how you will transfer your data from your existing system into your new software. Most 

database management systems allow you to import spreadsheets easily, but you should verify that your new 

software is compatible with your old software and make sure that you understand how to transfer your data. 

b. Incorporating Additional Monitoring Parameters 

When you expand your monitoring program, remember to modify your data management tools to account for 

those changes. If you begin to collect additional parameters, make sure that you update your data management 

procedures to include procedures for these parameters. Remember to adapt any other electronic tools you use 

(e.g., graphing tools, GIS tools) to reflect new data inputs. 

c. Using STORET or Electronically Compatible Formats 

EPA maintains a database that contains water quality information for the nation’s waters. The database, known as 

STORET, contains data collected since 1999, along with older data that have been properly documented and 

migrated. STORET contains raw biological, chemical, and physical data on surface water and ground water 

collected by federal, state, and local agencies, tribes, volunteer groups, academics, and others. All states, 

territories, and jurisdictions of the United States are represented in these systems. 

Each sampling result in STORET is accompanied by information on where the sample was taken (latitude, 

longitude, state, county, Hydrologic Unit Code, and a brief site identification), when the sample was gathered, the 

medium sampled (e.g., water, sediment, fish tissue), and the name of the organization that sponsored the 

monitoring. In addition, STORET contains information on why the data were gathered, sampling and analytical 

methods used, the laboratory that analyzed the samples, the personnel responsible for the data, and the quality 

control checks used when sampling and handling the samples. 

You will be required to submit electronic reports of certain data elements discussed in this guidance to EPA in a 

STORET-compatible format. Because of the technical challenges associated with submitting data to STORET, at 

this time EPA will not require you to report data directly to STORET. More information on reporting requirements 

is provided in chapter 8. If you would like to submit your data directly to the STORET data warehouse, you or a 

contractor must operate STORET locally. The local STORET system is a data management system with data 

entry and reporting software modules that operate on personal computers. If you are interested in using STORET 

as your water quality data repository, EPA will provide you with the system free of charge. To receive a free 

copy of STORET, call 1-800-424-9067 or send an e-mail to STORET@epa.gov. For more information, visit the 

STORET Web site, http://www.epa.gov/storet/. EPA is working on improvements to the system that will eliminate 

the need to run a local copy of STORET to submit data to the STORET central warehouse. 

d. Maintaining a Database with Graphing Capabilities 

As the amount of data that you have collected increases, making sense of it will be facilitated by electronic 

capabilities such as graphing. Graphs are useful tools to identify environmentally sensitive areas, produce historical 

water quality trends analyses, and create spatial and temporal representations of your water quality data. Some of 

the products you use to store your data may have graphing tools. A number of GIS tools that can create graphs 

are available. 

4-28 
3. Data Assessment and Analysis 

a. Evaluating Monitoring Program Effectiveness 

As noted in section I.14 of chapter 3, program evaluations are important to advancing program goals and 

objectives. As you begin to accumulate monitoring data, remember to evaluate whether your monitoring data are 

allowing you to meet your program goals. If you are not collecting the right data to achieve your goals and 

objectives, identify what additional information you will need to meet your monitoring goals and consider adjusting 

your monitoring program accordingly. 

b. Measuring Water Quality Improvement 

As you begin to implement mitigation or prevention programs to improve or protect water quality, your monitoring 

program should allow you to evaluate the results of your protection and restoration activities. For example, your 

monitoring results should enable you to determine WQS attainment for specific water bodies if you have 

developed WQS. Use your monitoring program not only as an informational tool to help you learn about the 

condition of your water resources but also as a diagnostic tool to evaluate the outcomes of your protection and 

restoration activities. 

III. Mature Program Activities 

1. Understanding and Using EPA’s “Elements” Guidance 

At this point in your program development, your monitoring program should incorporate all of the elements 

described in EPA’s Elements of a State Water Monitoring and Assessment Program. You should have many of 

these elements in place in your program already, but you may need to develop some elements to meet EPA 

requirements. The following are the ten elements you should include in your monitoring and assessment program: 

1. Monitoring Program Strategy: You should have a comprehensive monitoring program strategy that 

meets your water quality needs and addresses all tribal waters, including streams, rivers, lakes, Great 

Lakes, reservoirs, estuaries, coastal areas, wetlands, and ground water, as applicable. 

2. Monitoring Objectives: You should identify monitoring objectives that are critical to the design of a 

monitoring program that is efficient and effective at generating data that serve your decision needs. 

3. Monitoring Design: You should use an approach and rationale for selecting monitoring designs and 

sample sites that best serve your monitoring objectives. 

4. Core and Supplemental WQI: You should use a tiered approach to monitoring that includes core 

indicators selected to represent each applicable designated use, plus supplemental indicators selected 

according to site-specific or project-specific criteria. 

5. Quality Assurance: Your quality management plans and QAPPs should be established and maintained, 

and should be approved by your EPA regional office and peer reviewed according to EPA policy to make 

sure that your monitoring and laboratory activities are scientifically valid and that you are meeting all 

reporting requirements. 

4-29 
6. Data Management: You should use an accessible electronic data system for water quality, habitat, and 

biological data, enter data in a timely manner, and provide public access to your data. 

7. Data Analysis and Assessment: You should have a methodology for assessing attainment of your water 

quality goals for all water body types and all tribal waters based on analysis of various types of data (e.g., 

chemical, biological, land use) from various sources. To the extent possible, your program should include 

graphing spatial and temporal trends as a means of tracking water quality changes and identifying trends 

over time. 

8. Reporting: You should produce timely and complete water quality reports and lists called for under CWA 

Sections 303(d), 314, and 319 as applicable to your program responsibilities. 

9. Programmatic Evaluation: In consultation with your EPA regional office, you should conduct periodic 

reviews of each aspect of your monitoring program to determine how well it serves your needs for all 

tribal waters and all water body types. 

10. General Support and Infrastructure Planning: You should identify current and future resource needs to 

fully implement your monitoring program strategy. 

Refer to Elements of a State Water Monitoring and Assessment Program for more detailed information on 

these elements of a mature water quality monitoring program. 

Water quality monitoring. Photo courtesy of Gila River 

Indian Community. 

4-30 
Chapter 5: Nonregulatory

Approach

Introduction 

This chapter contains information on addressing water quality problems on a watershed basis through 

nonregulatory means, including watershed-based planning, nonpoint source (NPS) assessment reports and 

management programs, source water assessment and protection, and other voluntary programs. The information 

presented in this chapter is relevant for all tribes. Tribes that are developing regulation-based federally approved 

Activities Included in Chapter 5 

Fundamental Program Activities

1. Understanding Watershed-based Planning

2. Understanding NPS Pollution

3. Understanding Decentralized Wastewater Treatment Facilities

4. Understanding Source Water Protection

5. Choosing and Setting Water Quality Goals

6. Determining Areas with Water Quality Problems

7. Choosing and Setting Watershed-based Goals

8. Developing Projects to Meet Water Quality Goals

9. Conducting Public Outreach and Encouraging Public Involvement

Intermediate Program Activities

Tribes should begin these activities after having completed the relevant fundamental program activities.

1. Understanding Section 319 Grants

2. Section 319 Eligibility............................................................. Qualifying for TAS Eligibility for the Section 319 Program

Developing Section 319 NPS Assessment Reports

Developing Section 319 NPS Management Programs

3. Developing a Watershed-based Plan

4. Conducting a Source Water Assessment

5. Implementing Water Quality Protection and Restoration Activities

6. Implementing Section 106 Grant Activities Related to Decentralized Systems

7. Analyzing Water Quality Data and Defining Performance Measures

Mature Program Activities

Tribes should begin these activities after having completed the relevant fundamental and intermediate program activities.

1. Evaluating Restoration Activities

2. Providing Updated Information to Your Partners and Community

3. Refining Your Assessment Report, Management Program, Source Water Assessment, and Watershed-based Plan

4. Coordinating and Cooperating with Other Programs

5. Working in Partnership with Other Tribes and States

6. Other Voluntary Programs

5-1 
water quality controls or using tribal law to protect water quality could also benefit from applying the nonregulatory 

approaches described in this chapter. 

EPA has developed this approach in recognition of the fact that some tribes may lack the technical and financial 

resources to implement a regulatory program. In some cases, nonregulatory approaches may address water quality 

problems, including NPS pollution, more effectively. 

This approach uses nonregulatory water quality goals and objectives to measure program results. These goals may 

relate to the biology, chemistry, or habitat of the ecosystem and should focus on identifying the cause of the impact 

and possible ways of addressing the impact. See section I.1.a of chapter 4 for more information on goals and 

objectives. 

The tools described in this chapter can include the development of regulatory components, such as zoning 

ordinances or land use regulations, or coordination with a neighboring tribe or state in support of their regulatory 

program. The intent of this chapter, however, is to highlight nonregulatory solutions for water quality problems. 

Regulatory components will not be discussed in depth. 

Many watershed-based activities to control water pollution require “on-the-ground” restoration or construction 

activities that are not allowable activities under Section 106 grants. The discussion in this chapter is limited to 

activities that can be implemented using Section 106 funds but provides links to other grant programs that fund 

restoration or construction activities (e.g., CWA Section 319 grants). 

I. Fundamental Program Activities 

1. Understanding Watershed-based Planning 

A watershed is a geographic area in which all of the falling water drains to a common water body. Watersheds may 

be as small as a few acres or extend over thousands of square miles. Reservations often cover only part of a 

watershed. A watershed can cross tribal and state boundaries and fall under the jurisdiction of tribal, state, and local 

governments. It has been demonstrated that water quality improvements have been achieved when all the 

communities in a watershed work together. 

Watershed-based planning is a “place-based” method for maintaining, protecting, or restoring resources within a 

watershed that relies on collaboration among interested stakeholders. Working together with a diverse array of 

partners can help tribes identify and implement successful strategies to protect their waters. 

Watershed planning generally follows the steps listed below: 

Step 1: Build partnerships 

Step 2: Characterize the watershed 

Step 3: Finalize goals and identify solutions 

Step 4: Design an implementation program and assemble a watershed plan 

Step 5: Implement a watershed plan 

Step 6: Measure progress and make adjustments 

5-2 
EPA’s Watershed Planning Handbook 

EPA’s Office of Water has published a guide to watershed management to help various organizations develop 

and implement watershed plans. The Handbook for Developing Watershed Plans to Restore and Protect 

Our Waters is aimed toward communities, watershed groups, and tribal, local, state, and federal environmental 

agencies. 

The handbook is designed to supplement existing watershed planning guides that have been developed by

agencies, universities, and other nonprofit organizations by taking users through each step of the watershed

planning process (including monitoring and assessment, community outreach, selection and application of

available models, best management practices, effective databases, implementation, feedback, and plan

adjustment). The handbook is more specific than other guides about quantifying existing pollutant loads,

developing estimates of the load reductions required to meet WQS, developing effective management

measures, and tracking progress once the plan is implemented.

Available online at http://www.epa.gov/owow/nps/watershed_handbook, copies can also be ordered from the 

National Service Center for Environmental Publications. Call 1-800-490-9181 or email ncepimal@one.net. 

When ordering, please refer to EPA document number 841-B-05-005. 

Working with neighboring states and tribes on improving water quality on a watershed basis will allow you to 

address problems on your reservation that originate from activities outside of the reservation thereby improving 

the health of your watershed. Some states, tribes, or local governments may have watershed-based plans that you 

can help to implement or adapt. In some cases, you may want to enter into agreements with state and local 

governments, other agencies, or other tribes. 

EPA encourages the development of watershed-based plans to protect pristine waters and restore impacted 

waters in accordance with the requirements of the Section 319 program. Watershed-based plans provide a 

coordinating framework for solving water quality problems by providing a specific geographic focus, integrating 

partnerships, science, and data, and coordinating priority setting and integrated solutions. The watershed-based 

plan should address a large enough geographic area so that its implementation will address all of the sources and 

causes of impacts and threats to the water body in question. Where feasible, the plan should be designed to meet 

WQS. Tribes should refer to EPA’s Guidelines for Awarding Section 319 Grants to Indian Tribes, published 

each year in the Federal Register, for specific guidance in developing watershed-based plans (the guidelines will 

be made available each year on www.epa.gov/owow/nps/tribal.html when they are published). Section 106 grants 

can be used to develop watershed-based plans; however, tribes using 106 funds for this purpose should ensure 

that watershed-based plans meet programmatic requirements of the Section 319 program as described in the 

annual Guidelines for Awarding Section 319 Grants to Indian Tribes. Watershed-based plans cannot be 

implemented using Section 106 funds. 

EPA’s Office of Wetlands, Oceans, and Watersheds (OWOW) maintains a Web site with information about 

watersheds at http://www.epa.gov/owow/watershed/. OWOW has also developed a manual called the 

Community-based Watershed Management Handbook, available online at http://www.epa.gov/owow/estuaries/ 

nepprimer/handbook.htm. EPA’s Watershed Academy has developed a comprehensive Watershed Analysis and 

Management (WAM) Methodology for tribes, available online at http://www.epa.gov/owow/watershed/ 

wacademy/wam/. The Center for Watershed Protection also provides many tools and guidance materials on their 

Web site, http://www.cwp.org. In addition, the Michigan Department of Environmental Quality has written 

Developing a Watershed Management Plan for Water Quality: An Introductory Guide, available online at 

http://www.deq.state.mi.us/documents/deq-swq-nps-Watershe.pdf. These resources can help you develop an 

effective watershed-based plan. 

5-3 
The Houlton Band of Maliseet Indians 

The Houlton Band of Maliseet Indians (HBMI) is located in Aroostook County, Maine, on over 800 acres of 

reservation/trust land purchased in the late 1980s along the lower end of the Meduxnekeag River. This section 

of the river, downstream from a large portion of the watershed (and thus subject to upstream dischargers), 

can become choked with large mats of filamentous algae during the summer and turns brown with sediment 

after rainfall. 

In 1992, the Band began developing a water resources program with the Bureau of Indian Affairs (BIA) 

Water Resources Management, Planning, and Redevelopment funds to assess water quality impairments in 

the Meduxnekeag. By 1994, they were monitoring water quality for pH, dissolved oxygen, temperature, 

turbidity and conductivity. In 1995, funding from the Administration for Native Americans (ANA) 

Environmental Regulatory Enhancement program supported laboratory infrastructure and staff training to add 

alkalinity, E. coli, total suspended solids, benthic macroinvertebrates, and periphytic algae monitoring to their 

program. In 1995, the Band assisted the Maine Department of Environmental Protection’s (MDEP) data 

collection efforts in support of its Waste Load Allocation study for the River’s two dischargers. Currently, 

MDEP relies on the Band’s water quality data to set some discharge permit limits for two upstream 

dischargers. 

For the HBMI, developing a comprehensive, well-established, and reliable baseline monitoring program has 

paved the way for their water resources program to conduct special studies in partnership with other entities. 

Special studies are providing the information necessary to understand specific problems of the Meduxnekeag 

River ecosystem, notably the multiple-point and non-point causes of massive algal blooms. Ongoing study 

partners include the George Mitchell Center for Environmental and Watershed Research, University of Maine, 

and the USGS. 

The HBMI is involved in extensive nonregulatory efforts to improve water quality in the Meduxnekeag. They 

collect data to better understand the extent and underlying causes of water quality impairment and share this 

data with MDEP for use in regulatory efforts to address non-attainment in the Meduxnekeag. As part of an 

effort to ensure tribal activities do not impair water quality, they have begun developing tribal water quality 

standards that incorporate the Band’s cultural values and uses of water. This is coupled with an effort to 

develop culturally appropriate EPA-approved water quality standards to be enforced by EPA. 

5-4 
2. Understanding NPS Pollution 

NPS pollution threatens water quality in many watersheds. Unlike point sources of pollution, which generally are 

stationary, fixed facilities (e.g., wastewater treatment plants, industrial facilities) from which pollutants are 

discharged via a conveyance, NPS pollution generally is unconfined rainfall and snowmelt runoff from farms, 

lawns, landfills, streets, parking lots, and driveways that picks up natural pollutants such as sediment and topsoil 

and man-made pollutants such as pesticides, fertilizers, hazardous wastes, heavy metals, oil, and other automotive 

fluids. The rainfall and snowmelt may then flow into surface water or ground water, carrying these pollutants. 

A number of factors contribute to NPS pollution. Some of the leading contributors to NPS pollution are: 

z Agricultural activities including grazing, plowing, pesticide spraying, irrigation, fertilization, planting, and 

harvesting. Major NPS pollutants from these activities include pesticides, sediments, and excessive 

nutrients, which can occur through applications of crop fertilizers and manure from animal production 

facilities. 

z Urban development including road, bridge, building, and parking lot construction. Development can result in 

increased flows that cause stream erosion and can carry large amounts of runoff with a variety of 

pollutants including sediment from new development, oil and grease from vehicles, and nutrients and 

pesticides from turf management and gardening. Failing septic systems also carry pathogenic bacteria and 

viruses from inadequately treated sewage. 

z Hydromodification, or alteration of the hydrologic characteristics of coastal and noncoastal waters, can 

cause degradation of water resources. Hydromodification includes activities such as channelization, 

dredging, and construction of dams not covered under existing federal regulations. Excess sediment due to 

erosion can alter aquatic communities and carry other harmful pollutants into water bodies. 

z Habitat modification, including the removal of vegetation along streambanks and buffers that help filter 

runoff and provide shade to the adjacent water body. These modifications can result in an increase in 

water temperature and an increase in the quantity and velocity of runoff, making the river or stream less 

suitable for the organisms inhabiting it. 

EPA has placed a high priority on controlling NPS pollution. Because of the difficulty of tracing NPS pollution to a 

single source, Congress enacted Section 319 of the CWA, authorizing EPA to award grants to eligible states and 

tribes for the purpose of assisting them in implementing approved NPS management programs developed pursuant 

to Section 319(b). The principal goal of the NPS management control program is to control NPS pollution through 

implementation of management measures and practices to reduce pollutant loadings resulting from NPS pollution 

identified in the tribe’s assessment report developed pursuant to Section 319(a). Management measures are 

actions that your tribal environmental program, your community, or specific sectors of your community (e.g., 

farmers, builders) can take to minimize the impacts of NPS-pollution-generating activities – for example, 

restoring streambanks to prevent erosion and reduce sediment runoff or protecting wetlands to increase natural 

filtration of contaminants. Tribes can implement measures through a variety of programs, including nonregulatory 

or regulatory programs for enforcement, technical assistance, financial assistance, education, training, technology 

transfer, and demonstration projects. EPA encourages the development and implementation of watershed-based 

plans to guide implementation of management measures to achieve pollutant reductions from NPS. Remember 

that construction activities cannot be completed using Section 106 grants. 

NPS and Water Quality Impairment 

In its 2000 National Water Quality Inventory report (available online at http://www.epa.gov/305b/2000report/), 

EPA identified NPS pollution as the leading source of water quality impairment. 

5-5 
Because of the diffuse nature of NPS pollution, you will need to work with partners to implement effective NPS 

pollution control programs. Partners can include other tribal departments (e.g., fish and wildlife), neighboring 

states, local governments, EPA regional offices, other federal entities, and, perhaps most important, members of 

your community. NPS programs often rely on the voluntary implementation of management measures by all 

partners for success. Although collaboration with other entities is important in all areas of water quality protection, 

it is essential to control NPS pollution. 

Allowable NPS Control Activities 

NPS management measures requiring construction are implemented under Section 319 of the CWA and are 

thus ineligible for Section 106 funding. Section 106 funding can be used to develop NPS assessment reports 

and management programs, which are required elements when applying for Section 319 program 

authorization. Section 106 grants can also be used to develop watershed-based plans. 

3. Understanding Decentralized Wastewater Treatment Facilities 

Decentralized wastewater treatment systems (commonly called septic systems) are a significant component of 

the United States’ wastewater infrastructure. They derive their name from their location — they treat 

wastewater close to the source, typically on the property of individual homes and businesses. Unlike centralized 

urban wastewater treatment systems that pipe large amounts of wastewater many miles through sewers prior to 

reaching the treatment facility, decentralized wastewater treatment systems usually use small pipes for collecting 

small volumes of domestic wastewater. Decentralized systems (especially smaller ones) usually disperse treated 

waste underground, where the soil provides further treatment. Some decentralized systems are designed to 

discharge to surface waters following treatment. 

The performance of decentralized wastewater treatment systems is a national issue of great concern to EPA. 

These systems are used in 25 percent of the homes in the United States and 33 percent of new development, and 

they are permanent components of our nation’s wastewater infrastructure. Decentralized systems can be an 

effective option for protecting public health and the environment if properly designed, installed, and managed. 

Proper management of decentralized systems involves: implementation of a comprehensive, life-cycle series of 

elements and activities that address public education and participation; planning; performance; site evaluation, 

design, construction, operation and maintenance; residuals management; training and certification or licensing; 

inspections and monitoring; recordkeeping, inventorying, and reporting; and financial assistance and funding. 

Decentralized systems can be a significant threat to public health and water quality when they are not properly 

sited, designed, installed, operated, and maintained. “Failure” of onsite systems is a term subject to much debate; 

however, 1995 U.S. Census data show that over 10 percent of all systems back up into homes or have 

wastewater emerging on the ground surface, and that more than half the systems in the United States were 

installed more than 30 years ago, when onsite rules were nonexistent or poorly enforced. Few systems receive 

proper maintenance because homeowners are either unaware of the need for maintenance or find it a distasteful 

task. In addition, most regulatory programs do not require homeowner accountability for system performance 

after installation. 

5-6 
Although it is difficult to measure and document specific cause-and-effect relationships between onsite 

wastewater treatment systems and the quality of our water resources, it is widely accepted that improperly 

managed systems contribute to water quality problems. EPA’s National Water Quality Inventory 1996 Report to 

Congress states that “improperly constructed and poorly maintained septic systems are believed to cause 

substantial and widespread nutrient and microbial contamination to ground water.” In United States-classified 

shellfish growing areas, closures and harvest restrictions have occurred primarily because of the concentration of 

fecal coliform bacteria associated with human sewage and with organic wastes from livestock and wildlife. 

Onsite wastewater systems also may contribute to an overabundance of nutrients in ponds, lakes, and coastal 

estuaries, leading to an overgrowth of algae and other nuisance aquatic plants. EPA is also concerned with the 

presence of nitrates in ground water, particularly in rural areas where residents must rely on individual wells and 

onsite systems to serve relatively small lots. It is essential to improve the performance of decentralized 

wastewater systems through better management to improve the quality of our nation’s waters. 

Most water quality programs have a role, either direct or indirect, in managing or working with decentralized 

systems. Regardless of your program’s current involvement with decentralized wastewater treatment systems, 

effective watershed-based planning requires that you take these systems into account. Poorly managed or 

operated decentralized systems can significantly affect water quality on your reservation. Appropriate 

management programs for decentralized systems will support the activities and approaches being used in other 

EPA programs, such as watershed management, NPDES, TMDLs, WQS, source water assessment and 

protection, and NPS control, and contribute to achievement of water quality and public health goals. For more 

information on decentralized systems, visit EPA’s new National Management Measures to Control Nonpoint 

Source Pollution from Urban Areas Web site, http://www.epa.gov/owow/nps/urbanmm/index.html. 

4. Understanding Source Water Protection 

Source water is the water from reservoirs, streams, rivers, or underground aquifers that drinking water systems 

use to supply drinking water. Source water protection involves identifying any significant potential source water 

contaminants, taking steps to maintain the quality of source water and preventing contamination from occurring 

(i.e., contingency planning), and determining whether the best available water source is being used. As a key step 

in protecting source water, your tribe might want to conduct a source water assessment. A source water 

assessment provides the basic information needed to protect drinking water sources and is a foundation for 

ensuring the safety of your drinking water. See section II.4 of this chapter for more information on conducting 

source water assessments. 

EPA is committed to helping tribes assess the rivers, lakes, springs, and aquifers serving as tribal public water 

supplies and implement preventative measures against contamination of these water resources. See EPA’s Tribal 

Source Water Web site (http://www.epa.gov/safewater/protect/tribe.html) for additional resources on source 

water protection. 

5. Choosing and Setting Water Quality Goals 

If you have developed WQS, your water quality goal should be to enable all water bodies to meet their designated 

uses. If an NPS TMDL has been established for an impaired water body, then the water quality goal should be at 

a minimum to achieve the NPS TMDL. If you have not developed WQS, or if a TMDL has not been established 

for an impaired water body, you can establish quantifiable water quality-based goals, such as reducing the levels 

of a specific pollutant by a certain percentage or amount. You can also use standards from neighboring states or 

tribes as a proxy to measure water body impairment. Alternatively, you could use some basic parameters, such as 

sediment, nitrogen, phosphorus, nutrients, total suspended solids (TSS), and dissolved oxygen. For an example of 

using basic parameters to establish water quality goals, refer to the Gila River Indian Community case study 

presented in section I.1.b of chapter 4. The case study shows how the Gila River Indian Community uses water 

quality indicators (WQI) to measure water quality improvement. Although EPA encourages you to use numeric 

standards or proxies, in some cases, narrative goals (e.g., remove exotic or invasive species, eliminate nuisance 

algae blooms) may better reflect the goals for a water body. 5-7 
6. Determining Areas with Water Quality Problems 

After you have set water quality goals, you should evaluate your monitoring data to identify water bodies that are 

not meeting those goals. As noted in section I.4 of chapter 3, you can also use data from other sources if you do 

not have all the monitoring data you need. 

Depending on the expertise and resources available to your program, you may find it helpful to focus on one 

watershed or a subset of watersheds each year. You may find that different water bodies differ in topography, 

degree of surrounding urbanization, or land use, and some water bodies are more susceptible to pollution. If any of 

your water bodies face a severe pollution threat, you may want to evaluate monitoring data from these waters 

first. If your source water assessment shows that any of your ground water sources are likely to be contaminated 

or are vulnerable to contamination, then you may want to prioritize monitoring and protection of wellhead areas. 

Once you have identified areas with water quality problems, you should prioritize these areas. Although you 

should consider current conditions when prioritizing problems, the most severe problems may not necessarily be 

the problems you want to address first. For instance, a high-quality water resource may be in good condition but 

threatened by NPS pollution. You may want to address this problem first; preventing pollution is often more costeffective than restoring an impaired water body. In addition, consider cultural significance, biological and 

ecological factors, partner buy-in on the project, the cost and feasibility of possible solutions, and tribal members’ 

concerns when prioritizing water quality problems. 

Note than an NPS assessment report, developed in accordance with the Section 319 program, provides a good 

framework for determining areas with water quality problems. A source water assessment also can provide you 

with information on protecting water quality. Both of these tools are discussed in section II of this chapter. 

There are a number of other partners that you can work with to implement nonregulatory activities. Your EPA 

regional office, the USDA NRCS program, the USGS, and other government agencies may be implementing NPS 

activities in your area. In addition, local universities or community colleges may be able to assist you in developing 

management measures and implementing NPS pollution control programs. Talk to your EPA regional office to 

identify any NPS pollution control programs in your area. 

Rotating Basins Approach 

To maximize resources and at the same time address problems in different basins, many organizations have 

adopted a rotating basins approach to watershed planning. In this approach, watersheds are grouped into units 

of sub watersheds. A five-step watershed management process is followed to focus activities within each basin, 

while staggering the overall workload. Specifically, the assessment, planning, and management activities are 

grouped under five general categories: 

z Data collection/monitoring z Basin plan review/approval

z Assessment/prioritization z Implementation

z Strategy development

Implementation of the rotating basins approach involves beginning the five-step management cycle in one basin 

the first year (data collection/monitoring). In the second year, step two (assessment/prioritization) occurs in 

that basin, while in another basin step one activities (data collection/monitoring) are undertaken. Moving 

sequentially through the five management steps in each basin focuses resources associated with that activity 

rather than scattering them. 

5-8 
7. Choosing and Setting Watershed-based Goals 

Your watershed-based goals should relate to your water quality goals and ultimately help you achieve them. 

Watershed-based goals can address current and historical distribution and condition of important resources in a 

watershed, or the physical and ecological setting of the watershed. Some common watershed-based plan goals 

that can be funded with Section 106 grants include: 

z Characterize water quality 

z Evaluate the impacts of forestry, agriculture, urbanization, septic systems, or construction and effects of 

land use on pollution 

z Protect natural resources 

z Develop watershed-based plans 

z Identify causes of streambank erosion 

z Investigate causes of declines in ground water quantity 

z Characterize stormwater runoff 

z Conduct community education and outreach about the watershed 

z Develop watershed maps showing water body types, tribal cultural sites, species distribution, and sites of 

water quality impairment 

z Develop local and community watershed organizations 

z Inventory possible restoration sites 

z Determine causes of floods 

8. Developing Projects to Meet Water Quality Goals 

An initial assessment of your water pollution issues can help you identify appropriate goals to address them. For 

example, NPS problems are typically addressed through management measures. As noted above, NPS 

management measures are practices, techniques, principles, or activities that have been shown to help reduce 

NPS in the most effective and practical ways. The goal of these management measures is to reduce NPS 

pollution by keeping pollutants out of the water rather than removing them once they are in the water. 

Management measures can be sector specific (e.g., agriculture, timber, construction, stormwater, marinas, septic 

systems) or cover broader activities that address all sources of NPS pollution (e.g., planting vegetative buffers 

around your water bodies, maintaining your streambanks). 

Asset Management 

Although point sources such as wastewater treatment facilities are not eligible for the use of Section 106 

grants, EPA provides extensive information on the management of treatment facility assets. Additional 

information is available at http://www.epa.gov/owm/assetmanage and http://www.epa.gov/water/ 

infrastructure/. 

5-9 
EPA, states, and many other organizations have developed documents with information on controlling NPS 

pollution through management measures. Your EPA regional office can provide you with information on 

management measures that have successfully addressed NPS issues similar to the ones you face. In addition, 

OWOW maintains a comprehensive list of EPA and non-EPA documents on NPS pollution and management 

measures at http://www.epa.gov/owow/nps/pubs.html. EPA’s Office of Ground Water and Drinking Water 

(OGWDW) offers electronic training on protecting source water at http://epa.gov/safewater/dwa/electronic/ 

ematerials.html#SWP. EPA’s Office of Wastewater Management (OWM) offers information and guidance on 

implementing management programs for septic systems at http://cfpub.epa.gov/owm/septic/home.cfm. 

Many solutions to water quality problems will require you to work with partners to implement them successfully. A 

watershed-based plan can provide the coordinating framework for identifying your partners and prioritizing the 

management measures you want to implement. Sections I.9, III.4, and III.5 of this chapter contain more 

information on building networks. 

9. Conducting Public Outreach and Encouraging Public Involvement 

Water quality protection programs will require active public participation to succeed. A successful tribal water 

quality program, particularly one that involves voluntary activities, depends on community involvement and 

participation. In addition, informed and involved members of the community are more likely to support your 

program’s efforts to protect the environment. For example, if you want to address leaching from septic systems, 

you will have to work closely with homeowners and small businesses that use septic systems. Sections I.12, II.5, 

and III.3 of chapter 3 contain some general information on encouraging public participation and involvement. 

Depending on the activities you choose to implement, you will need 

to target different groups of your population. For example, if you 

want to implement a pesticide and fertilization management 

program, you will have to work with farmers in your community. 

In addition, because of the characteristics of NPS pollution, 

watershed-based planning, and source water protection, 

community awareness and involvement are especially important in 

these areas. Consider carrying out public education programs to 

raise awareness on issues such as the proper disposal of car 

fluids. The text box on page 5-12 provides some information on 

basic activities members of your community can take to reduce 

NPS pollution. Some methods that communities have used to raise 

public awareness about all water quality issues include: 

z Tours of restored or impaired water bodies 

z Educational workshops on NPS pollution, source water 

protection, and septic system management 

z Events and programs such as “adopt-a-river,” river 

cleanup days, and volunteer monitoring networks 

z Brochures, flyers, and newsletters on NPS pollution, source water protection, and septic system 

management 

z No-penalty hazardous waste collection programs 

z Solicitation of public input in developing a septic system management program 

Bishop Paiute Tribe Analytical Lab. Photo 

courtesy of Bishop Paiute Tribe. 

5-10 
EPA has developed a comprehensive guide for conducting watershed outreach campaigns that includes specific 

information about understanding the audiences in your watershed, creating messages that resonate with them, 

finding appropriate ways to communicate your message, and understanding how outreach can help change 

behavior (see Getting in Step: A Guide for Conducting Watershed Outreach Campaigns, available online at 

www.epa.gov/owow/watershed/outreach/documents/getnstep.pdf). EPA is also in the process of releasing a new 

NPS Outreach Digital Toolbox, which will include sample materials and templates of successful outreach 

materials (e.g., public service announcements) from across the country that you can customize to meet your own 

outreach needs (see www.epa.gov/owow/nps/toolbox.html). 

Colorado River Indian Tribes Youth Day. Photograph Courtesy of the Colorado 

River Indian Tribe. 

NPS and Public Outreach 

The Red Lake Band of Chippewa Indians, located in EPA Region 5, has developed a project called “NPS/ 

Stormwater Management Planning and NPS Reduction/Buffer Zone Education.” As part of this project, they 

worked with the Natural Resources Conservation Service (NRCS) to produce a folder of informational 

pamphlets and resources to be mailed to watershed residents in an effort to raise awareness about 

stormwater and NPS pollution issues. Other sponsors of the project included the University of Minnesota 

Extension Service, the Beltrami County Soil and Water Conservation District, and USDA’s Farm Service 

Agency. 

The resource packet offers residents the opportunity to contribute to regional NPS management by evaluating 

their own households and properties. In addition to providing an overview of NPS pollution, each folder 

contains several pamphlets on topics such as septic system maintenance, reducing the use of hazardous 

household products, and agricultural practices. The folder also lists the names and Web sites of numerous 

organizations that can offer more information and technical support. 

In addition to the mailing, the Band hosts an after school River Watch Program that helps get students 

involved in river conservation and an annual Water Festival that provides a variety of educational opportunities 

for 5th grade students. During the Water Festival, students participate in fun-filled activities while developing 

awareness for the protection of the Band’s valuable water resources. 

5-11 
Examples of Management Measures for Your Community 

The management measures listed below are simple actions that members of your community can take to help 

reduce NPS pollution. You may want to expand on this list and distribute it to members of your community to 

raise their awareness of NPS issues or develop programs to support related NPS prevention activities. 

z Properly dispose of pet waste and other animal waste to help prevent runoff of nutrients and 

pathogens into your water bodies. 

z Report septic system leaks to the proper tribal authority for repair. 

z NEVER dump automotive fluids down a drain or on the ground. Recycle used auto fluids at your local 

recycling facility; see EPA’s Web site for information on recycling waste: http://www.epa.gov/ 

epaoswer/osw/index.htm. 

z NEVER dump household hazardous wastes (HHWs) down a drain or on the ground. Dispose of 

HHWs (e.g., cleaners, pesticides, paint) at the proper disposal facility; for more information on HHWs, 

see EPA’s Web site at http://www.epa.gov/epaoswer/non-hw/muncpl/hhw.htm. 

z Educate yourself on the proper use and application of pesticides. Information is available online at 

http://www.epa.gov/pesticides/. 

z Fence off streams and wetlands from livestock and provide alternate water sources. Livestock in 

streams and wetlands affect plant life and cause soil erosion. 

z Rotate grazing on lands to prevent overgrazing and stabilize soil. 

z Use ground cover, such as jute netting or ground cover plants, on bare ground to prevent soil erosion. 

z Plan or participate in community cleanup programs or events. 

z Promote and provide environmental education and NPS pollution awareness in your community. 

5-12 
II. Intermediate Program Activities 

1. Understanding Section 319 Grants 

This section discusses nonregulatory components of the 319 program, which supports both regulatory and 

nonregulatory activities. As noted in section II.1 of chapter 3, Section 319 grants can be used to implement NPS 

activities. Each year, EPA awards Section 319 grants to eligible tribes either as base funding or competitive 

funding. Base funding is issued on a non-competitive basis at $30,000 or $50,000 (depending on land area) to 

implement the full range of activities in a tribe’s approved NPS management program. The remaining funds are 

awarded on a competitive basis for the purpose of developing and implementing watershed-based plans and 

implementing on-the-ground water quality improvement projects that are expected to achieve actual water quality 

benefits in waters impacted by NPS pollution. Tribes are encouraged to submit on-the-ground projects that 

implement watershed-based plans. In FY 2005, EPA awarded $7 million to 84 tribes, with approximately $2.8 

million awarded to 84 tribes as base funding and $4.2 million awarded to 31 tribes on a competitive basis. Tribes 

should refer to the annual guidelines on awarding Section 319 grants for more information about the process for 

awarding Section 319 funding, including the criteria for proposed work plans (see http://www.epa.gov/owow/nps/ 

tribal.html). 

You can use Section 106 grants to fund some NPS control activities, including the development of NPS 

assessments and management programs, as well as the development of watershed-based plans for implementing 

NPS projects and management measures. Section 106 grants may also be used for additional NPS activities, such 

as inventorying NPS, attending NPS meetings and trainings, and forming partnerships to address NPS issues. 

Construction activities and remediation activities are generally prohibited under Section 106 grants. Contact your 

EPA grant project officer for more information on specific projects that are authorized for funding under Section 

106. Section I.3.b of chapter 3 contains more information on projects that can be funded under a Section 106 

grant. 

2. Section 319 Eligibility 

To be eligible for Section 319 grants, tribes must have (a) TAS eligibility in accordance with CWA Section 518; (b) 

an approved NPS assessment report in accordance with CWA Section 319(a); and (c) an approved NPS 

management program in accordance with CWA Section 319(b). Section 319 grants cannot be used to develop 

NPS assessment reports or management programs (but can be used to update approved NPS management 

programs). Section 106 funds can be used for these purposes. You should consider applying for Section 319 

grants, especially if you want to implement NPS control activities not allowed under the conditions of your Section 

106 grant. 

Tribes should work with the EPA grant project officers and refer to EPA’s Tribal Nonpoint Source Planning 

Handbook (EPA 841-B-97-004) for information on applying for Section 319 grants. The Handbook is available 

for order through EPA’s Office of Water Publications Web site (http://yosemite.epa.gov/water/owrccatalog.nsf/). 

In some cases, state NPS funds may be available to tribes through state pass-throughs. Consult your EPA 

regional office to see if this option is available in your region. 

a. Qualifying for TAS Eligibility for the Section 319 Program 

You will need to qualify for TAS eligibility for the purposes of administering the Section 319 program to become 

eligible for Section 319 grants. If you have qualified for Section 106 TAS eligibility, you already may have met 

some of the requirements for Section 319 TAS eligibility (e.g., federal recognition and demonstration of substantial 

governmental duties). See section I.1 of chapter 3 and contact your EPA grant project officer for more 

information on these requirements. 

5-13 
b. Developing Section 319 NPS Assessment Reports 

An NPS assessment report describes existing and potential NPS-related water quality problems in reservation 

waters using existing water quality data. The report identifies the nature, extent, effect, and causes of NPS 

pollution. It should also describe existing programs and methods used to control the pollution. The report must be 

approved by your EPA regional office. 

NPS assessment reports should include four elements: 

1. An identification of waters that cannot be expected to attain or maintain WQS without NPS pollution 

control. If you have not developed tribal WQS, you can use state standards as a proxy to identify impacted 

water bodies. 

2. An identification of the sources of NPS pollution (e.g., agriculture, urban runoff, construction) that 

contribute to the water quality problems of the identified water bodies. 

3. A description of how you will first identify management measures to control NPS pollution and how you 

will then use those management measures to control the pollution. Include public participation and 

intergovernmental coordination if applicable. 

4. A description of any existing tribal, state, federal, and other programs you can use to help control NPS 

pollution. 

See EPA’s Tribal Nonpoint Source Planning Handbook for detailed information on developing an NPS 

assessment report. 

As your NPS program evolves, you will learn more about NPS pollution and the most effective ways of 

controlling different types of pollution. As your program matures and as conditions change, you should continue to 

revise and update your assessment to account for this information. 

c. Developing Section 319 NPS Management Programs 

As set forth in Section 319(b)(1) of the CWA, an NPS management program describes how you intend to control 

pollution added from NPS to navigable waters within the reservation and improve the quality of such waters. If 

you cannot address all NPS categories, you can focus your management program on NPS pollution that you have 

identified as a priority. An NPS management program must have six elements: 

1. A description of the management measures you will use to reduce pollutant loadings from each category 

of sources you identified in your NPS assessment report. 

2. A description of the programs you will use to implement the management measures you have identified, 

including nonregulatory or regulatory (e.g., zoning laws) approaches, technical assistance, financial 

assistance, education, training, technology transfer, and demonstration projects. 

3. A schedule containing annual milestones for the implementation of management measures identified under 

element (1) and the programs identified under element (2). 

4. A certification by legal counsel that your tribal laws provide authority to implement the programs identified 

under element (2) or a list of additional authorities your tribe will need to implement the management 

program. If you need to seek additional authorities, you should submit a schedule and commitment to seek 

those authorities as quickly as possible. 

5-14 
5. A list and description of additional sources of funding (federal or other) for the implementation of NPS 

pollution control measures. 

6. A list of any assistance programs or development projects (e.g., USDA NRCS) that your tribe will review 

to determine their effects on water quality and consistency with your tribe’s NPS program. 

See EPA’s Tribal Nonpoint Source Planning Handbook for detailed information on developing an NPS 

assessment report. 

If you choose not to apply for Section 319 grants, you should still consider developing an NPS assessment report 

and management program. Completing these documents will give you important information to help you assess 

your NPS pollution control efforts and plan effectively for the future. 

3. Developing a Watershed-based Plan 

EPA encourages tribes to develop watershed-based plans to guide the implementation of their NPS programs. 

EPA’s annual Guidelines for Awarding Section 319 Grants to Indian Tribes provide guidance in developing 

watershed-based plans and encourage tribes to use competitive funding for projects that are designed to develop 

or implement a watershed-based plan (see http://www.epa.gov/owow/nps/tribal.html). The watershed-based plans 

incorporate specific elements designed to help tribes identify significant sources of NPS pollution, identify the 

management measures that will most effectively address those sources, and estimate the expected water qualitybased goals that will be achieved. Without such information to provide focus and direction, it is less likely that a 

project that implements the watershed-based plan can address the sources of water quality impairments 

efficiently and effectively. Section 106 grants can be used to develop watershed-based plans; however, tribes 

using Section 106 funds for this purpose should ensure that watershed-based plans meet programmatic 

requirements of the Section 319 program as described in the annual Guidelines for Awarding Section 319 

Grants to Indian Tribes. 

The nine elements of a watershed-based plan are: 

1. An identification of the causes and sources or groups of similar sources that will need to be controlled to 

achieve the goal identified in element (3) below. Sources that need to be controlled should be identified at 

the significant subcategory level with estimates of the extent to which they are present in the watershed 

(e.g., X number of dairy cattle feedlots needing upgrading, including a rough estimate of the number of 

cattle per facility; Y acres of row crops needing improved nutrient management or sediment control; or Z 

linear miles of eroded streambank needing remediation). 

2. A description of the NPS management measures that will need to be implemented to achieve a water 

quality-based goal described in element (3) below, as well as to achieve other watershed goals identified in 

the watershed-based plan, and an identification (using a map or a description) of the critical areas in which 

those measures will be needed to implement the plan. 

3. An estimate of the water quality-based goals expected to be achieved by implementing the measures 

described in element (2) above. To the extent possible, estimates should identify specific water qualitybased goals, which may incorporate, for example, load reductions, water quality standards for one or more 

pollutant/use, NPS total maximum daily load (TMDL) allocations, measurable in-stream reductions in a 

pollutant, or improvements in a parameter that indicates stream health (e.g., increases in fish or 

macroinvertebrate counts). If information is not available to make specific estimates, water quality-based 

goals may include narrative descriptions and best professional judgment based on existing information. 

5-15 
PYRAMID LAKE PAIUTE TRIBE

The Pyramid Lake Paiute Indian Reservation is located in western Nevada, about 30 miles northeast of 

Reno, and encompasses about 474,000 acres. Pyramid Lake, a slightly saline terminal desert lake, is located 

entirely within the reservation. The lake covers approximately 114,000 acres and is the focal point of the 

reservation. The Lower Truckee River, which originates in the Sierra Nevada, flows through the reservation 

for 31 miles and terminates in Pyramid Lake. The beneficial uses of Pyramid Lake and Truckee River 

include provision of a cold freshwater habitat, protection of threatened or endangered species, preservation 

of indigenous aquatic life, and the protection of aquaculture. Other water resources at Pyramid Lake 

include ground water, streams, creeks, wetlands, springs, and seepages. The beneficial uses of groundwater 

and wetlands include cultural, indigenous aquatic life, livestock watering, and water quality enhancement. 

According to the tribe, it has depended upon Pyramid Lake and the Truckee River for food, clothing and 

shelter materials, as well as cultural and spiritual health 

since time immemorial. 

In 1994, the tribe’s NPS Assessment Report and 

Management Program was approved by EPA and the tribe 

became eligible for Section 319 funding. The tribe has 

been awarded multiple competitive NPS grants to carry 

out its NPS pollution control program to address pollutants 

found through its water quality monitoring program. 

Specifically, the NPS program mitigated and prevented the 

effects of uncontrolled grazing by cattle that led to turbidity 

from soil erosion, nutrient loads, loss of native vegetation, 

and destabilized streambanks. This was accomplished 

through the implementation of management measures such 

as fencing and providing alternate water sources. 

From 1999 to 2004, water quality monitoring and sampling on the Lower Truckee River has shown that 

riparian habitat has improved as a direct result of the implementation of NPS on-the-ground projects 

including the fencing out of livestock and improved water flow management for cottonwood and willow 

trees. The environmental results of the NPS projects show reduction in velocity and sedimentation and 

increased bank stability in the Truckee River. Specifically, nitrate and nitrite levels have declined from 0.17 

mg/L in May 2000 to 

about 0.01 mg/L in July 

2004 (see attached chart). 

The riparian areas 

restored under the NPS 

Nitrate and Nitrite 

1999-2004 

Lower Truckee River PLPT Data 

grant program will 

continue to recover 

0.18 

0.16 

through the intensive 

management of cattle 

grazing, which will allow 

0.14 

0.12 

0.10 

0.08 

(mg/L) 3 

Wadsworth 

Nixon 

Linear 

(Wadsworth) 

the water level to rise 

back to support native 

0.06 

0.04

No & NO 2 

Linear 

(Nixon) 

vegetation and become 0.02 

properly functioning 0.00 

systems. 7/21/99 

1/3/00 

5/1/00 

/2/00 

4/9/01

1

1

1

1

Sample Date 

/14/01 

4/5/02 

7/14/03 

7/7/04 

Images courtesy of Pyramid Lake Paiute Tribe 

5-16 
4. An estimate of the amounts of technical and financial assistance needed, associated costs, and/or the 

sources and authorities that will be relied upon to implement the plan. As sources of funding, tribes should 

consider other relevant federal, state, local, and private funds that may be available to assist in 

implementing the plan. 

5. An information and education component that will be used to enhance public understanding and encourage 

early and continued participation in selecting, designing, and implementing the NPS management measures 

that will be implemented. 

6. A schedule for implementing the NPS management measures identified in this plan that is reasonably 

expeditious. 

7. A description of interim, measurable milestones for determining whether NPS management measures or 

other control actions are being implemented. 

8. A set of criteria that can be used to determine whether the water quality-based goals are being achieved 

over time and substantial progress is being made towards attaining water quality-based goals and, if not, 

the criteria for determining whether the watershed-based plan needs to be revised. 

9. A monitoring component to evaluate the effectiveness of the implementation efforts over time, measured 

against the criterion established under element (8) above. 

4. Conducting a Source Water Assessment 

A source water assessment characterizes sources of drinking water (rivers, lakes, reservoirs, springs, and ground 

water wells) to identify significant potential sources of contamination and to determine how susceptible the 

sources are to these threats. The assessments provide the basic information needed to protect drinking water 

sources and a foundation for ensuring drinking water safety. Tribes might also choose to conduct a source water 

assessment to determine the quality of their water. The final product of a source water assessment is a report that 

provides basic information about a drinking water source. 

These source water assessments should include the following four major elements: 

z A delineation (or map) of the source water assessment area. This determines the boundaries of the area 

from which your source water is drawn, i.e., the area that you will need to protect. 

z An inventory of all significant potential sources of contamination by regulated contaminants in the 

delineated area. 

z A determination of how susceptible the water supply is to those contamination sources. 

z Assessment results are summarized and made available to the public. 

Assessment report summaries help tribes to understand the potential threats to their water supplies and to identify 

priority needs for protecting the water from contamination. Tribes can make the assessment summaries available 

to the public in a variety of ways. Tribes may: convene public workshops; make copies available at public libraries, 

local government offices, or water suppliers; or post their assessment information on the internet. 

5-17 
Source Water Assessments 

For more information on Source Water Assessments, please visit EPA’s Source Water Assessment Web site 

at http://www.epa.gov/safewater/protect/assessment.html or call the EPA Safe Drinking Water Hotline at 1­

800-426-4791. 

5. Implementing Water Quality Protection and Restoration Activities 

Your NPS assessment report and management program, watershed-based plan, or source water assessment will 

provide you with a road map for your water quality protection and restoration activities. Begin to implement those 

activities, prioritizing them as needed. Involve members of your community and other tribal, federal, state, or local 

partners, as necessary. Remember that you may not be able to use Section 106 funds to implement all the 

management measures you have identified. 

6. Implementing Section 106 Grant Activities Related to Decentralized

Systems

If decentralized systems pose a threat to water quality on your reservation, you may be able to use Section 106 

funds for a variety of activities related to improving the performance of decentralized systems (remember that 

Section 106 funds cannot be used for wastewater treatment facility construction or operation). Activities related 

to decentralized systems that can be funded through Section 106 grants include: 

z Public outreach, education, and involvement programs 

z Programs to promote stakeholder and partner agency involvement 

z Development of effective management programs to ensure that performance requirements for 

decentralized systems are met 

z Watershed and ground water assessments 

z Establishment of public health and water resource protection goals related to decentralized systems 

z Targeted surface and ground water monitoring 

z Studies to characterize the impact of malfunctioning decentralized systems, discharging and nondischarging, on surface and ground water quality 

z Inventory and assessment of decentralized systems 

z Identification of critical areas where decentralized systems pose elevated risks (e.g., sites with poor soils, 

high water tables, high densities of existing systems, near sensitive surface waters, or in floodplains) 

Contact your EPA regional office for more information on eligible activities related to decentralized wastewater 

treatment systems. EPA and other organizations provide construction funding through various grant programs: 

EPA Programs 

To help prevent decentralized system failure and improve management practices, EPA has issued Voluntary 

National Guidelines for Management of Onsite and Clustered (Decentralized) Wastewater Treatment 

5-18
Systems (EPA 832-B-03-001) and the Handbook for Management of Onsite and Clustered (Decentralized) 

Wastewater Treatment Systems (EPA 832-D-03-001), available online at http://cfpub.epa.gov/owm/septic/ 

home.cfm. These documents are designed to enhance the performance and reliability of decentralized 

wastewater treatment systems through improved management programs. Proper management of decentralized 

systems involves implementation of a comprehensive group of elements and activities, such as public education 

and participation, planning, operation and maintenance, and financial assistance and funding. The Management 

Guidelines will help improve system performance by encouraging the institutionalization of management concepts 

and raising the quality of state, tribal, and local management programs. Improved management will minimize the 

occurrence of failures by ensuring (with proper planning, siting, design, installation, operation and maintenance, 

and monitoring) that pollutants are adequately treated and dispersed into the environment, thereby reducing risks 

to both public health and local water resources. 

z The Alaskan Native Village and Rural Communities Sanitation Grant Program Provides grants to Alaska 

Native Villages and rural communities for drinking water and wastewater facility construction, and training 

and technical assistance in facility operation. Visit http://www.epa.gov/owm/mab/indian/anvrs.htm for 

more information. 

z The Clean Water Indian Set-Aside Grant Program provides grants to Indian tribes and Alaskan Native 

Villages for the planning, design, and construction of wastewater treatment systems. More information on 

the Clean Water Indian Set-Aside Grant Program is available online at http://www.epa.gov/owm/mab/ 

indian/cwisa.htm. 

Section 319 funds also can be used for projects that implement management measures to address the proper 

siting, design, and installation of on-site wastewater treatment systems, upgrading of existing systems, inspections, 

assessments, development of local codes and ordinances, and education and training on proper management 

practices. Section 319 funds may be used to fund any urban storm water activities that are not specifically 

required by a draft or final National Pollutant Discharge Elimination System (NPDES) permit. See section III.6 of 

chapter 7 for more information on NPDES permits. 

Other Organizations 

z The Indian Health Service (IHS) — Sanitation Facilities Construction Program provides funding for 

drinking water, wastewater, and solid waste disposal facilities for American Indians. IHS also provides onsite training and technical assistance for the planning, design, construction, and operation and maintenance 

of facilities. The Division of Sanitation Facilities Construction’s Web site (http://www.dsfc.ihs.gov/) 

contains more information on this program. 

z USDA’s Rural Utilities Service Water and Waste Disposal Program provides both loans and grants to rural 

communities and Indian tribes (with 10,000 or fewer persons) for drinking water and wastewater systems, 

and for solid waste and storm drainage products. More information is available through the program’s Web 

site, http://www.usda.gov/rus/water/. 

7. Analyzing Water Quality Data and Defining Performance Measures 

Your water quality program should strive to show quantifiable improvements in water quality when possible. As 

you implement your water quality protection activities, you should begin to develop performance measures to help 

you determine whether the management measures are addressing the water quality problems for which they were 

developed. The performance measures you use will vary based on the management measure. For example, if you 

have implemented a fertilizer management program in partnership with the agricultural community, you may be 

able to use changes in phosphorus concentrations to measure success. If a management measure is not meant to 

5-19 
Penobscot Indian Nation DNR staff collaborating 

with state, EPA, and dischargers on a wasteload 

allocation study of the Penobscot River. Photo 

courtesy of the Penobscot Indian Nation. 

address a sector-specific water quality problem but instead addresses all NPS (e.g., streambank stabilization and 

restoration projects), you may be able to use attainment of your WQS or proxies for tribal standards (e.g., state 

standards) as performance measures. A watershed-based plan can help you make these determinations because 

in addition to incorporating specific water quality-based goals, a watershed-based plan also incorporates a specific 

set of criteria that can be used to determine whether these 

goals are being achieved over time. 

III. Mature Program 

Activities 

1. Evaluating Restoration Activities 

Using the performance measures you identified in section II.7, 

you can begin to evaluate the effectiveness of your water 

quality protection activities. To the extent possible, try to 

collect enough information through monitoring to make 

definitive statements about the number or percent of water 

bodies meeting or moving towards meeting WQS or water 

quality goals. If you do not have enough data to determine the 

effectiveness of your activities, identify which data points you 

need to collect and adjust your monitoring program as necessary. The data requirements for making decisions 

about whether waters support WQS or water quality goals should be included in your tribe’s QAPP or a related 

document. 

If you find that your measures are not affecting water quality as you anticipated, try to determine why. Are all 

affected parties implementing the management measures? Are there other sources of the pollutant you are trying 

to address that are not covered by your management measures? Do you need to implement additional measures 

that supplement the ones you already have in place? Answer these questions to the best of your ability and modify 

your approach as appropriate. 

As part of your evaluation, you may find it helpful to consider the cost-effectiveness of different types of 

activities. Calculating the costs for program activities and measuring their benefits can be very challenging, but 

even a rough analysis may give you valuable information about your program. To the extent possible, see if you 

can associate specific costs with the implementation of specific program activities. This may be easy to do with a 

small construction project but more difficult to calculate for a large, multi-year public outreach program. If you 

can determine rough cost estimates for certain types of activities and understand the general effectiveness of 

those management measures, you can use that information to help prioritize your pollution control activities. For 

example, if your monitoring results show that NPS pollution from car fluids has decreased dramatically since you 

distributed a simple one-page flyer to all community residents, you may want to assign a higher priority to other 

simple community outreach activities. 

2. Providing Updated Information to Your Partners and Community 

As your program grows and you begin to see results for your NPS pollution control programs, keep your 

community informed of changes in water quality. Improved water quality that results from management measures 

can serve as a source of pride to those people involved in the implementation of the management measure and 

can spur interest in the program. If the results show that your partnerships have achieved their goals effectively, 

your partners may be more likely to agree to participate in and commit resources to other projects in the future. 

5-20 
3. Refining Your Assessment Report, Management Program, Source Water 

Assessment, and Watershed-based Plan 

Based on your performance measures and your assessment of your restoration activities, you should refine your 

assessment report, management program, source water assessment, and watershed-based plan. As noted in 

section II.1-3 of this chapter, it is important to update and revise your management program and watershed-based 

plan as you collect more data on NPS pollution and your understanding of your NPS problems improves. You 

should also update your assessment report to account for changing conditions or new problems on your 

reservation. Even if you are not applying for Section 319 grants, these tools will help you continue to address NPS 

pollution on your tribe’s land effectively. 

4. Coordinating and Cooperating with Other Programs 

In some situations, you may find it useful to engage other programs within your tribe (e.g., fish and game 

programs, tribal planning offices) to avoid duplication of effort, maximize resources, and expedite your program 

development. You may find coordination and cooperation with other tribal programs especially valuable in 

developing NPS pollution control programs because of their reliance on voluntary activities and universal 

participation. You may also find it useful to coordinate with external organizations such as states, universities, or 

other tribes or coalitions of tribes. Some tribal environmental programs have developed memoranda of agreement 

(MOAs) or memoranda of understanding (MOUs) with other programs and organizations that identify areas of 

mutual interest and define the role and responsibility for each tribal program within those areas. For example, in 

some instances, GIS programs are not part of tribal environmental programs. In these cases, an MOA or MOU 

between your program and the program that houses the GIS activities could give you access to GIS services and 

valuable GIS data. 

5. Working in Partnership with Other Tribes and States 

Other tribes and states, as well as local governments and non-governmental organizations, may conduct water 

quality protection activities in your watershed. To use limited resources more effectively, you may find it helpful to 

collaborate with these entities. Jointly sponsoring events or programs can lead to greater participation, raised 

awareness in the community, and cost savings for each program. 

Depending on the types of activities being conducted in your watershed, you may be able to support regulatory 

programs of neighboring states and tribes, even if your program is nonregulatory. For example, the Penobscot 

Indian Nation shares its water quality monitoring data with the Maine Department of Environmental Protection 

not only for resource management and planning purposes but also Section 305(b) reporting to Congress, which 

Maine is required to perform. More information is provided in the case study below. For other examples of 

partnerships you can pursue, see section 1.4 of chapter 6 and section 1.7 of chapter 7. 

The Houlton Band of Maliseet Indians (HBMI) and USGS 

The partnership that has evolved over the past several years between the HBMI’s Water Resources 

Program and USGS has had numerous benefits for both parties involved as well as the riverine ecosystem 

that they are mutually working to protect. USGS provides strong technical and scientific expertise, 

advanced field sampling equipment, staff training, and QA/QC. In turn, the HBMI offers a vast background 

of historical information, can effectively respond to storm events, and processes sediment and water 

samples in their own lab. By combining their efforts, the amount of data collected and analyzed is far 

greater than what either group could do individually. 

5-21 
6. Other Voluntary Programs 

The information included in this chapter does not include all possible voluntary activities your tribal program can 

support. If voluntary activities not described in detail in this chapter will allow your tribal program to further its 

water quality goals more effectively, you should consider implementing those activities. EPA maintains information 

on additional voluntary programs and partnerships on its Voluntary Partnerships Web site, http://www.epa.gov/ 

partners/. 

Penobscot Nation DNR staff deploying artificial substrates for sampling aquatic macroinvertebrates. Photo courtesy of 

the Penobscot Indian Nation. 

5-22 
Why Monitor? Successes of Penobscot Nation Water Quality Monitoring 

Section 106 funding has been a critical asset to the Penobscot Indian Nation’s (PIN) successful 

development of an invaluable water quality monitoring program. The PIN, whose unique reservation is the 

Penobscot River and its islands from Old Town northward, uses Section 106 funds to help carry out water 

quality monitoring throughout the PIN’s reservation, as well as trust land waters. This program is integral to 

the tribe’s efforts to protect its reservation waters, aquatic resources, and traditional uses. Data collected 

from these monitoring activities are used for a variety of purposes including: 

z Short- and long-term water resources planning 

z Setting fish consumption advisories for the Nation 

z Tracking water quality 

z Surveying water near dischargers to collect indicators of possible noncompliance 

z Identifying sources of pollution and developing plans for reduction and future pollution prevention 

z Contributing to research projects conducted by academics and consultants who ultimately share their 

results with the Nation 

z Educating Native and non-Native community members on the health of the Penobscot River 

The benefits of these efforts flow well beyond the Nation. Through a cooperative agreement with the 

Maine Department of Environmental Protection (MDEP), the Nation shares its data with them for water 

resources management and planning purposes as well as 305(b) reporting to Congress. Furthermore, the 

technical capabilities, flexibility in scheduling, more frequent and widespread presence on the river, and 

ability to respond to emergency situations more quickly have led to the PIN identifying many water quality 

problems including: 

1. A jet fuel spill from a local airport that was detected by a PIN employee, who was doing a routine 

sampling run, and reported and taken care of in a more timely manner than would have otherwise 

been possible. 

2. A leak from a local gas station that released several thousands of gallons of gasoline into the ground 

water and ultimately into the Penobscot River, but, because of the PIN, was contained, stopped, and 

remediated, protecting ground water wells of adjacent neighbors and the river. 

3. A lumber mill where the Nation’s questions about permit compliance resulted in a $800,000 fine and 

a consent agreement between the company and the State of Maine. 

4. Episodic algae blooms in the river. Nutrient, chlorophyll, and other water quality data have 

heightened the Maine DEP’s awareness of the severity and frequency of algae blooms in the river, 

leading to improvements in the river model and providing an impetus for developing instream criteria 

and discharge permit levels for nutrients. 

5-23 
Through the Cooperative Agreement with Maine DEP, the PIN Water Resources Program also provides 

technical and logistical assistance on a variety of projects including: 

1. Wasteload allocation studies that provide important scientific data for the development of a model of 

the Penobscot and Piscataquis Rivers. These studies are ultimately used to help determine discharge 

license limits and conditions. 

2. Maine’s Dioxin Monitoring Program, which examines levels of dioxin in fish above and below 

suspected sources, including kraft paper mills. 

3. A surface water ambient toxic program that examines levels and effects of a variety of toxic 

contaminants in fish and other biota. 

For more information contact: 

Daniel H. Kusnierz 

Water Resources Program Manager 

Penobscot Indian Nation - DNR 

12 Wabanaki Way, Indian Island 

Old Town, ME 04468 

Tel. (207)817-7361

 or 

(207)827-7776 ext. 7361 

Fax (207)827-1137 

pinwater@penobscotnation.org 

Penobscot Indian Nation Department of Natural Resources staff 

monitoring water quality of the West Branch of the Penobscot River with 

Mount Katahdin in the background. Photo courtesy of the Penobscot 

Indian Nation. 

5-24 
Chapter 6: Tribal Law Water

Quality Protection Approach

Introduction 

This chapter is designed for tribes that do not want to develop EPA-approved standards but would nonetheless 

like to use tribal law to protect water quality on their reservations. Many of the activities described in chapter 7 

may be helpful if you are developing tribal standards. Rather than repeat that information here, this chapter 

includes references to relevant sections in chapter 7 where appropriate. Like those discussed in chapter 7, the 

activities in this chapter are most appropriate for sophisticated tribal programs. 

Many tribal communities have maintained and protected watersheds and waterways for centuries. In those cases, 

tribes may already have laws and legal systems to protect water quality. These measures may be rooted in tribal 

law and linked to long-standing tradition and culture. The information provided in this chapter is not intended to 

supersede any existing tribal law but to provide guidance for tribes that would like basic information on developing 

standards. You may find that due to the unique culture and traditions of your tribe, some of the information 

provided in this chapter may not apply. 

You should work with your tribal attorney general or equivalent office and the tribal council during this process to 

make sure that you understand how you can use tribal law to protect water quality. You should also work with 

your tribal council to make sure you cover all applicable requirements under tribal law for adoption of standards. 

Activities Included in Chapter 6 

Fundamental Program Activities

1. Understanding Water Quality Standards

2. Understanding What Tribal Standards Can Do

3. Identifying Goals of Tribal Standards

4. Working in Partnership with EPA, Tribes, and States

Intermediate Program Activities

Tribes should begin these activities after having completed the relevant fundamental program activities.

1. Developing Draft Standards

2. Sharing Draft Standards with EPA, Tribes, and States for Review, as Appropriate

3. Conducting Public Outreach

4. Drafting Tribal Code Based on Standards

5. Formally Adopting Standards through Tribal Council

Mature Program Activities

Tribes should begin these activities after having completed the relevant fundamental and intermediate program activities.

1. Implementing Standards

2. Reviewing Standards

3. Developing MOAs with EPA for Permitting Purposes

6-1 
I. Fundamental Program Activities 

1. Understanding Water Quality Standards 

Chapter 7 explains the basic structure of standards. Review section I.1 of chapter 7 to understand this structure. 

2. Understanding What Tribal Standards Can Do 

Developing tribal standards and goals may enable you to protect water on your reservation without EPA-approved 

standards. In addition, EPA may use technically sound tribal standards as guidance in permitting actions under the 

CWA based on the circumstances. You may also use tribal standards when reviewing and providing comments to 

EPA on proposed permits. Section III.3 of this chapter provides more information on working with EPA on 

permitting issues. 

Your tribal legal staff can help you determine where your standards will apply. If you do not have clear authority 

over some water resources you wish to regulate, you may want to work cooperatively with neighboring 

governments to ensure adequate protection. 

3. Identifying Goals of Tribal Standards 

Chapter 7 discusses identifying goals of tribal standards. Review the information in section I.6 of chapter 7 for 

more information on considerations to keep in mind when defining objectives of standards. Consider any relevant 

cultural or traditional goals when thinking about your standards goals. If you are not pursuing EPA approval for 

your standards, you may still want to consider some of the goals the CWA has identified as essential for standards 

(e.g., protect public health; enhance water quality; restore and maintain the chemical, physical, and biological 

integrity of waters; achieve protection and propagation of fish/shellfish/wildlife; and recreation). 

You may find that the goals and standards appropriate for your tribe (e.g., protecting tribal treaty rights) differ 

from state standards or national recommendations. 

4. Working in Partnership with EPA, Tribes, and States 

Working in cooperation with neighboring tribes and 

states will help you make full use of information and data 

already developed that may apply to your reservation. As 

discussed in sections I.5 and I.7 of chapter 7, you can 

use standards from neighboring tribes and states to help 

you develop your tribal standards. 

If you do not plan to seek EPA approval for your 

standards, you are not required to take downstream 

standards into consideration, but doing so may give you a 

better understanding of the uses water bodies that cross 

tribal boundaries can meet. You should also consider 

reviewing upstream standards to gain a better 

understanding of the quality of waters entering the 

reservation. 

Klamath River Mouth. Photo courtesy of Yurok Tribe. 

6-2 
II. Intermediate Program Activities 

1. Developing Draft Standards 

Section II.3 of chapter 7 contains information on developing uses, criteria, and antidegradation policies, the key 

components of standards. If you do not seek EPA approval for your tribal standards, you will not need to comply 

with the requirements or structure outlined in those sections; however, depending on your tribal needs, you may 

want to consider those requirements and structure when developing standards. 

2. Sharing Draft Standards with EPA, Tribes, and States for Review, as

Appropriate

Even if you are not seeking EPA approval for standards, the appropriate EPA Regional WQS Coordinator can 

serve as a valuable resource to help you develop standards. Consider sharing your draft tribal standards with EPA 

and neighboring tribes and states for an informal review. Your WQS Coordinator may be able to help you make 

sure that the standards you have developed will help you achieve the goals you have established. Neighboring 

tribes and states may be able to offer you suggestions based on their experience implementing standards 

programs. Working in partnership with your EPA region and neighboring tribes and states may help you develop a 

more successful standards program and may help you ensure that your standards will work in coordination with 

neighboring standards. 

3. Conducting Public Outreach 

Your tribe may have public participation requirements that apply to changes to tribal law. Consult your tribal 

attorney general or equivalent officer to see if any tribal public participation requirements apply. 

In addition, a successful tribal water quality program depends on community involvement and participation. (See 

section I.12 of chapter 3 for more information on community involvement and participation.) Similarly, community 

involvement in standards development can lead to successful standards programs. Working in partnership with 

your community (including potentially regulated entities), watershed groups, and others will help you understand 

your community’s perspective and may give you access to data and information that could increase the 

effectiveness of your program. In addition, enlisting the support of those affected by the quality of your 

reservation waters may build support for the standards development process. 

4. Drafting Tribal Code Based on Standards 

Once you have drafted standards, you should pursue some mechanism (e.g., amendment to the tribal code) to 

incorporate those standards into law on your reservation. You may wish to work with your tribe’s legal department 

during this process. The department can help you with the structure and language of the standards, and it can help 

you acquire the appropriate approvals and signatures. You may want to share a draft of your tribal code with your 

tribal council, EPA, and neighboring tribes and states for informal review. They may be able to identify any 

potential problems, point out additional topics you may want to address, and confirm that the standards you have 

drafted will help you meet your program goals. 

5. Formally Adopting Standards through Tribal Council 

Work with your tribe’s legal department and your tribal council to formally adopt the standards. Make sure that 

you have followed all applicable requirements for approval. Once your tribal council has formally adopted your 

standards, you may be required to notify your community. You should consider doing this as a follow-up to your 

standards development public outreach activities even if it is not a requirement. An informed and educated 

community will make it easier for you to implement your standards. 

6-3 
III. Mature Program Activities 

1. Implementing Standards 

You can implement your tribal standards through a variety of mechanisms, such as limits placed on pollutants 

discharged by point sources or through controls developed to reduce NPS pollution. You may be able to develop 

MOAs with EPA for permitting purposes. See section III.3 of this chapter for more information on MOAs. In 

cases where control of pollution through permits will not allow you to attain standards, or where NPS are the 

principal sources of pollution, you may rely on your NPS control program to reduce the NPS pollutant load. 

Chapter 5 contains more information on developing and implementing NPS control programs. 

2. Reviewing Standards 

Even if you are not required to do so under tribal law, you should consider reviewing your standards periodically 

and modifying or adopting new standards, if necessary. EPA recommends triennial reviews of standards. When 

reviewing your standards, consider using the same community involvement mechanisms you used to develop the 

standards to keep the public up to date and involved. Your tribe may have specific public notification requirements 

with which you must comply to modify or change standards. Prior to any public hearing, consider making any 

proposed revisions, including supporting analyses, available to the public. When you begin activities to revise or 

adopt new standards, consider consulting with your EPA regional office, neighboring states, watershed groups, 

and others. 

During your standards review, you may want to consider the following: 

z New federal or tribal statutes, regulations, or guidance 

z Legal decisions involving the application of standards 

z Water bodies or segments that do not meet designated uses 

z Water bodies with designated uses that do not meet the fishable/swimmable use 

z Other necessary clarifications or revisions 

3. Developing MOAs with EPA for Permitting Purposes 

Even if you have not developed EPA-approved WQS and cannot issue federally approved permits, you can work 

in collaboration with EPA and states to help them enforce permits and make compliance determinations. In many 

cases, states and tribes have developed cooperative agreements that promote consultation, sharing of technical 

information, notification of permitting issues, and joint tribal/state programming. You can expand your role in 

assisting permitting authorities through MOAs with neighboring states. Some states and tribes have entered into 

MOAs to share enforcement-related files and information that may have an adverse impact on tribal water 

bodies. In addition, some tribes have entered into formal agreements with states developing TMDLs on rivers and 

lakes that include transboundary waters. This approach enables tribes to use their own or EPA-approved WQS in 

setting appropriate protection levels. 

Depending on the nature of your MOA, you may want to consider taking the lead in investigating complaints and 

other issues. You can also document and report any compliance problems to EPA or to the appropriate permitting 

authority. 

6-4 
Chapter 7: EPA-Approved

Water Quality Protection

Approach

Introduction 

This approach to water quality management uses a regulatory framework based on the CWA structure to control 

water quality. Tribes that use this approach will develop and establish federally approved water quality standards 

(WQS). This is an approach that many tribes have followed already to develop their tribal water quality programs. 

WQS will serve the dual purpose of establishing the water quality goals for a specific water body and serving as 

the regulatory basis for establishment of water quality-based treatment controls. These water quality-based 

treatment controls include Section 401 certification, National Pollutant Discharge Elimination System (NPDES) 

permits, and enforcement actions. The activities discussed in the chapter are most appropriate for sophisticated 

programs with many years of experience. 

EPA has published detailed guidance on issues related to EPA Water Quality Standards developing WQS, including specific guidance for tribes.

This guidance is not intended to duplicate these Note: EPA water quality standards are only for the

technical guidance documents; instead, it provides protection of surface waters of the U.S. They are

an overview of the major elements of WQS and not applicable to ground water.

directs you to appropriate sources of information.

Consult the appropriate Regional WQS

Coordinator before you begin to develop WQS.

Because tribes choosing this approach will be developing regulatory programs for federal approval, they must 

comply with specific requirements. EPA’s Office of Science and Technology (OST) has written a general 

guidance for developing standards and a reference guide for Indian tribes. In addition, OST maintains a WQS 

Web site that includes links to all approved tribal WQS. More information on these resources is provided in the 

box below. 

Reference Materials Related to WQS Development 

EPA’s Reference Guide to Water Quality Standards for Indian Tribes (EPA 440/5-90-002), available online 

at http://epa.gov/waterscience/library/wqstandards/indianguide.pdf, contains more information on tribal 

considerations in developing WQS. It also lists sources of information that you can consult to help you 

understand and develop standards. 

EPA’s Water Quality Standards Handbook: Second Edition (EPA-823-B-94-005), available online at http:// 

www.epa.gov/waterscience/standards/handbook/, contains technical information on all aspects of WQS 

development, including requirements for tribes and issues related to adoption of tribal standards. 

OST’s Water Quality Standards Policy and Guidance Web site, http://www.epa.gov/waterscience/standards/

policy.htm, contains links to policy and guidance documents. Consult this site for a complete list of all EPA

WQS resources. Approved standards for states, tribes, and territories are posted on http://www.epa.gov/

waterscience/standards/wqslibrary/.

7-1 
Activities Included in Chapter 7 

Fundamental Program Activities

1. Understanding Water Quality Standards

2. Understanding Section 401 Certification

3. Understanding Section 404 Permitting

4. Using EPA WQS Trainings and Educational Materials

5. Reviewing Existing Tribal and State Water Quality Standards

6. Identifying Goals of Tribal Regulatory Program

7. Working in Partnership with EPA, Tribes, and States

Intermediate Program Activities

Tribes should begin these activities after having completed the relevant fundamental program activities.

1. Applying for TAS Eligibility for a WQS Program and a Section 401 Certification Program

2. EPA Review of Tribal Application for TAS Eligibility for WQS Program and Section 401 Certification Program

3. Developing Standards................................................. Working With EPA, Tribes, and States

Reviewing EPA Regulation and Guidance

Designating Uses

Developing Criteria

Developing an Antidegredation Policy

Developing General Policies

4. Submitting Draft WQS for Formal Public Hearing and Comment

5. Formally Adopting WQS through Tribal Council

6. Submitting Adopted WQS for EPA Approval

7. Understanding EPA's WQS Review Process..................... Approved WQS

Disapproved WQS

8. Understanding EPA's Dispute Resolution Mechanism

Mature Program Activities

Tribes should begin these activities after having completed the relevant fundamental and intermediate program activities.

1. Implementing WQS

2. Conducting Triennial Reviews

3. Implementing Section 401 Certifications

4. NPDES Program Overview

5. Sources Regulated Under the NPDES Program

6. Understanding NPDES Permits

7. Reviewing Permits

8. Considering NPDES Program Authorization

9. Developing Capabilities for Permitting, Compliance, and Enforcement

10. Preparing for NPDES Program Authorization.................... Developing Tribal Code and Obtaining Approval from the Tribal Government

Inventorying Existing Point Sources

Establishing Sources of Funding to Run the NPDES Program

11. Obtaining NPDES Program Authorization

12. Assuming the Section 404 Program

13. Working with EPA to Transition from Federal to Tribal Implementation

14. Conducting Public Outreach

7-2 
Testing water quality on the Verde River. Photo courtesy of Salt 

River Pima-Maricopa Indian Community 

EPA Regional WQS Coordinators 

EPA’s Regional WQS Coordinators play a key role in working one-on-one with tribes to develop WQS. You 

should work closely with your regional WQS Coordinator throughout the WQS development process. You 

can obtain contact information for your regional WQS Coordinator on OST’s Web site, http://www.epa.gov/ 

waterscience/standards/regions.htm. 

This chapter also provides information about the WQS program authorization process. Before EPA can approve a 

tribe’s water quality standards under the CWA, it must approve the tribe’s application for TAS eligibility to 

administer the WQS program. 

As noted in chapter 4, analysis of your monitoring data 

can provide useful inputs to development of your 

WQS. Before you attempt to regulate the quality of 

waters on your reservation, you should know their 

current condition. Monitoring data will help you 

understand the natural variability in water quality data, 

make informed management decisions, and identify 

sources most severely affected by point source and 

NPS pollution. Monitoring results will also help you 

identify specific parameters of concern (e.g., high 

levels of toxic chemicals) for water bodies on your 

land. Once you have developed and implemented a 

WQS program, your monitoring program will help you 

assess whether your water bodies are meeting the 

criteria for their designated uses and determine the 

effectiveness of your standards. A strong monitoring 

and assessment program complements and improves a 

WQS program. 

EPA-approved WQS serve as the basis for water quality-based effluent limits for facilities with NPDES permits 

that are discharging to waters of a reservation covered by the standards. A tribe may also evaluate whether 

discharges under a federal license or permit will be consistent with its WQS when granting, denying, or 

conditioning a water quality certification under Section 401 of the CWA. Facilities developing or renewing 

NPDES permits or other federal licenses or permits for discharging to waters of a reservation must have their 

federal permits or licenses certified by the tribe under CWA Section 401 (unless certification is waived). The tribe 

and EPA will refer to the tribal WQS when identifying whether waters are impaired and developing total 

maximum daily loads (TMDLs) under Section 303(d) of the CWA. Finally, effluent limitations for a permit to 

discharge upstream from tribal waters must assure compliance with downstream federally approved standards. 

Federal WQS for Reservation Waters 

Tribes may adopt EPA-approved WQS to enhance the ability to include appropriate effluent limits in CWA 

permits for point source discharges into reservation waters. In situations where tribes have not adopted 

EPA-approved WQS, EPA may consider adopting federal WQS for reservation waters. EPA, however, 

prefers to work cooperatively with tribes and states on WQS issues and to initiate federal promulgation only 

when absolutely necessary. 

7-3 
I. Fundamental Program Activities 

1. Understanding Water Quality Standards 

WQS apply to “waters of the United States.” For tribes, these can include rivers, streams, intermittent streams, 

lakes, natural ponds, wetlands, estuaries, and near-shore coastal waters that are within the tribe’s reservation. The 

statutory basis for EPA’s WQS program is located in Section 303(c) of the CWA. According to this Section, the 

purpose of WQS is to support the following goals found in Section 101(a) of the CWA: 

z Restoring and maintaining the chemical, physical, and biological integrity of waters 

z Achieving, whenever attainable, a level of water quality that provides for the protection and propagation of 

fish, shellfish, and wildlife and for recreation in and on the water 

WQS consist of three components: designated uses, water quality criteria, and an antidegradation policy. WQS 

define the water quality goals for a water body by designating its use(s) (e.g., recreation, water supply, aquatic 

life) and setting water quality criteria (e.g., numeric pollutant concentrations, narrative requirements) to protect 

the use(s). WQS must also include an antidegradation policy. The policy must at a minimum maintain and 

protect existing uses (i.e., prevent water quality from deteriorating), protect high-quality waters, and maintain 

water quality in water bodies designated as Outstanding National Resource Waters (ONRWs). In addition, tribes 

may, but are not required to, include in their WQS policies that address implementation issues (e.g., low-flow 

conditions, variances from WQS, mixing zones near point source discharges). 

Outstanding National Resource Waters 

ONRWs are generally regarded as the highest quality waters of the United States; however, other water 

bodies that are unique, or ecologically sensitive but of lower quality (e.g., wetlands), also can be classified as 

ONRWs. This classification is intended to protect and maintain current water quality. Therefore, no 

degradation or change in water quality is allowed, except on a short-term, temporary basis (i.e., weeks or 

months). California’s Lake Tahoe, Florida’s Biscayne Bay, and Tennessee’s Reelfoot Lake are examples of 

water bodies designated as ONRWs. 

WQS serve as the basis for water quality-based control actions (e.g., a NPDES permit, a water quality 

certification for a federal license). WQS do not impose any directly enforceable requirements on any party, 

however. WQS will have no direct effect on any entity until they are implemented in a permit or some other CWA 

decision. Once WQS have been implemented in a permit, the permit can be enforced. The CWA does not require 

authorized tribes to regulate NPS pollution through enforceable controls, although tribes can determine what, if 

any, controls on NPS pollution are needed to attain WQS. 

EPA recognizes that tribes have varying abilities to develop WQS. Some tribes have more technical capability and 

experience in drafting and implementing regulations and may be capable of adopting more complex standards. 

Regardless of your tribe’s level of expertise, as a first step you should focus on the basic structure of WQS (i.e., 

designated uses for identified water segments, appropriate narrative and numeric criteria, an antidegradation 

policy). The complexity and sophistication of the structure you adopt will depend on your program’s abilities and 

the environmental concerns you wish to address. 

WQS development is an ongoing process. The CWA and federal regulation require triennial revisions of WQS 

(see section III.2 of this chapter for more information on triennial reviews). Tribes and states use triennial reviews 

to fine tune WQS. EPA anticipates that tribal staff will also use triennial revisions to further refine their WQS. 

7-4 
Examples of EPA-approved tribal WQS, including designated uses, are available online at http://www.epa.gov/ 

waterscience/standards/wqslibrary/tribes.html. 

2. Understanding Section 401 Certification 

Section 401 of the CWA provides eligible tribes with a powerful mechanism to control discharges to waters on 

Indian reservations. Under Section 401 of the CWA, tribes with approved WQS can review any application for 

federal permits or licenses that may result in a discharge to reservation waters for which the tribe has developed 

approved WQS. As stated in 40 CFR 131.4, your tribe is eligible for TAS for Section 401 certification purposes if 

your tribe is determined to be eligible for TAS for the WQS program. 

The Section 401 certification process allows your tribe to certify whether the discharge will comply with your 

tribe’s EPA-approved WQS. In addition, you can examine whether the discharge will violate effluent limitations, 

toxic pollutant limits, and other water resource requirements of tribal law or regulation. This means that a facility 

with a NPDES permit or other federal license or permit discharging into reservation waters for which you have 

developed approved WQS will be required to obtain a 401 certification from your tribe when renewing the permit 

or license. If you determine that the proposed discharge will not comply with the tribe’s approved water quality 

standards or other appropriate requirements of tribal law, you may in your certification set forth license conditions 

necessary to do that. Those conditions shall become part of the federal license or permit. More information about 

Section 401 certifications is available online at http://www.epa.gov/OWOW/wetlands/regs/sec401.html. 

3. Understanding Section 404 Permitting 

Section 404 of the CWA establishes a program to regulate the discharge of dredged and fill material into waters of 

the United States, which includes wetlands. Discharges into waters of the United States that are regulated under 

this program include, but are not limited to, fills for development, water resource projects (such as dams and 

levees), infrastructure development (such as highways and airports), and conversion of wetlands to uplands for 

farming and forestry. The basic premise of the program is that no discharge of dredged or fill material can be 

permitted if a practicable alternative exists to achieve the project purpose that is less damaging to the aquatic 

environment or if a water body would be significantly degraded by the placement of dredged or fill material. The 

U.S. Army Corps of Engineers (the Corps) issues Section 404 permits based on CWA Section 404(b)(1) 

guidelines written by EPA (40 CFR Part 230). EPA and the Corps both have enforcement authority over 404 

discharges. 

States and tribes can assume administration of the Section 404 permit program in certain waters within their 

jurisdictions. Since authority has been available to states and tribes, only two states have elected to assume the 

federal program. 

4. Using EPA WQS Trainings and Educational Materials 

EPA holds a number of training sessions, workshops, and meetings related to WQS development and 

implementation. If you would like more information on the basics covered in this guidance, you should consider 

using EPA’s educational materials. The WQS Academy, for instance, offers a basic WQS course that introduces 

students to all aspects of the WQS program, including the interpretation and application of WQS regulation, 

policies and program guidance, the development of water quality criteria, and other facets of the water program. 

From time to time, EPA also conducts specialized workshops on WQS development for Indian tribes. More 

information on the WQS Academy, other long-distance training opportunities, and guidance documents are 

available online at http://www.epa.gov/waterscience/standards/training.htm. 

7-5 
5. Reviewing Existing Tribal and State Water Quality Standards 

As you begin to develop WQS for your tribe, EPA recommends that you work closely with the water quality 

standards coordinator in the appropriate EPA regional office to obtain the latest criteria recommendations and to 

discuss the adjacent state and tribal WQS as an option or starting point for your tribal WQS. You are required to 

take into consideration and ensure the attainment and maintenance of downstream WQS when developing your 

WQS (40 CFR 131.10). Hence, as a first step you may benefit from reviewing downstream tribal and state 

standards. You may decide to use them as a basis for your standards. This is an expedient way of getting WQS in 

place. If necessary, they can then be revised during the triennial review process. You can also use downstream 

tribal and state standards to gain an understanding of existing conditions in your area, EPA’s expectations for 

approved standards, and WQS in general. 

OST maintains a list of all EPA-approved state standards online at http://www.epa.gov/waterscience/standards/ 

states/. EPA-approved tribal standards are available online at http://www.epa.gov/waterscience/standards/ 

wqslibrary/tribes.html. 

6. Identifying Goals of Tribal Regulatory Program 

WQS should achieve the goals outlined in section I.1 of this chapter (protect public health or welfare, enhance 

water quality, and otherwise serve the purposes of the CWA). Before developing WQS, however, tribes may 

want to consider specific environmental problems that standards could address. WQS can be a very useful tool 

for some environmental programs. Some tribes have used WQS to help the program achieve goals such as 

providing guidance about existing water quality, protecting aquatic life, defining allowable levels and types of 

discharges, helping to establish priorities for the allocation of treatment resources and cleanup efforts, and 

ensuring additional protection for waters used as drinking water supplies. EPA-approved WQS do not apply to 

ground water; hence, tribes where surface water is scarce may find that standard development may not help 

them achieve their goals most effectively. After an evaluation of standards in relation to its overall program goals, 

a tribal water quality program may decide that development of WQS will not help achieve its goals in the most 

effective way. Tribes reaching this determination may elect to pursue one of the other routes for program 

development presented in this guidance and described in chapters 5 and 6. 

7. Working in Partnership with EPA, Tribes, and States 

Sound environmental planning and management suggest that you collaborate with neighboring tribes and states 

and EPA. Particularly in the field of environmental regulation, your tribe, neighboring states, and EPA often share 

the same problems, and coordination may help you to address them comprehensively. Working together to resolve 

these problems serves the interests of all parties. You may also benefit by contacting other organizations in your 

watershed, including local governments and watershed organizations. 

EPA can provide technical expertise and guidance, and thus strongly encourages tribes to work with their EPA 

Regional WQS Coordinator well before adopting and submitting WQS to EPA for approval. Working together 

early in the development process will help prevent problems that may lead to EPA disapproving a tribal submission 

later on. Likewise, working with your neighboring states as you develop your standards may be helpful. 

In some cases, you may want to work even more closely with neighboring tribes and states. Depending on 

circumstances, you may choose to negotiate a cooperative agreement with a neighboring tribe or state regarding 

standards on common water bodies or adopt the standards of an adjacent state as your own, making modifications 

as needed. When available, these options can be quick and cost-effective ways of establishing WQS and may be 

more likely to result in consistent upstream and downstream standards for water bodies that flow through the 

reservation. 

7-6 
Even if you find that your tribe and neighboring tribes or states disagree on some topics, many points of 

agreement and cooperative partnership between states and tribes that can benefit both parties can be negotiated. 

Usually, these agreements have focused on information exchanges and transboundary coordination, much like 

agreements commonly reached between states. Some agreements have also allowed tribes to access state 

resources, such as training and on-the-ground work to protect water resources. 

Approaches to WQS Development 

Remember that the development of WQS is an iterative process. As your WQS program evolves, you may 

change your approach for establishing standards. You may adopt existing state standards initially and modify 

them as necessary in subsequent years. The WQS regulation requires that you review EPA-approved WQS 

at least once every 3 years and revise them if necessary. 

II. Intermediate Program Activities 

1. Applying for TAS Eligibility for a WQS Program and a Section 401

Certification Program

As is the case with obtaining eligibility for Section 106 grants, you must obtain EPA approval for TAS for the 

WQS program to have your standards approved by EPA under the CWA. To be approved for WQS program 

eligibility, you must meet the TAS requirements of CWA Section 518 and 40 CFR 131.8. See section I.1 of 

chapter 3 for a summary of some of the CWA Section 518 statutory requirements. If you have TAS eligibility for 

Section 106, you may have met some of these requirements already. You may have to submit only information not 

submitted previously or submit updated information where previously submitted information is no longer current. 

Refer to appendix B, Requirements for Authorization of Tribal Administration of the WQS Program, for a 

checklist of some of the items to be included with WQS program authorization applications. See CWA Section 518 

and 40 CFR 131.8(b) and contact the EPA Regional WQS Coordinator for information on specific requirements 

that you must include in your application to the EPA Regional Administrator (RA). 

EPA will work individually with the tribe making the application for eligibility for the WQS program to ensure that 

the application is complete and meets all of EPA’s requirements. EPA strongly recommends that you contact the 

appropriate EPA WQS Coordinator and the Office of Regional Counsel to discuss specifics before you submit 

your application for program eligibility. EPA’s WQS Coordinators are also available to assist you in developing 

WQS for your reservation prior to obtaining authorization to conduct the WQS program. 

Although a tribe can submit a TAS eligibility application and an application for WQS approval together, EPA will 

not approve a tribe’s WQS until it has approved the eligibility application. A tribe that receives eligibility approval 

for WQS from EPA is also approved to conduct the Section 401 certification program on reservation lands and 

certify that federally licensed or permitted discharges comply with the tribe’s EPA-approved WQS. There is no 

separate application for the Section 401 certification program. 

7-7 
2. EPA Review of Tribal Application for TAS Eligibility for WQS Program and 

Section 401 Certification Program 

The EPA process for reviewing tribal applications for TAS eligibility for the WQS program consists of five steps. 

They are: 

z Step 1: The Tribe Submits an Application. Tribes are encouraged to work with EPA staff in 

developing their eligibility applications to administer a WQS and certification program. Drafts or 

components of the applications may be shared with EPA staff before being formally submitted to EPA. 

EPA will examine the tribe’s application and may request additional information. 

z Step 2: Comment Period. EPA then provides appropriate governmental entities with notice of the tribe’s 

application, including information as to the substance and basis of the tribe’s claims regarding authority to 

regulate reservation water quality, and provides 30 days for comments on the tribe’s application. EPA also 

publishes a notice in relevant newspapers, offering the public the opportunity to provide comments through 

appropriate governmental entities. EPA then affords the applicant tribe the opportunity to provide a 

response to the comments. 

z Step 3: EPA Review. A team of EPA regional and Headquarters staff reviews the application to 

determine whether the tribe meets the requirements for eligibility listed above. If necessary, EPA may 

request additional information from the tribe. 

z Step 4: Proposed Findings of Fact (if needed). Where appropriate, EPA prepares a proposed findings 

of fact document regarding tribal authority that would form a basis for EPA’s decision on whether the tribe 

has adequate authority as described above. EPA provides the tribe, appropriate governmental entities, and 

the public with the opportunity to comment on the analysis in the proposed findings of fact. The tribe 

applying for eligibility is given the opportunity to respond to comments received. 

z Step 5: Final Decision. The EPA team reviews all of the materials — including the original application, 

any proposed findings of fact, and all comments submitted — prepares draft decision documents, including 

a response to comments, and submits them for final review within the Agency. The RA (or delegatee) then 

makes a final decision and, if EPA approves the application, produces a decision document with the 

findings of fact as an appendix if needed. The regional office will notify the tribe in writing of EPA’s 

approval of the tribe’s application. The approval letter and the decision document are transmitted to the 

tribe. 

3. Developing Standards 

a. Working with EPA, Tribes, and States 

You should consider sharing your draft standards with your EPA region and neighboring states and tribes or 

working with them to develop your draft standards. Working with your EPA Regional WQS Coordinator as you 

develop your standards may help prevent problems that could lead to EPA disapproving your submission later on. 

Similarly, working with neighboring states and tribes as you develop your standards will promote coordinated 

water quality protection. 

EPA’s Water Quality Standards Handbook (referenced on page 7-1 of this chapter) contains technical guidance 

on developing standards. In addition, this section provides some basic information you should consider. 

As mentioned in section I.7 of this chapter, it is important to work with your EPA regional office early in the WQS 

development process and share drafts of your tribe’s WQS as they are developed. Once you have developed 

draft standards and have completed the public participation requirements as laid out in section II.2 of this chapter, 

7-8 
your tribe may adopt the WQS. When the WQS are tribally adopted, you must submit them to EPA to receive 

approval for your WQS. 

b. Reviewing EPA Regulation and Guidance 

Although you have some flexibility in the standards you adopt, they must meet some basic requirements. At a 

minimum, EPA expects that tribal WQS, at least initially, should focus on basic contents and reflect existing uses 

and existing water quality. The standards must be established for all “waters of the United States” within the 

reservation area covered by the application. Tribes should focus on the basic structure of a WQS system 

(designated uses, water quality criteria to protect the uses, and an antidegradation policy). How complex or 

sophisticated these elements need to be depends on the tribes’ technical capacity and the environmental concerns 

to be addressed. 

Tribal WQS should be developed considering the quality and designated uses of waters entering and leaving 

reservations. It is important that tribes be aware of the WQS of surrounding states and tribes. Even though there 

is no requirement to match those standards, WQS regulation requires that tribes consider and ensure the 

attainment and maintenance of downstream WQS (40 CFR 131.10). 

See section 1.9.1 of EPA’s Water Quality Standards Handbook for more information on EPA’s basic 

expectations for tribal WQS. Section 2.2 of the handbook discusses consideration of downstream uses. 

c. Designating Uses 

Use classifications refer to the types of activities you expect water bodies to support. You must develop a 

classification system to designate uses for water bodies or segments of water bodies on your reservation. You 

may adopt and use any categories appropriate for your tribe that meet all applicable requirements when 

developing uses. You may also adopt subcategories of a use (e.g., you could divide the “recreation” use into two 

subcategories – recreation in the water and recreation on the water). For more information on designated uses, 

see 40 CFR 131.10. General categories for designated use include: 

z Public Water Supplies: Waters that are drinking water sources. They may require treatment prior to 

distribution by public water systems. 

z Protection and Propagation of Fish, Shellfish, and Wildlife: This category is often divided into 

subcategories (e.g., cold-water fish, warm-water fish). It can also include protection of aquatic flora. You 

should designate aquatic life uses that appropriately address biological integrity and adopt biological criteria 

necessary to protect those uses. 

z Recreation: This category is traditionally divided into primary and secondary contact recreation. Primary 

contact includes activities likely to result in immersion in the water (e.g., water skiing, swimming, surfing). 

Secondary contact includes activities when immersion is unlikely (e.g., boating, fishing, rafting). 

z Agriculture and Industry: Agricultural use defines waters suitable for crop irrigation, livestock 

consumption, support of vegetation for range grazing, and other uses that support farming and ranching 

and protect livestock and crops from injury. Industrial uses include industrial cooling and processed water. 

z Navigation: This use protects ships and crews and maintains water quality to avoid restricting or 

preventing navigation. 

z Other Uses: You may adopt other uses that you think are necessary, such as any tribally relevant 

traditional or cultural uses, aquifer protection, or hydroelectric power. 

7-9 
When designating uses, remember that water bodies can support more than one use. Criteria for waters with 

multiple use designations must support the most sensitive use, as required by 40 CFR 131.11(a). You can 

designate uses for entire water bodies or segments of water bodies. When designating uses, you should take 

physical, chemical, and biological characteristics of the water body into account. You should also consider its 

geographical setting, scenic qualities, and any relevant economic considerations. In addition to the minimum uses 

required by the CWA (i.e., aquatic life use, wildlife use, and primary contact recreation use), you can designate 

other uses as appropriate, but you must ensure that your water quality criteria (discussed below) protect the most 

sensitive use, as required by 40 CFR 131.11(a). 

CWA Section 101(a)(2) states that it is a national goal that wherever attainable: 

1. protection and propagation of fish, shellfish, and wildlife, and 

2. recreation in and on the water 

be achieved. As a result, all waters are designated for these two uses at a minimum unless a use 

attainability analysis is provided. A use attainability analysis is a structured scientific assessment of the factors 

affecting the attainment of a use that may include physical, chemical, biological, or economic factors described in 

40 CFR 131.10(g). It also examines whether the water body can attain fishable/swimmable use through effluent 

limits for point dischargers and cost-effective management measures for NPS. As required by 40 CFR 131.20(a), 

every 3 years you must re-examine those water bodies where designated uses of fishable/swimmable were not 

deemed attainable to determine whether new information has become available that indicates the fishable/ 

swimmable uses can be attained. 

Waste Transport and Waste Assimilation 

In no case may you adopt waste transport or waste assimilation as a designated use for any waters of the 

United States. You also may not replace a designated use with a designated use that is lower than the use 

currently being attained. 

When establishing WQS for the first time, you should carefully consider the uses that are appropriate for each 

water body or segment. Removing or downgrading a designated use, while possible, requires a substantial 

demonstration that attaining the use is not possible. (See section 2.7 of the Water Quality Standards Handbook 

for more information on removing designated uses.) You may always add a use and develop scientifically 

defensible criteria to protect that use. 

Chapter 2 of EPA’s Water Quality Standards Handbook contains information on developing water body uses. 

For more information on use attainability analyses, consult EPA’s Technical Support Manual for Conducting 

Use Attainability Analyses (EPA 440-486-038). Pages 1-233 apply to rivers and streams, pages 234-422 apply to 

estuarine systems, and pages 422-622 apply to lakes. The manual is available online at http://www.epa.gov/ 

waterscience/library/wqstandards/uaavol123.pdf. 

7-10 
Use Classifications for Wetlands (from EPA’s Water Quality Standards for Wetlands 

Handbook, EPA 440/S-90-011) 

z Ground water recharge/discharge z Nutrient removal/transformation 

z Flood flow alteration z Wildlife diversity/abundance 

z Sediment stabilization z Aquatic diversity/abundance 

z Sediment/toxic retention z Recreation 

You can obtain the Water Quality Standards for Wetlands handbook online at http://www.epa.gov/ 

waterscience/library/wqstandards/wetlandsguidance.pdf. 

d. Developing Criteria 

Water quality criteria are levels of individual pollutants, water quality characteristics, or descriptions of a water 

body that, if met, protect designated uses. Water quality criteria can consist of numeric criteria or narrative 

descriptions of conditions a water body must meet (narrative criteria). In some cases, narrative criteria can 

supplement numeric criteria. 

Numeric criteria establish values expressed as levels, concentrations, toxicity units, or other numbers, deemed 

necessary to protect designated uses. Numeric criteria can refer to chemical (e.g., phosphorus), physical (e.g., 

temperature), or biological (e.g., the types and numbers of aquatic species that should be present in the water 

bodies) parameters. Numeric criteria are appropriate for known causes of toxicity and for protection against 

pollutants with potential human health effects. Numeric criteria may be values not to be exceeded (e.g., toxic 

chemicals), values that must be exceeded (e.g., dissolved oxygen), or a range (e.g., pH). 

Narrative criteria are general statements designed to protect a specific designated use or set of uses (e.g., “free 

from substances that will produce undesirable or nuisance aquatic life”). Narrative criteria are especially 

important for the control of NPS, chemicals with no numeric criteria, and activities that may affect the physical or 

biological aspects of water quality. 

See 40 CFR 131.11 for more information on numeric and narrative criteria. 

EPA publishes recommended water quality criteria consisting of scientific information on concentrations of 

specific chemicals or levels of parameters in water that protect aquatic life and human health, as required by 

Section 304(a) of the CWA. You should consider this information, along with recommended criteria, as the basis 

for developing WQS. Criteria must be based on a sound scientific rationale and must contain appropriate 

parameters or constituents to protect designated uses. Section 303(c)(2)(B) requires that you adopt numeric 

criteria for priority toxic pollutants for which EPA has developed Section 304(a) recommendations and that may 

be discharged or present in your waters and impair designated uses. You are also encouraged to adopt numeric 

and narrative criteria for other pollutants. If you adopt narrative criteria, you must develop implementation 

procedures to explain how you will regulate point source discharges of priority toxic pollutants in impaired waters. 

In adopting criteria, tribes may: 

z Adopt the criteria that EPA publishes periodically as required under Section 304(a) of the CWA 

z Modify the Section 304(a) criteria to reflect site-specific conditions 

z Adopt criteria based on other scientifically defensible methods 

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Narrative Criteria 

EPA’s most recent Section 304(a) criteria summary document includes the following narrative criteria:

All waters [shall be] free from substances attributable to wastewater or other discharges that:

z Settle to form objectionable deposits

z Float as debris, scum, oil, or other matter to form nuisances

z Produce objectionable color, odor, taste, or turbidity

z Injure or are toxic or produce adverse physiological responses in humans, animals, or plants

z Produce undesirable or nuisance aquatic life

The most recent criteria published under Section 304(a) of the CWA are available online at http://www.epa.gov/ 

waterscience/criteria/wqcriteria.html. Other than the requirement to adopt criteria for a specific list of priority 

toxic pollutants wherever they are reasonably expected to interfere with designated uses, EPA has not established 

mandatory lists of criteria. For numeric criteria for toxics, states and tribes usually rely on EPA’s recommended 

values, rather than on monitoring results. At a minimum, however, you should consider all of EPA’s published 

Section 304(a) criteria. These include: 

z Narrative “free froms” (e.g., free from substances that will produce undesirable or nuisance aquatic life) 

z Dissolved oxygen 

z pH 

z Temperature 

z Bacteriological criteria (for recreational use, and potentially for cultural and traditional uses) 

z The list of non-priority pollutants in EPA’s Section 304(a) recommended water quality criteria 

Great Lakes Basin Requirements 

Tribes located within the Great Lakes Basin are required to comply with all of the requirements of the Great 

Lakes Water Quality Guidance when adopting WQS under the CWA, including adopting specific water quality 

criteria. Information on Great Lakes Basin requirements is available online at http://www.epa.gov/ 

waterscience/gli/. 

If you think these regulations may apply to you, you should consult your EPA regional office. For further 

information, contact the Great Lakes National Program Office. To see a map of the Great Lakes Basin, visit 

http://www.epa.gov/glnpo/atlas/ and click on “Ecoregions, Wetlands, and Drainage” under the heading List of 

Maps near the bottom of the page. 

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Chapter 3 of the Water Quality Standards Handbook contains more information on adopting criteria that protect 

designated uses. Chapter 4 of EPA’s Water Quality Standards for Wetlands contains additional information on 

narrative and numeric criteria. In addition, a compendium of EPA’s National Recommended Water Quality 

Criteria can be found at http://www.epa.gov/waterscience/criteria/wqcriteria.html. 

e. Developing an Antidegradation Policy 

Your WQS must include an antidegradation policy. In addition, you must identify the methods for implementing the 

policy. Stated simply, antidegradation policies must ensure that all existing water body uses are maintained in all 

water bodies. Antidegradation policies must maintain and protect high-quality waters, as well as water quality of 

ONRWs. Tribes must identify their antidegradation implementation procedures. Antidegradation implementation 

procedures identify the steps and issues to be addressed when proposed regulated activities (e.g., new 

development projects) may affect water quality. Your policy must be consistent with 40 CFR 131.12. 

For those tribes located within the Great Lakes Basin, antidegradation policies must be consistent with both 40 

CFR 131.12 and 40 CFR Part 132, Appendix E. There are additional implementation procedures for 

bioaccumulative chemicals of concern that tribes in the Great Lakes Basin are required to adopt. 

The federal antidegradation policy (listed in 40 CFR 131.12(a)) consists of three tiers protecting different levels of 

uses: 

z Tier 1: Protects existing uses (i.e., those uses actually attained in the water body on or after November 

28, 1975, whether or not they are included in the WQS), applying a minimum level of protection to all 

waters. 

z Tier 2: Applies to waters whose quality exceeds that necessary to support the goals of the CWA. The 

quality of these waters cannot be lowered to less than the level necessary to protect the fishable/ 

swimmable uses and other existing uses and can only be lowered to these levels after you show that 

allowing lower water quality is necessary to accommodate important economic or social development in 

the area in which the waters are located. 

z Tier 3: Applies to ONRWs where ordinary use classifications or supporting criteria may not be sufficient 

or appropriate. You may choose to classify specific waters as ONRWs. This may be an appropriate 

classification for unique waters such as those located in tribal wilderness areas or wildlife refuges. 

Classifying a water body as an ONRW is often the most effective approach to protecting high-quality or 

ecologically significant water resources, but remember that this classification may restrict or preclude 

significant development activities both on and off your reservation because of its stringent prohibitions 

against any lowering of water quality. 

Some tribes have developed an additional Tier, Tier 2 1⁄2. This tier is more stringent than Tier 2 but less stringent 

than Tier 3. 

Your antidegradation policy cannot permit any activity that would partially or completely eliminate any existing 

use. 

Public participation and intergovernmental coordination can make a tribe’s antidegradation policy and 

implementation procedures more effective. Requirements for public participation and intergovernmental 

coordination when determining whether to allow lower water quality in high-quality water are detailed in 40 CFR 

131.12(a)(2). 

Consult chapter 4 of EPA’s Water Quality Standards Handbook for more information on antidegradation 

policies. 

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Members of the Karuk Tribe of California fishing for salmon. 

Photo courtesy of the Karuk Tribe of California. 

f. Developing General Policies 

You may also adopt policies in your standards that affect how you apply and implement those standards. Policies 

on mixing zones, variances, and low flows are the most common general policies. These policies are subject to 

EPA review and approval. You may implement other general policies that apply to your standards with the 

approval of your EPA regional office. 

A mixing zone is a limited area or volume of water 

where a discharge enters a water body and numeric 

criteria may be exceeded as long as acutely toxic 

conditions are avoided. It serves as an area where the 

original discharge is diluted. In some cases, it may be 

appropriate for you to designate a mixing zone. If you 

implement a mixing zone policy, your WQS should 

describe the methodology for determining the location, 

size, shape, outfall engineering design, and in-zone water 

quality of mixing zones. You should give careful 

consideration to the appropriateness of mixing zones 

where the substance discharged is persistent in the 

environment (i.e., only slowly decomposes into other 

substances), accumulates in aquatic life, or causes cancer. 

Mixing zones for bioaccumulative chemicals are prohibited 

in the Great Lakes Basin because of the threat that these 

chemicals pose to human health, aquatic health, and 

wildlife. For more information on this prohibition, see 40 

CFR Part 132 or visit http://www.epa.gov/waterscience/ 

gli/mixingzones/. 

Variances can serve as an alternative to downgrading the 

designated use of a water body through a use attainability 

analysis if you believe that the use ultimately can be 

achieved. You may grant variances for specific pollutants 

to an individual discharger. Controlling discharges via a 

variance instead of designating a use requiring less 

stringent criteria can help you ensure that water quality in 

the water body continues to improve. The variance must 

be justified based on one of the six factors listed in 40 

CFR 131.10(g). 

You may designate a critical low-flow volume below which numerical criteria do not apply; however, narrative 

criteria should be applied even in low-flow situations. Low-flows are used in developing water quality-based 

effluent limits and waste load allocations. These policies are also subject to review and approval by EPA. 

Consult chapter 5 of EPA’s Water Quality Standards Handbook for more information on general policies. 

4. Submitting Draft WQS for Formal Public Hearing and Comment 

Development of WQS under the CWA requires public involvement and participation. CWA Section 303(c)(1) 

requires that, at a minimum, you hold a public hearing to review proposed WQS and make the results of that 

review available to the Administrator. EPA urges you to involve the public even more actively in helping to 

establish WQS through public hearings and workshops. Public hearings must comply with applicable tribal law, 

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EPA’s Public Participation Regulation (40 CFR Part 25), and EPA’s WQS regulation. Prior to the hearing, you 

must make the proposed WQS and any applicable supporting materials (e.g., analyses of water quality) available 

to the public. Section I.12 of chapter 3 and section II.3 of chapter 6 have more information on conducting public 

outreach. 

5. Formally Adopting WQS through Tribal Council 

Before you can submit your standards to EPA for approval, you must adopt the standards as tribal law. EPA will 

not formally approve any tribal WQS unless they have been adopted by the tribal council, and you have submitted 

a certification stating that the WQS have been approved by the tribal council to EPA. You must include a 

certification from your tribal attorney general or equivalent officer with your WQS package to indicate that the 

WQS were adopted in accordance with tribal laws and codes and can be implemented in accordance with tribal 

laws and codes. Sections II.4 and II.5 of chapter 6 contain more information on adoption of standards as part of 

tribal law. 

6. Submitting Adopted WQS for EPA Approval 

After your tribe has approved your WQS, you must formally submit the tribally adopted WQS to EPA for review. 

Include the following elements in your submission: 

z Use designations consistent with CWA Sections 101(a)(2) and 303 (c)(2) 

z Methods used and analyses conducted to support WQS 

z Water quality criteria sufficient to protect designated uses (including those for priority toxic pollutants and 

biological criteria) 

z An antidegradation policy consistent with WQS regulation 40 CFR 131.12 

z Certification by the appropriate legal authority within your tribe that the WQS were duly adopted 

according to tribal law 

z General information to help EPA determine the adequacy of the WQS’ scientific bases for uses not 

specified in CWA Section 101(a)(2), including any sound scientific rationale on which water quality criteria 

are based 

z Information on general policies that may affect the application and implementation of WQS 

z Use attainability analyses (UAA) for all waters not classified as fishable/swimmable, as required by 40 

CFR 131.10(j) (UAAs may or may not touch on the supporting water quality criteria) 

z A record of public participation, including public comments made and your responses to comments 

In addition, your EPA regional office, in consultation, as appropriate, with the Fish and Wildlife Service and/or the 

National Marine Fisheries Service, will review your WQS to ensure, consistent with the federal Endangered 

Species Act, that they protect federally listed endangered or threatened species that may be present within the 

tribe’s boundaries. The two Services and EPA will work cooperatively with your tribe to address concerns about 

protecting endangered or threatened species. For more information on this process, consult the Endangered 

Species Act implementing regulations at 50 CFR Part 402 and the Memorandum of Agreement between EPA, the 

U.S. Fish and Wildlife Service, and the U.S. National Marine Fisheries Service (published in the Federal Register 

on February 22, 2001, 66 Fed. Reg. 11202-11217), available online at http://www.epa.gov/ost/standards/esa.html. 

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Your EPA regional office may request additional information. Check with the appropriate EPA Regional WQS 

Coordinator to determine if you should include anything else in your submission. 

7. Understanding EPA’s WQS Review Process 

After you submit adopted WQS, EPA reviews them, assessing whether: 

z You have adopted water uses that are consistent with CWA requirements and criteria that protect the 

designated water uses 

z You have followed your legal procedures for revising or adopting standards 

z Your tribal standards are based on appropriate scientific and technical data and analysis 

z You meet the submission requirements discussed above in section II.6 

EPA’s regional offices review WQS with assistance from the WQS Branch at Headquarters, if necessary. EPA 

uses the same regulatory requirements when reviewing tribal standards as when reviewing state standards. 

If the submitted WQS meet the regulatory requirements in 40 CFR Part 131 and Part 132, EPA will approve 

them. If some or all of the provisions fail to meet these requirements, EPA will notify you and specify the 

necessary changes. 

a. Approved WQS 

If EPA determines that you have met all appropriate requirements and approves your WQS, the appropriate 

Regional Administrator (RA) or other designated regional official will notify your tribal chair and the tribal agency 

responsible for the WQS program through an approval letter. If EPA approves only a portion of the standards you 

submitted, the RA will provide information on the sections that need modification in this letter. 

b. Disapproved WQS 

If your standards do not meet the requirements of the CWA and EPA’s regulations, the appropriate EPA RA or 

designee will notify you and specify the necessary revisions. It is EPA policy to encourage tribes to work with 

their appropriate EPA regional office in making such revisions. If a tribe does not adopt the changes specified by 

EPA within 90 days after notification of EPA’s disapproval, EPA shall promulgate such standards pursuant to 

Section 303(c)(4)(A) of the CWA, which provides that EPA is to “promptly prepare and publish proposed 

regulations setting forth a revised or new [WQS]...if a revised or new [WQS] submitted by such [tribe]...is 

determined by the Administrator not to be consistent with the applicable requirements of the [CWA].” 

8. Understanding EPA’s Dispute Resolution Mechanism 

Section 518 of the CWA requires EPA to establish a mechanism to resolve any unreasonable consequences that 

may arise as a result of differing WQS set by states and tribes located on common bodies of water. This 

mechanism is promulgated at 40 CFR 131.7. Either a state or a tribe may request EPA involvement in a dispute, in 

which case the RA, if appropriate, will work with the parties in an effort to reach an agreement. The RA may 

include other parties besides the tribe and state (e.g., permittees, landowners) in the dispute resolution mechanism. 

EPA may use mediation, nonbinding arbitration, and the Agency’s default procedure to resolve disputes. 

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To resolve disputes through mediation, the RA may appoint a mediator to facilitate discussions between the state 

and the tribe. Under nonbinding arbitration, the RA may appoint an arbitrator or panel of arbitrators to work with 

parties and recommend a nonbinding solution to EPA. Under the default procedure, EPA will review all available 

information and issue a recommendation for resolving the dispute. 

For more information on EPA’s dispute resolution mechanism, see section 1.7 of the Water Quality Standards 

Handbook. 

III. Mature Program Activities 

1. Implementing WQS 

Many of the CWA’s mechanisms for protecting water quality rely on WQS as the foundation for water qualitybased decisions. For example, WQS can be used to develop NPDES permit requirements, and WQS serve as a 

basis for identifying impaired waters under the CWA. WQS are also used as a basis for tribes (or EPA where a 

tribe is not administering the WQS program) to protect water quality from upstream discharges. For example, if 

an upstream permit applicant proposes a discharge that cannot ensure compliance with applicable CWA water 

quality requirements of downstream affected tribes, that discharge is prohibited under the CWA. They are also a 

basis for assessing and reporting on water quality biannually under Section 305(b) of the CWA. 

In addition, WQS are important for programs other than those associated with the CWA. For example, under 

EPA’s Superfund program, water quality standards promulgated pursuant to the CWA are generally considered 

“Applicable or Relevant and Appropriate Requirements” (ARARs) that must be attained or waived during 

Superfund remedial actions. See EPA’s CERCLA Compliance with Other Laws Manual, EPA/540/G-89/006, 

Interim Final, August 8, 1988, http://www.epa.gov/superfund/resources/remedy/pdf/540g-89006-s.pdf. 

If regulation-based actions are not enough to attain WQS, or NPS are the principal sources of pollution, you may 

also rely on your NPS control program to reduce the NPS pollutant load. Chapter 5 contains more information on 

developing and implementing NPS control programs. 

2. Conducting Triennial Reviews 

EPA’s regulations require that a tribe’s WQS approved under the CWA be reviewed at least once every 3 years 

and revised if necessary. You must hold a public hearing when any element of a WQS is modified or changed, and 

the public hearings must meet the same requirements as the public hearings held during standards development 

(discussed in section II.4 of this chapter). Prior to the hearing, you must make any proposed revisions, including 

supporting analyses, available to the public. When you begin activities to revise or adopt new standards, you 

should consult with your EPA Regional WQS Coordinator. 

Remember that you must re-examine water bodies or segments with designated uses that do not meet the 

fishable/swimmable use to determine if any new information or technology has become available that would make 

fishable/swimmable uses attainable. In addition, if designated uses for any water bodies are less restrictive than 

those uses currently being attained, you must revise your standards to reflect the uses attained. You must also 

review any variances you have granted and decide whether to issue new variances. 

Change in use designation requires that you consider the need for a change in criteria. If a use is removed, the 

criteria developed to protect that use may be deleted or revised. If a use is added, you will need to develop 

adequate criteria to protect the use. 

See chapter VIII of the Reference Guide to Water Quality Standards for Indian Tribes for more information 

on conducting triennial reviews. 

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During triennial reviews, you can also establish procedures for identifying and reviewing standards on specific 

water bodies in detail. These water bodies are likely to be those where: water quality-based permits are scheduled 

to be issued or reissued; CWA goals are not being met; toxics have been identified and may be precluding a use or 

posing an unreasonable risk to human health; or potential impacts on threatened or endangered species may exist. 

See section 6.1.4 of the Water Quality Standards Handbook for more information on identifying and reviewing 

specific water bodies. 

When revising standards, you must review all available information to determine whether the discharge or 

presence of a toxic pollutant is interfering with or likely to interfere with the attainment of designated uses of any 

water body segment. If so, you must adopt water quality criteria for that toxic pollutant sufficient to protect the 

designated use (40 CFR 131.11(a)(2)). 

You should consult with the appropriate EPA Regional WQS Coordinator before you begin this process. For 

information on EPA’s review process, see section 6.2 of the Water Quality Standards Handbook. 

3. Implementing Section 401 Certifications 

Once you have received EPA approval for your WQS, you may want to consider developing a comprehensive set 

of Section 401 certification implementing regulations to facilitate and enhance the defensibility of your control over 

the certification process. The language of Section 401(a)(1) of the CWA is written very broadly with respect to 

the activities it covers. Any federally licensed or permitted activities that may result in discharges into navigable 

waters, including CWA 404 permits and FERC (Federal Energy Regulatory Commission) licenses, require Section 

401 water quality certification. This includes, but is not limited to, the construction or operation of facilities. The 

purpose of the certification is to ensure that no license or permit is issued for any activity that could become a 

source of pollution through inadequate planning or otherwise. Carefully considered Section 401 certification 

regulations can be very effective in conserving water quality and in ensuring that you apply all appropriate criteria 

to every certification decision. Some considerations to include in your Section 401 certification implementing 

regulations include the timeframe for review, application requirements, permit fees, and basis for decisions. 

Section VI of EPA’s 1989 Wetlands and 401 Certification: Opportunities and Guidelines for States and 

Eligible Indian Tribes contains more information on these considerations and is available online through the 

Office of Water’s Online Publication Web site, http://yosemite.epa.gov/water/owrccatalog.nsf/. Appendix D of 

that document also contains some example certification conditions. 

After you receive WQS and Section 401 certification program authorization, entities must apply for and obtain 

certification from your tribe before obtaining a federal license or permit for any activity that may result in a 

discharge into waters on your reservation. When evaluating applications from these regulated entities for Section 

401 certification, you should consider all potential water quality impacts over the life of the project (e.g., direct and 

indirect, short and long term, upstream and downstream), as well as impacts resulting from construction and 

operation of the facility when making your decision. 

If your tribe has received an application for 401 certification for an activity that may affect the water quality of a 

downstream jurisdiction, you may wish to notify EPA. When an activity requiring 401 certification in one 

reservation or state will have an impact on the water quality of another reservation or state, EPA will notify any 

other tribe or state with water bodies that could be affected by the decision after receiving notice of application 

from a federal permitting or licensing agency within 30 days of the date of notice. EPA will also notify the 

licensing or permitting agency and the applicant. If within 60 days after receipt of such notification, other affected 

7-18 
states or tribes determine that issuance of the permit will affect the quality of their waters so as to violate any 

water quality requirements of the state or tribe, and notify EPA and the licensing or permitting agency in writing of 

their objections, the licensing or permitting agency will hold a hearing at which EPA will submit its evaluation and 

recommendations on the proposed permit. The licensing or permitting agency must then condition the permit or 

license to ensure compliance with all applicable water quality requirements. 

4. NPDES Program Overview 

The NPDES program is a cornerstone of the CWA. The program regulates the discharge of pollutants into the 

waters of the United States by means of permits issued to industrial, municipal, and other point source 

dischargers. Across the United States, more than fifty categories of industry (including several hundred thousand 

businesses) and the nation’s network of more than 16,000 municipal sewage treatment systems are required to 

comply with standards implemented in NPDES permits. These permits remove billions of pounds of conventional 

pollutants and millions of pounds of toxic pollutants each year. Today, more than 400,000 facilities are required to 

have NPDES permits. EPA regional offices currently issue and enforce NPDES permits in Indian Country. 

If your tribe has EPA-approved WQS and wishes to use the NPDES program to regulate point source discharges 

based on your standards, you will find helpful information in the pages that follow. However, if your tribe has 

EPA-approved WQS, you are not required to seek NPDES program authorization. The process for tribal 

authorization of the NPDES permitting program is similar to the WQS authorization process and is described 

below. However, the elements that must be in place prior to tribal authorization are considerably more complex 

than those required for other CWA programs, such as WQS or Section 319. These requirements are found at 40 

CFR Part 123. 

EPA’s NPDES and Sewage Sludge Program Authority, a Handbook for Federally Recognized Indian 

Tribes (EPA 833-B-94-004) contains more information on the NPDES program for tribes. You may download the 

Handbook from http://www.epa.gov/owm/rmes/tribalcwas106_app-e.pdf. You can also visit EPA’s NPDES Web 

site at http://cfpub.epa.gov/npdes/index.cfm for general information and links to guidance, regulations, and training 

information. 

5. Sources Regulated under the NPDES Program 

Pollutant discharges may come from direct and indirect sources. Direct sources discharge wastewater directly 

into a receiving water body; indirect sources discharge wastewater to a publicly owned treatment works 

(POTW), which in turn discharges into the receiving water body. Under the national program, NPDES permits 

are issued only to direct point source discharges. The primary focus of the NPDES permitting program is 

individual permit issuance for municipal and industrial direct discharges. The NPDES program has other 

components, such as general permits, pretreatment programs, the industrial stormwater program, the construction 

stormwater program, confined animal feeding operations, and biosolids. If you would like more information on 

these components, visit EPA’s NPDES Web site (http://cfpub.epa.gov/npdes/index.cfm). 

z Municipal Sources: Municipal sources are POTWs that receive primarily domestic sewage from 

residential and commercial customers. Larger POTWs also typically receive and treat wastewater from 

industrial facilities (indirect dischargers) connected to the POTW sewerage system. The types of 

pollutants treated by a POTW always include conventional pollutants (e.g., human wastes, ground-up food 

from sink disposals, laundry and bath waters) and may include nonconventional pollutants (e.g., nutrients 

such as nitrogen and phosphorus) and toxic pollutants (e.g., pesticides, solvents, dioxin, lead, silver, 

mercury, copper) depending on the characteristics of the commercial and industrial sources discharging to 

the POTW. The treatment provided by POTWs typically includes physical separation and settling (e.g., 

screening, grit removal, primary settling), biological treatment (e.g., trickling filters, activated sludge), and 

disinfection (e.g., chlorination, UV, ozone). Some older POTWs have the additional concern of combined 

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sewer overflow (CSO) systems that can release untreated effluent during storms. CSOs were an 

economic way for municipalities to collect both sanitary sewage and stormwater and are controlled under 

the NPDES program. A number of municipalities have municipal separate storm sewer systems (MS4s) 

that are also subject to NPDES requirements. 

z Nonmunicipal Sources: Nonmunicipal sources, which include industrial and commercial facilities, have 

unique products and processes. At industrial facilities, the types of raw materials, production processes, 

treatment technologies, and pollutants discharged vary widely and depend on industry and facility 

characteristics. The operations at industrial facilities are generally carried out within a clearly defined plant 

area; thus, the collection systems are typically less complex than those for POTWs. Examples of 

nonmunicipal commercial sources include concentrated animal feeding operations, which are required to 

obtain NPDES permits to control runoff of nutrients and manure, especially in non-agricultural areas, and 

the construction stormwater program. 

6. Understanding NPDES Permits 

A permit is a license for a facility to discharge a specified amount of a pollutant into a receiving water, subject to 

certain conditions. Pollutant limitations are based on the more stringent of technology-based or water qualitybased requirements. Permits may also authorize facilities to process, incinerate, send to a landfill, or beneficially 

use sewage sludge. The two basic types of permits that can be issued under the NPDES program are individual 

permits, which are tailored for particular facilities, and general permits, which are developed and issued to cover 

multiple facilities within a single category. If your tribe has many facilities of the same kind or that have certain 

elements in common, a general permit may be appropriate. A general permit can help you ensure that similar 

facilities are subject to consistent conditions. 

A tribe’s WQS serve as a basis for establishing water quality-based effluent limitations for facilities with NPDES 

permits that are discharging to those reservation waters covered by the standards. Most facilities with permits 

issued by EPA that could be affected by a tribe’s WQS probably have been operating with technology that has 

satisfied the WQS set outside the reservation. Whether the facilities will need to undertake different or additional 

pollution control measures when their NPDES permits are reissued will depend in part on any differences 

between the tribe’s and state’s WQS, and on EPA’s technical procedures in applying the two sets of standards. 

An NPDES permit contains effluent limitations (e.g., restrictions on the amount of specific pollutants that a facility 

can discharge into a water body) as well as monitoring and reporting requirements to ensure compliance with the 

effluent limitations. You can find more information on NPDES permits in EPA’s NPDES Permit Writer’s Manual 

(EPA 833-B-96-003), available online at http://cfpub.epa.gov/npdes/writermanual.cfm?program_id=45. 

7. Reviewing Permits 

As noted in section III.2, you must hold public hearings to review applicable WQS and modify or adopt standards, 

if necessary, at least once every 3 years. During your tribe’s triennial review, tribal staff responsible for 

administration of the NPDES program should revisit any variances that have been granted. If the conditions that 

necessitated the variance still apply, no permit modification need be made. Otherwise, the permit containing the 

variance should be modified to reflect the new circumstances. 

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8. Considering NPDES Program Authorization 

Before deciding to pursue NPDES program authorization, you should consider all the benefits and costs 

associated with it. You may want to consider: 

z Tribal interest in furthering autonomy and self-determination 

z The role the tribal program plays in the protection of tribal interests 

z The abilities of your tribal program (i.e., whether your program has the organizational ability to develop and 

maintain a permitting authority) 

z New tribal statutes or regulations you will need to manage the NPDES program 

z Costs associated with expanding your regulatory role and ability to protect public health and the 

environment 

z The infrastructure necessary to implement the program 

z Your ability to support this type of program for many years 

If you plan on seeking NPDES program authorization, you should contact your EPA regional office to discuss the 

process. The regional office can help guide you through the application process. 

Photo Courtesy of EPA Great Lakes National Program Office, National Park Service, Indiana Dunes National 

Lakeshore. 

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9. Developing Capabilities for Permitting, Compliance, and Enforcement 

You must have the ability to implement all portions of an NPDES program, including writing permits, tracking 

compliance, and enforcing permit conditions at the time of approval (40 CFR 123.23(a)). To help you meet this 

requirement, you should consider training engineers and permit writers. EPA offers various training courses and 

workshops that explain the regulatory framework and technical considerations of the NPDES permit program. 

These courses are designed for permit writers, dischargers, EPA officials, and other interested parties. Updated 

information about courses and workshops is available on the Internet at http://cfpub.epa.gov/npdes/ 

outreach.cfm?program_id=0&otype=1. 

The extent to which permit writers are involved in monitoring, compliance, and enforcement activities will depend 

on the size of the organization set up by your tribal program. In smaller programs, a single individual or a small 

group of individuals may be responsible for all activities. In larger programs, individuals may specialize in different 

functions, so that the permit writer, while aware of the general activities of the permittee, may not be as closely 

involved with monitoring, compliance, and enforcement as are the individuals who specialize in each of those 

activities. 

EPA has issued a number of guidances for permit writers that contain information on developing, issuing, ensuring 

compliance with, and enforcing NPDES permits. You can find general guidance and documents related to specific 

permit types online at http://cfpub.epa.gov/npdes/pubs.cfm?program_id=0. 

10. Preparing for NPDES Program Authorization 

a. Developing Tribal Code and Obtaining Approval from the Tribal Government 

You will need to follow your tribal mechanisms to develop any necessary legal authority required to administer the 

NPDES program. Section II of chapter 6 includes some general considerations for developing tribal code and 

obtaining approval from your tribal government. Consult this section for more information. 

Remember that you should work with your tribal attorney general or equivalent office during this process to 

produce tribal code that meets tribal as well as NPDES program requirements. You should also work with your 

tribal council to make sure you cover all applicable tribal requirements for adoption of your NPDES program. 

b. Inventorying Existing Point Sources 

Typical point source discharges come from POTWs and industrial facilities. The NPDES program does address 

certain types of agricultural activities (e.g., concentrated animal feeding operations), but the majority of 

agricultural facilities are defined as nonpoint sources and are exempt from NPDES regulation. You should 

coordinate with the existing (state or federal) permitting authority on your reservation to make sure that you have 

a complete list of all municipal and nonmunicipal point source dischargers currently regulated by NPDES permits. 

c. Establishing Sources of Funding to Run the NPDES Program 

In obtaining authorization for an NPDES program, your tribe will have to consider whether it is willing to commit 

to the long-term financial support of the program. The decision to ask for authorization will have environmental 

and economic consequences over many years. The tribe must determine whether it has (or plans to obtain) the 

revenue to hire and train the staff needed to run the NPDES program. You may be able to collect some funding 

through program and permit fees, but you may need additional dedicated tribal appropriations or other sources of 

EPA funding to fully support your program. Your EPA regional office may be able to help you locate sources of 

additional funding. A portion of your Section 106 grant could be used to support a NDPES program, but there is no 

separate CWA funding program for state or tribal permit programs. 

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11. Obtaining NPDES Program Authorization 

As with obtaining eligibility for the standards program, you must meet basic requirements to be eligible for TAS 

under the NPDES program (40 CFR 123.32). You must be recognized by DOI, and you must demonstrate 

existing substantial governmental duties and powers, defined authority over water resources, and tribal capacity to 

administer the program. Remember that if you have already met any of these requirements, you may have to 

submit only information not submitted previously or resubmit information that is no longer current. 

As established in 40 CFR 123.32, your application for eligibility for TAS for the NPDES program must include: 

z A statement that the tribe is recognized by the Secretary of the Interior 

z A descriptive statement demonstrating that the tribal governing body is currently carrying out substantial 

governmental duties and powers over a defined area 

z A map or legal description of the area over which the Indian Tribe asserts authority under section 

518(e)(2) of the Act; a statement by the Tribal Attorney General (or equivalent official authorized to 

represent the Tribe in all legal matters in court pertaining to the program for which it seeks approval) 

which describes the basis for the tribe’s assertion (including the nature or subject matter of the asserted 

regulatory authority); copies of those documents such as tribal constitutions, by-laws, charters, executive 

orders, codes, ordinances, and/or resolutions which the tribe believes are relevant to its assertion under 

section 518(e)(2) of the Act; and a description of the location of the surface waters for which the tribe 

proposes to establish an NPDES permit program 

z A narrative statement describing the capability of the Indian Tribe to administer an effective, 

environmentally sound NPDES permit program 

The Regional Administrator may, at his or her discretion, request further documentation necessary to support a 

tribe’s eligibility. If the Administrator or his or her delegatee has previously determined that a tribe has met the 

prerequisites that make it eligible to assume a role similar to that of a state as provided by statute under the Safe 

Drinking Water Act, the Clean Water Act, or the Clean Air Act, then that tribe need provide only that information 

unique to the NPDES program which is requested by the Regional Administrator. 

In evaluating whether your tribe is capable of implementing an NPDES program in a way that is consistent with 

the CWA and applicable regulations, EPA will consider: 

z Your tribe’s previous management experience 

z Environmental or public health programs that your tribe currently administers 

z Existing mechanisms to carry out the executive, legislative, and judicial functions of tribal government 

z The relationship between the entities that will be regulated and the agency of the tribal government that is 

designated as the primacy agency 

z The technical and administrative capabilities of the staff responsible for administering and managing the 

program 

7-23 
12. Assuming the Section 404 Program 

To be eligible to assume the federal program, a tribe must have TAS status for the Section 404 program. In 

addition, to assume the program, a tribe must develop a wetlands permit program no less stringent than the federal 

program and submit an application to EPA. The tribal program must meet the requirements in CWA Section 518 

and 40 CFR 233.60-233.61. 

While tribes can assume the Section 404 program for all surface waters on tribal land, the U.S. Army Corps of 

Engineers (the Corps) retains jurisdiction for Section 404 permits for certain waters as provided in CWA Section 

404(g)(1). 

If a tribe wishes to regulate jurisdiction over these “Section 10” waters and adjacent wetlands (Section 10 of the 

Rivers and Harbors Act), it must either develop a parallel permit program with the Corps or assume a State 

Programmatic General Permit (SPGP) with the Corps. If a tribe develops a parallel permit program, a permittee 

would need to receive a permit from the Corps and from the tribe for activities in these waters. An SPGP is a 

type of general permit founded on an existing state, local, or other federal agency program and designed to avoid 

duplication with that program. 

When tribes assume administration of the Section 404 program, the Corps no longer processes Section 404 

permits in waters included within the tribal program. Instead, your tribe would assume responsibility for the 

program, determine what areas and activities are regulated, process individual permits for specific proposed 

activities, and carry out enforcement activities. Tribes may issue general permits in addition to individual permits. 

Note that there are regulatory requirements that apply to general permits issued by the tribe. More information 

about Section 404 permitting is available from http://www.epa.gov/owow/wetlands/facts/fact23.html and http:// 

www.epa.gov/owow/wetlands/pdf/reg_authority.pdf. 

13. Working with EPA to Transition from Federal to Tribal Implementation 

The transition from a federal to a tribal NPDES program will be laid out in the MOA between EPA and the tribe. 

Upon approval of a tribal program, EPA will suspend the issuance of federal permits for activities covered by the 

tribal program. After program approval, EPA will retain jurisdiction over any permits (including general permits) 

that it has issued unless your MOA with EPA calls for you to assume responsibility for them. During the transition 

from a federally administered NPDES program to a tribally administered NPDES program, tribal staff should 

work with EPA to identify and review existing permits and establish mechanisms for tribal permit implementation. 

14. Conducting Public Outreach 

You should meet any public notification requirements particular to your tribe that are associated with NPDES 

permits prior to and after program authorization. Consult your tribal attorney general or equivalent officer to see if 

any public participation requirements apply. 

In addition, the NPDES administrative procedures require that the public be notified and allowed to comment on 

NPDES permit applications. Once you assume authority for the NPDES program, you will be required to provide 

public notice and allow for comments on NPDES permit applications in accordance with federal regulations. See 

40 CFR 124.10-124.12 for more information on public comments requirements. 

7-24 
Chapter 8: Reporting

Introduction 

As noted in the introduction to this guidance, one of this document’s goals is to make it possible to aggregate data 

in a way that allows EPA to begin to assess national results associated with the Section 106 Tribal Program. 

Establishing consistent reporting requirements and data formats across all tribal water quality programs is the first 

step in aggregating and using the data to make statements about tribal water quality nationwide. This chapter 

discusses the annual Assessment Report that tribes will have to submit as a requirement of their work plan for 

their Section 106 tribal grants. 

The Assessment Report consists of three components: a description of your monitoring strategy; a water quality 

assessment; and electronic copies of water quality data. It is different from progress reports required under the 

grant. Progress reports help your EPA regional office ensure that you are meeting your work plan objectives and 

project schedule. See section I.13 of chapter 3 for more information on progress reports. The Assessment Report 

contains information about water quality on your reservation and will help EPA begin to compile data that 

demonstrate national results for the Section 106 Tribal Program. EPA will also use the data provided in the 

Assessment Report to understand national trends and overall water quality. Tribes are critical partners in helping 

to develop this national picture. See appendix A for more information on what to include in your Assessment 

Report. 

In addition to helping EPA assess national results, the elements required in tribal Assessment Reports provide a 

foundation to tribes for assessing water quality for reservation waters. The assessments will allow tribes to 

compare water quality data over time and serve as tools to help tribes make informed decisions about their 

program’s future. 

Some tribes already submit 305(b) water quality reports and other types of assessments. However, greater 

consistency among these reports is needed to assess water quality on a national scale. This document is intended 

to provide guidance on reporting that will lead to greater consistency among tribal reports and ultimately allow 

EPA to demonstrate environmental results for the Section 106 Tribal Program. 

The reporting requirements outlined in this chapter reflect EPA’s minimum reporting expectations for tribes. Tribes 

that currently collect and report more than the minimum required elements should not reduce their efforts to the 

minimum but continue to collect and report additional elements of interest to their programs. 

Reporting Requirements 

While EPA expects tribes able to do so to report on all of the parameters discussed in this chapter, it is 

understood that labor and financial contraints, relevant parameters, and other factors will vary among tribes. 

Individual reporting requirements will be determined on a case-by-case basis by EPA regional offices. A 

specific reporting requirement may be waived, for instance, if it can be demonstrated with data collected by 

the tribe or another entity that a required parameter does not affect a specific water body, or that the 

reporting requirements would cause an undue economic hardship. 

8-1 
In selecting tribal reporting components, EPA has attempted to balance tribal non-disclosure issues with EPA’s 

goals of documenting national results for the Section 106 Tribal Program and assessing water quality nationwide. 

Certain information may be protected from release. For example, confidential business information, some personal 

privacy information, and limited other tribal information may be exempt from disclosure under the Freedom of 

Information Act (FOIA) or special provisions worked out at the regional level. There are also significant 

technological challenges associated with reporting raw data directly to STORET, and many tribes do not have the 

resources to meet those challenges. On the other hand, EPA has an obligation to demonstrate results for the 

Section 106 Tribal Program and to understand conditions on Indian reservations in sufficient detail to make 

effective decisions at a national level. The Agency believes the reporting requirements presented in this chapter 

reflect a balance between tribal data sensitivity issues and EPA data needs, take resources available for water 

quality monitoring into account, and reflect the goals outlined in AIEO’s Tribal Leader Letter on Tribal Data 

Access (see appendix C for a copy of the Letter). 

The diagram below is a summary of the reporting requirements for the Section 106 Tribal Program. 

Summary of Reporting Requirements for the Section 106 Tribal Program 

Item Description

1. Description of Your Monitoring Strategy

A description of the needs, goals, and objectives you have

identified, as well as a full description of the methodology and

parameters sampled within your monitoring program.

2. Water Quality Assessment

A narrative account detailing the types of water sampled,

sampling procedures, and resulting data summaries. The

summary report must also include the tribe's interpretation of the

data and the assessment methodology used.

3. EPA's Nine Basic Parameters Submitted in an Electronic Format

Fundamental

Monitoring

Parameters

1. Dissolved Oxygen DO testing kits and multi-parameter probes are readily available

on the market.

2. pH pH testing kits and multi-parameter probes are readily available

on the market.

3. Water Temperature Thermometers and multi-parameter probes are available from

laboratory supply stores.

6. Turbidity Turbidity data should be collected in lakes and reservoirs using

a Secchi disc method, probes, or meters. In streams, turbidity

should be collected using a turbidity tube, kits, probes, or

meters.

Intermediate

Monitoring

Parameters

4. Phosphorus While total phosphorus data is preferred, ortho-phosphorus data

is acceptable. Ortho-phosphorus may be measured using kits,

probes, or contract laboratories.

5. Total Nitrogen Total nitrogen should be reported separately as the sum of total

Kjeldahl nitrogen (TKN), ammonia, and nitrate-nitrite.

Mature

Monitoring

Parameters

8. Macroinvertebrates Multiple monitoring methods are acceptable.

7. E. coli or

enterococci

Samples can be measured with a market kit and an incubator or

sent to a laboratory for analysis.

9. Basic habitat

information

For each reach, include existing streambank erosion, existing

hydrologic modification, stream bottom characteristics, and land

use patterns near sampling sites.

8-2 
Reporting Requirements 

As a grant requirement for continuing to receive Section 106 funds, tribes must submit to their EPA 

regional offices annual tribal Assessment Reports that consist of the three components listed below. 

Tribes, however, will not be required to upload their raw data into STORET. EPA expects that all tribal 

data will be uploaded into STORET, but recognizes that in many cases the burden for data 

management will lie with EPA regions or EPA Headquarters. When tribes have approved Section 106 work 

plans, they will be required to submit the assessment in accordance with their approved work plan. In some 

instances (e.g., when a tribe can demonstrate through its own data or data collected by another entity, such as a 

state or watershed council, that a required parameter does not affect a specific water body or when the reporting 

requirements would cause an undue economic hardship), EPA may waive specific reporting requirements. Unless 

EPA has waived specific reporting requirements for your tribe, you must include all the elements listed below in 

your assessment: 

1. A description of your monitoring strategy. If you have followed the procedures outlined in this 

guidance, you already should have developed a monitoring strategy, and you may have included it as part 

of your QAPP (See section I.1.a of chapter 4 for more information on developing a monitoring strategy.) 

As stated in chapter 4, characteristics of monitoring strategies will vary from tribal program to tribal 

program based on program goals and objectives, the level of program sophistication, and resources 

available. The complexity of the strategy you describe will depend on the sophistication of your monitoring 

program. Your strategy description can vary in length as long as you adequately describe a program that 

meets your data and information needs and considers future needs. If you have a monitoring strategy in 

place, you do not need to develop a new monitoring strategy to meet this requirement. Tribes will be 

allowed to report strategies they already have developed using Section 106 funds or other funds. 

Information on strategies is included in appendix A. This requirement will help EPA measure success 

towards subobjective 2.2.1 of the National Water Program Tribal Targets for FY 2005-2008, “protect and 

improve water quality on a watershed basis,” in particular the monitoring component of that target, 

“number of tribes that currently receive EPA funding that have developed comprehensive monitoring 

strategies.” Understanding existing water quality is a key step in protecting and improving water quality. 

Comprehensive monitoring strategies help tribes understand existing water quality conditions. 

2. A water quality assessment. This narrative and graphical account should include your assessment of 

water quality. Assessments will vary based on the tribal program’s sophistication. A tribe just beginning to 

implement a water quality program might submit a short assessment covering only a single year of 

monitoring results, while a tribe with a more advanced program might submit a more detailed and complex 

assessment that is based on several years of monitoring and includes GIS maps. At a minimum, the 

assessment must include summary information on the types of water sampled (e.g., rivers, lakes, wetlands, 

ground water), including the total extent (acres, miles) on the reservation and the total extent assessed, 

numbers of samples taken, and the complete set of parameters for which samples were collected. For the 

parameters discussed below, the summary report must also include mean/median values, the range of 

concentrations found, a threshold against which comparisons are being made, and the number of sampling 

locations (or miles of streams, acres of lakes, etc.) for which samples were above or below (as 

appropriate) the threshold value. EPA encourages tribes to provide this information for all parameters, 

including the minimum nine parameters. The summary report must also include the tribe’s interpretation of 

the data and the assessment methodology used. If the tribe has EPA-approved WQS or tribally adopted 

standards, or has otherwise assigned designated uses to its waters, this report should include a summary of 

the number of stream miles, lake acres, etc. that are meeting designated uses, not meeting designated uses 

(i.e., impaired water bodies), or are unassessed. More advanced tribes should also consider including a 

table of water body-specific assessment information. (Information on assessments is included in appendix 

A.) This requirement will also help EPA measure success towards subobjective 2.2.1, in particular the 

strategic target showing water quality improvement in tribal waters. 

8-3 
3. Electronic copies of surface water quality data for nine basic parameters (submitted in a 

STORET-compatible format). This requirement will (1) ensure that tribes formulate their water quality 

assessments using consistent parameters; (2) provide EPA with data to assess water quality on Indian 

reservations at a national level; and (3) prepare tribes for submitting data to STORET, a possible grant 

requirement in future years. Although tribes are encouraged to report all data they collect, tribes are 

required to report only the nine basic parameters listed below. These parameters will enable EPA to make 

national comparisons and assess the health of all tribal waters. EPA believes that most tribal monitoring 

programs already include most of these nine basic parameters. Many tribes will not need to conduct 

additional monitoring to collect these parameters. In some cases, one or more of these requirements may 

be waived by EPA. For instance, if your tribal program has determined that pathogens are not a concern in 

your water bodies and you have data to support this determination, your EPA regional office may waive 

the pathogen monitoring requirement. While EPA recommends monitoring for these parameters biannually, 

individual monitoring requirements will be negotiated between individual tribes and the appropriate EPA 

region on a case-by-case basis. 

You may submit electronic copies of your water quality data via e-mail or on a CD-ROM or floppy disk. EPA 

strongly encourages tribes to submit additional parameters to EPA in this STORET-compatible format. Standard 

templates for data reporting will be developed through coordination among EPA Headquarters, EPA regional 

offices, and tribes, and will be available through EPA regional offices before tribes begin implementing the 

reporting requirements outlined in this guidance. For more information, see the text box titled “QAPPs and 

Monitoring” on page 4-4. 

Although all tribes are encouraged to report data for all required parameters even if that data is reported 

elsewhere (such as in state 305(b) reports), as well as any additional parameters for which the tribe has 

monitored, tribes’ abilities to monitor and report on some of the parameters may vary. EPA recognizes that it will 

not be possible for all tribes to begin collecting information on all nine parameters immediately. EPA understands 

that lack of resources and training may prevent some tribes from collecting and reporting data for all parameters. 

EPA has classified each of the nine parameters as fundamental, intermediate, or mature based on the level of 

complexity required by the monitoring and reporting activities associated with that parameter. EPA regions will 

use these classifications as guidelines in determining reporting requirements for each tribe, but ultimately 

will decide which parameters a tribe is required to report on a case-by-case basis. In situations where tribes 

cannot monitor for all nine parameters, EPA regional offices and tribes should negotiate ways to build tribal 

capacity (e.g., training, technical assistance, purchase of laboratory equipment) so that the tribe ultimately can 

collect information on all parameters. The nine parameters are: 

Fundamental Reporting Parameters 

1. Dissolved oxygen 

2. pH 

3. Water temperature 

4. Turbidity 

Intermediate Reporting Parameters 

1. Phosphorus. Total phosphorus data is preferred, but ortho-phosphorus data is acceptable. 

2. Total nitrogen. Total nitrogen data should be reported separately as the sum of total Kjeldahl 

nitrogen (TKN), ammonia, and nitrate-nitrite. 

8-4 
Mature Reporting Parameters 

1. Macroinvertebrates 

2. E. coli or enterococci 

3. Basic habitat information. For each reach (i.e., stream segment), you must include the basic 

habitat information listed below in your report: 

z Existing streambank erosion 

a. Undercutting bank 

b. Widening channel 

z Existing hydrologic modification 

a. Dams or water restriction structures 

b. Drainage pipes into stream 

c. Diversion of stormwater into stream through culverts or pipes 

d. Burying of streams in pipes 

e. Bridge abutments 

f. Rerouting stream channel 

z Stream bottom characteristics 

a. Soft muddy bottom 

b. Firm sandy bottom 

c. Hard rocky bottom 

z Land use patterns near sampling sites 

a. Forested 

b. Pasture/crops/open land 

c. Wetlands 

d. Residential 

e. Commercial/industrial 

f. Roads/highways 

g. Construction underway 

h. Cleared right-of-ways 

Tribes should use analytical methods consistent with 40 CFR Part 136 or other approved alternate test 

procedures, as documented in a tribe’s approved QAPP. Each of these nine parameters is discussed in detail in 

section I.1.b of chapter 4. 

The nine parameters described in this chapter reflect the minimum monitoring expectations for tribal water quality 

programs. Tribes that are currently monitoring additional parameters should not curtail their current monitoring 

programs. In addition, as less experienced tribal programs begin to develop expertise, EPA expects that these 

tribes will begin to incorporate additional parameters. 

8-5 
Data Formatting and STORET 

As noted in chapter 4, STORET is a repository for water quality, biological, and physical data that can be used by 

tribal and state environmental offices, EPA and other federal agencies, universities, private citizens, and many 

other organizations to assess water quality across the nation. 

Each sampling result in STORET is accompanied by appropriate metadata (section I.2.a of chapter 4 contains 

more information on metadata). These metadata allow other users of the data to put them in their proper context 

when using them. You can visit http://www.epa.gov/storet/index.html for more information on STORET. Sample 

metadata templates will be available from your EPA regional office. 

Currently, there are limitations to using STORET. In addition, tribes must be trained on STORET to submit data. 

Although several tribes report data to STORET, EPA recognizes that technical limitations prevent many tribes 

from reporting their data via STORET. EPA is working to address this issue and create simpler mechanisms (i.e., 

a Web-based interface) to allow users to submit data. Until this update to STORET is completed, EPA will 

not require tribes to report data directly into STORET. Tribes that already report data are encouraged to 

continue to do so. At this time, all tribes should focus on assembling data sets that include adequate metadata and 

are in a STORET-compatible format. Properly formatted data are not only a Section 106 requirement, they are 

also a key component of effective data management. As discussed in chapter 4, you will need properly formatted 

data sets to use your data as effectively as possible. Properly formatted data will allow you to make valid 

comparisons among water bodies, use data for purposes besides those for which you originally collected the data, 

and ensure that the data remain useful as personnel changes. Tribes that wish to submit data may do so through 

one of several options: 

z Run a local copy of STORET or access a hosted version. You can run a local copy of STORET to 

record your results. EPA can provide translation formats for upload to the national STORET database, but 

your tribe must either run a local copy of STORET or have access to a hosted version of STORET to use 

this option. 

z Use a contractor with STORET experience to upload STORET data. Several tribal programs have 

used contractors to upload their data into STORET. Other tribes in your region may be able to provide you 

with information about contractors they have used to do this. This option does not require tribes to use 

specialized software packages, but may require them to pay software licensing fees and setup costs. 

z Provide water quality data to EPA via a CD, DVD, or diskette. Tribes can save the data they have 

collected onto a CD-ROM, DVD, or diskette and arrange to submit it to their EPA region for STORET 

upload. 

EPA recognizes that it will not be possible for all tribes to begin to report data in a STORET-compatible format 

immediately. In situations where tribes cannot report data in a STORET-compatible format, EPA regional offices 

and tribes should negotiate ways to build tribal capacity (e.g., training, technical assistance) so that the tribe can 

ultimately store and report data in a properly formatted electronic file. 

Where feasible, EPA encourages all tribes to submit all their data to STORET. Not only will the data help EPA 

build a comprehensive picture of water quality, but tribes will have free access to an offsite storage site they can 

rely on if their data are lost. 

8-6 
Appendix A: Assessment

Reports

As described in chapter 8, tribes receiving Section 106 grants are required to submit an annual Assessment 

Report consisting of the following three components: 

1. A description of your monitoring strategy 

2. A water quality assessment 

3. Electronic copies of surface water quality data for nine basic parameters 

The information to be included in each component of the report is described below, along with suggested formats 

for your report. 

I. Monitoring Strategies 

A tribal monitoring strategy is simply an implementation plan that describes how a monitoring program will serve 

tribal water quality management needs and address tribal waters over time. It should be comprehensive in scope 

(i.e., addressing all water body types within tribal boundaries) and it should identify the issues and needs that are 

currently impediments to an adequate monitoring program. An adequate monitoring program should include the 

following: 

z Water quality indicators (WQI) and/or other parameters to be monitored 

z Monitoring frequency for each WQI and parameter 

z Monitoring sites 

z Monitoring data use and display 

See section I.1 and II.2 of chapter 4 for more information on WQI and other parameters, monitoring site 

selection, and monitoring data use and display. 

The requirements for tribal water monitoring strategies are described below in three tiers for fundamental, 

intermediate, and mature tribal water quality programs. EPA anticipates that over time, all tribal monitoring 

programs will advance to the highest level practical. The tribal strategy should be reviewed regularly to determine 

if goals are being achieved and if the tribal monitoring program is advancing toward maturity. 

Example Monitoring Objectives 

z Initial ground water monitoring conducted under the previous grant period indicated the presence of 

nitrates and nitrites within shallow ground water. The tribe has implemented management measures 

to lower total nitrogen levels. The tribe will continue monitoring at existing ground water locations to 

assess the impact of the management measures. 

z Our tribal waters are experiencing significant eutrophication, but we do not have existing surface 

water data. We will conduct monitoring of the two lakes on our reservation to determine the extent 

of the problem and use the results to attempt to determine possible causes. 

z Waters on our reservation are pristine. Our monitoring strategy will aim to maintain and protect our 

excellent water quality and attempt to identify any potential causes of concern or possible sources of 

pollution. 

A-1 
1. Monitoring Strategies for Fundamental-Level Tribal Programs 

A monitoring strategy for a tribal program at a fundamental level of development should include the following: 

Monitoring Objectives — This should be a narrative describing the major goal(s) and measurable objectives of 

the monitoring program. These objectives may include identifying water quality problem areas, tracking trends 

over time, or identifying NPS impacts. 

Monitoring Design — The strategy should describe the tribe’s approach for selecting sampling sites that best 

serve its monitoring objectives. Fundamental monitoring programs will most probably be designed using a fixed 

station design to begin to locate problem areas. 

Core Water Quality Indicators (WQI) — The strategy should define the core set of WQI that will be 

monitored (for fundamental programs, temperature, pH, DO, and turbidity are required parameters, as described 

in chapter 8). The strategy also should identify any supplemental indicators the tribe may choose to monitor. 

Quality Assurance — A Quality Management Plan (QMP) and Quality Assurance Project Plan (QAPP) must 

be developed and approved to ensure the validity of monitoring and laboratory activities. The QAPP should reflect 

the level of quality that is appropriate for the specific uses of the data. EPA guidance on developing QMPs and 

QAPPs is available at http://www.epa.gov/quality. See the introduction to chapter 4 for more information on 

QAPPs. 

Data Management — The strategy should describe how tribal data are stored in an electronic data system that

can be used to manage tribal data and is in a format that will allow data sharing with EPA. Data collected on the

four core indicators and metadata (date, time, location, etc.) should be managed electronically. EPA Headquarters

will work with tribes and EPA regional offices to develop a standard format for data reporting, including metadata.

Standard templates will be available through EPA regional offices before tribes begin to implement the reporting

requirements outlined in this document. See section I.2 of chapter 4 for more information on metadata.

Data Analysis and Assessment — The strategy should describe the tribe’s assessment methodology — how

data collected will be compiled and analyzed to make assessment decisions. Assessments should address whether

water quality is attaining available standards or criteria. If the tribe has EPA-approved WQS, the methodology

should use them for determining attainment. If the tribe does not have EPA-approved WQS, the methodology

should use one of the following sets of alternative standards or criteria:

z Tribal standards adopted and submitted to EPA, but not yet approved by EPA.

z Tribal standards adopted under tribal law for application solely under tribal law.

z Proposed or draft tribal standards prepared for use under either federal or tribal law, preferably consistent

with EPA’s guidance at http://www.epa.gov/waterscience. 

z Standards adopted by an adjacent or nearby tribe or state and approved by EPA for similar types of 

waters. The full text of each tribe’s and state’s EPA-approved WQS is available at http://www.epa.gov/ 

waterscience/standards/wqslibrary/. 

z EPA’s recommended water quality criteria published under Section 304(a) of the CWA, adjusted for sitespecific application in tribal waters. The recommended criteria are available at http://www.epa.gov/ 

waterscience. 

z EPA’s recommended water quality criteria published under Section 304(a) of the CWA, without sitespecific adjustment. 

If any of the non-tribal standards approaches are used (i.e., the last three bullets above), the tribe would be free to 

apply all of the standards or criteria available, or to use selected designated uses and associated criteria depending 

on what needs to be protected for that tribe. Depending on the tribe and the waters, some designated uses and 

criteria may not be appropriate. 

A-2 
Reporting — The strategy should describe the tribe’s procedures and protocol for preparing and submitting its 

annual tribal Assessment Report, which includes a description of the tribe’s monitoring strategy, a water quality 

assessment, electronic copies of water quality data, and any other reporting needs identified by the tribe, in 

accordance with its approved grant work plan. Standard templates will be available through EPA regional offices. 

Programmatic Evaluation and Needs Planning — The strategy should describe the process for conducting 

regular reviews of the tribal water quality monitoring program with the EPA region. These reviews will help 

determine how well the program is serving water quality decision needs. The tribe should also identify any current 

and future monitoring resources needed to fully implement a comprehensive program. 

2. Monitoring Strategies for Intermediate-Level Programs 

Monitoring Objectives — Similar to the fundamental level, this should be a narrative describing the major goals 

and measurable objectives of the monitoring program. The tribe should be considering CWA goals and objectives 

such as identifying problem areas needing protection. See section II.1 of chapter 4 for more information on 

updating monitoring objectives. 

Monitoring Design — The strategy should describe the tribe’s approach for selecting sampling sites that best 

serve its monitoring objectives. The tribe should consider several monitoring designs (e.g., rotating watersheds) to 

meet a broader range of monitoring objectives and to ensure comprehensive coverage of all water body types. 

See section II.1 of chapter 4 for more information on updating monitoring objectives. 

Core and Supplemental WQI — The strategy should define the core WQI that will be monitored (in addition to 

the fundamental core parameter requirements, the intermediate level should include measurement of total nitrogen 

and total phosphorus). The strategy should also identify any supplemental indicators the tribe may choose to 

monitor to better meet its program objectives. Core and supplemental WQI are discussed in section I.1.b of 

chapter 4. 

Quality Assurance — The strategy should describe protocols for expanding and refining the existing tribal QMP 

and QAPP to ensure the validity of monitoring and laboratory activities. The QAPP should reflect the level of 

quality that is appropriate for the specific uses of the data. EPA guidance on developing QMPs and QAPPs is 

available at http://www.epa.gov/quality. 

Data Management — The strategy should describe how tribal data are stored in an electronic data system that 

can be used to manage tribal data and is in a format that will allow data sharing with EPA. Data collected on the 

six core indicators and metadata (date, time, location, etc.) should be managed electronically. Standard templates 

will be available through EPA regional offices before tribes begin to implement the reporting requirements outlined 

in this document. Section II.2 of chapter 4 has more information on data management for intermediate programs. 

Data Analysis and Assessment — The strategy should describe the tribe’s assessment methodology — how 

data collected will be compiled and analyzed to make assessment decisions. Progress toward tribal water quality 

objectives should be discussed. Section II.3 of chapter 4 has more information on data analysis and assessment. 

Reporting — The strategy should describe the tribe’s procedures and protocol for preparing and submitting its 

annual tribal Assessment Report, which includes a description of the tribe’s monitoring strategy, a water quality 

assessment, electronic copies of water quality data, and any other reporting needs identified by the tribe, in 

accordance with its approved grant work plan. 

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Programmatic Evaluation and Needs Planning — The strategy should describe the process for conducting 

regular reviews of the tribal water quality monitoring program with the EPA region. These reviews will help 

determine how well the program is serving water quality decision needs. The tribe should also identify any current 

and future monitoring resources — such as staff and training, lab resources, and funding — needed to fully 

implement a comprehensive program. 

3. Monitoring Strategies for Mature-Level Programs 

Tribal water quality programs at the mature level should generally follow the guidance of EPA’s Elements of a 

State Water Quality Monitoring and Assessment Program guidance. While not required, mature tribal programs 

are encouraged to submit 305(b) reports. Comprehensive, detailed reports are expected at this level. In addition to 

the six parameters required in the other two levels, tribal programs must add, at a minimum, reporting on 

macroinvertebrates, physical habitat, and E. coli parameters. Data should be managed electronically and provided 

to EPA on an annual basis in an accessible format. 

II. Water Quality Assessment Report 

Under this Guidance on Awards of Grants to Indian Tribes under Section 106 of the Clean Water Act, tribes 

are required to collect, assess, and report annually on water quality monitoring data that were gathered using EPA 

Section 106 funding. The tribal water quality assessment should contain a basic set of information presented in a 

consistent fashion, as described below. EPA expects that each tribe’s water quality assessment will become 

increasingly comprehensive as its monitoring program matures. 

1. Fundamental Water Quality Program 

The major components of an Assessment Report for a tribe with a fundamental water quality monitoring program 

should include the following: 

1. An atlas table of tribal water resources. This atlas should include the estimated number of stream 

miles, lake acres, wetland acres, or estuarine square miles on your reservation. 

2. A narrative description of tribal water quality monitoring programs and assessment methods. 

Refer to chapter 4 for general information on developing a water quality monitoring program. Sections I.3 

and II.3 of chapter 4 contain information on assessment methods. This discussion should include: 

z The purpose of the monitoring program (e.g., to identify problem areas, track trends over time, 

identify NPS impacts, address public health concerns) 

z The number of stream miles/lake or wetland acres/estuary square miles monitored 

z Parameters monitored 

z Monitoring frequency 

z Discussion of any applicable WQI, tribal goals and objectives, or standards 

z Coordination or collaboration with other organizations 

z Any lab support 

z How data are interpreted and managed 

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3. Narrative description of results of water quality monitoring on your reservation. This should 

include an interpretation and summary of the findings of tribal monitoring activities, including probable 

causes and sources of impairment. Tribes that are in the early stages of developing a monitoring program 

should consider conducting simple watershed surveys and/or stream or lake habitat walks to learn about 

potential sources of impairment to their waters. EPA’s Volunteer Stream Monitoring: A Methods 

Manual contains field sheets and explanatory information on conducting watershed surveys and habitat 

walks. Section I.3 of chapter 4 contains more information on interpreting your monitoring results through 

data assessment and analysis. 

4. Brief narrative descriptions of issues of tribal concern. This discussion should identify any issues of 

special concern, such as: 

z Outbreaks of waterborne disease

z Fish kills

z Fishing or shellfishing advisories

z Restrictions on surface drinking water supplies

z Restrictions on bathing

5. Monitoring data, submitted electronically, for each assessed water body. Latitude/longitude 

location of the sites monitored, the water body name, and the name of the watershed are integral parts of 

this information. Standard templates will be available through EPA regional offices. 

2. Intermediate and Mature Water Quality Program 

The major components of a tribal Assessment Report for an intermediate or mature program should include the 

following components. A standard format is provided below and is recommended for use by tribes. 

1. An atlas table of tribal water resources. This atlas should include the estimated number of stream 

miles, lake acres, wetland acres, or estuarine square miles on your reservation. 

Table 1

Atlas of Tribal Waters

Total number of stream miles 95

Total number of lake acres 250

Total number of wetland acres 140

Total number of estuary square miles 10

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2. Brief narrative descriptions of monitoring programs and assessment methods. This discussion 

should include: 

z The purpose of the monitoring program (e.g., to identify problem areas, track trends over time, 

identify NPS impacts, address public health concerns) 

z The number of stream miles/lake or wetland acres/estuary square miles monitored 

z Parameters monitored 

z Monitoring frequency 

z Monitoring network design (e.g., rotating basin, fixed station) 

z Discussion of any applicable WQI, tribal goals or objectives, or standards 

z Coordination or collaboration with other organizations 

z Nature of laboratory support 

z How data are interpreted and managed 

Note: The table below shows a suggested approach for determining support of designated uses or tribal goals 

using the nine basic parameters for tribes with EPA-approved or tribally-adopted WQS. Tribes with WQI or tribal 

codes can use a similar approach. 

Table 2

Making Assessment Decisions

Designated Use or Tribal Goal Parameter(s) to be Measured to Determine

Support of Use or Goal

Contact recreation/swimming/cultural uses E. coli or enterococci, nitrogen, phosphorus

Aquatic life and wildlife DO, temperature, pH, turbidity,

macroinvertebrates, habitat, nitrogen,

phosphorus

Drinking water E. coli or enterococci, nitrates, turbidity

Shellfish/fish consumption E. coli or enterococci

3. Summary tables of the extent to which streams, lakes, and estuaries meet designated uses or 

tribal goals (including cultural uses of waters). Tribes should use WQI or EPA-approved or triballyadopted WQS to determine whether streams, lakes, and estuaries meet designated uses or tribal goals. 

Table 3

Use/Goal Support in Tribal Streams

Designated Use

or Tribal Goal

No. of Stream

Miles Monitored/

Assessed

No. of Stream Miles

Fully Supporting

Use or Goal

No. of Stream

Miles Supporting

Use or Goal but

Threatened*

No. of Stream Miles

Not Supporting Use

or Goal

Swimming 50 40 5 10

Aquatic life 45 20 20 25

Cultural 30 30 5 0

Fish consumption 20 10 5 10

*Note: Threatened miles are a subset of those miles fully supporting the use or goal.

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For tribes whose monitoring programs are in the intermediate stages, assessment decisions should be made on the 

best available information. Mature programs should consult EPA’s Consolidated Assessment and Listing 

Methodology (CALM) guidance, available online at http://www.epa.gov/owow/monitoring/calm.html, and 

Elements of a State Water Monitoring and Assessment Program, available online at http://www.epa.gov/owow/ 

monitoring/elements/, for more information on making assessment decisions. 

4. Summary tables of causes and sources of impairment. 

Table 4

Causes of Impairment in Tribal Streams

Parameter

No. of Stream Miles

Monitored or Assessed

No. of Stream Miles Not

Supporting Use or Goal

E. coli 50 10

Dissolved oxygen 45 25

Turbidity 45 20

Habitat degradation 45 25

Table 5

Sources of Impairment in Tribal Streams

Source of Impairment No. of Stream Miles

Monitored or Assessed

No. of Stream Miles Not

Supporting Use or Goal

Hydrologic modification 45 25

Agriculture (livestock grazing) 45 30

Stormwater runoff 20 20

Unregulated septic systems 50 25

III. Monitoring Data, Submitted Electronically, for

 Each Assessed Water Body 

Latitude and longitude of the sites monitored, the water body name, and the name of the watershed are integral 

parts of this information. EPA Headquarters will work with tribes and EPA regional offices to develop a standard 

format for data reporting, including metadata. Standard templates will be available through EPA regional offices 

before tribes begin to implement the reporting requirements outlined in this document. 

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" "

Appendix B: Requirements for

Authorization of Tribal

Administration of the WQS

Program

Summarized below are some, but not all, of the requirements a tribe must meet in order to be authorized to 

administer a WQS program. A full statement of the requirements is contained in CWA Section 518 and regulations 

at 40 CFR 131.8(b). You are encouraged to consult your Tribal Attorney General or equivalent and the appropriate 

EPA Regional Administrator as you begin to develop your TAS application. 

1. Tribe is federally recognized by the Secetary of the Department of the Interior. See Further Information below.

2. Tribe has a governing body carrying out substantial governmental duties and powers

Description of the form of tribal goverment

Description of governmental functions being carried out

Sources of tribal government's authority to carry out govermental

functions

3. WQS Program pertains to the management and protection of reservation water resources

Map and/or legal description of area where tribe asserts authority

Where are the boundaries of the reservation areas over

which the tribe asserts authority?

Are there tribal trust lands?

Are there non-member owned fee lands on the reservation?

Narrative statement describing legal basis of tribe's authority

Include description of authority over member and nonmember

activities.

Include description of authority over areas/waters covered by

the application.

Include a statement by the tribe's legal counsel that describes

the tribe's authority over member and nonmember activities.

Obtain copies of imporant tribal documents

Constitution, codes, by-laws, charters, resolutions, executive

orders, treaties, etc.

Identify surface waters where tribe proposes to establish WQS

What rivers, lakes, reservoirs, and wetlands are within the

reservation boundaries?

Map the important features.

4. Tribe exhibits capability to administer the WQS Program

Desciption of the tribe's previous management experience

List of existing environmental or public health programs

administered by the tribal government Copies of related tribals laws, policies, and regulations.

Description of the entities that exercise the executive, legislative,

and judicial functions of goverment

Description of the agency that will assume primary responsibility

for the WQS program

Description of the technical and administrative capabilities of the

program staff

Alternately, describe how this capacity will be developed.

The plan must also address how tribe will obtain the funds

required to develop technical and administrative expertise.

Further Information

1. The DOI maintains a list of all federally recognized Indian tribes, which is published periodically in the Federal Register.

The list can be found at www.doi.gov/bureau-indian-affairs.html.

2. Additional documentation may be required by the Regional Administrator to support a tribal application.

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Appendix C: Letter to Tribal

Leaders on Information Access

Dear Tribal Leader: 

We are writing today to discuss an issue that is of importance to both the 

Environmental Protection Agency (EPA) and tribes. The issue concerns records, 

information, and data which are generated under an EPA assistance agreement and 

required to be submitted to EPA under the agreement. We wish to inform you of the 

Agency’s position on this issue, to promote use of EPA’s national data systems, and to 

discuss what, if any, legal protections may be available to exempt this information from 

release in the event EPA receives a Freedom of Information Act (FOIA) request for it. 

On May 11, 2005, EPA circulated a draft tribal leaders’ letter with a call for 

comments throughout Indian country by way of the Tribal Caucus of EPA’s Tribal 

Operations Committee. These issues were also discussed with tribes in June at the 

National Tribal Environmental Management Conference in Traverse City, Michigan and 

prior to that in May at the River Network’s 2005 River Rally in Keystone, Colorado. 

Thank you for the thoughtful comments EPA received. Enclosed is a Comment and 

Response document to provide a more detailed explanation of the information in this 

letter. 

Be assured that EPA’s primary purpose in collecting this information is to help us 

implement the purpose of the relevant assistance agreement. EPA awards assistance 

agreements to tribes to carry out various statutory and program goals established in the 

Federal laws that EPA administers. In addition, by obtaining appropriate environmental 

data and information from tribes, EPA can ensure that it has a long-term and complete 

record of tribal environments from which to make necessary decisions, allocate 

resources, direct efforts, and mark progress over time. Using EPA’s national data systems 

also provides EPA and tribes the ability to understand the tribes’ important positioning 

within air sheds and watersheds that cross tribal-state boundaries, and will allow all 

parties to work together to improve the environment and human health. 

At this time when Congress and the President are requiring EPA to clearly 

demonstrate accountability and results from the financial assistance we provide to 

recipients, it is necessary for EPA offices to have this information available to make this 

showing. The Federal assistance agreements law makes clear that Federal agencies have 

full rights to information and data generated from activities financed by assistance 

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agreements. The American Indian Environmental Office (AIEO) supports making this 

information available. We believe that a lack of tribal information may hinder EPA’s 

ability to justify and account for its programs in Indian country to the overall detriment of 

tribes. 

Once information is obtained by EPA, any person may request a copy of the 

information through FOIA. FOIA contains nine exemptions from releasing records, but 

no specific restrictions preventing public access to tribal information in general. You 

should not assume that tribal information generated under an assistance agreement is 

automatically exempt from release. Certain information may be protected from release, 

for example, confidential business information, some personal privacy information, and 

limited other tribal information may be exempt from disclosure under FOIA. 

Please be assured that EPA will continue to work closely with our tribal partners 

on a government-to-government basis to discuss EPA’s program needs and ensure the 

appropriateness of our information collection requirements. We have heard many 

thoughtful comments regarding the need to protect tribally known sacred sites, medicinal 

plant locations, and particular species. In general such information is beyond the scope 

of EPA funded activities and would not be requested by EPA. AIEO will continue to 

emphasize to all EPA offices the importance of becoming knowledgeable about the 

effects that these requests have on tribal program capacity, the differences between 

working with states and tribes, and the overall sensitivity that the issue has in Indian 

country. 

If you have any questions please contact me, Carol Jorgensen, Director, AIEO, at 

(202) 564-0303, or have your staff contact Jeff Besougloff, AIEO, at (202) 564-0292.

 Sincerely,

 Benjamin H. Grumbles 

Assistant Administrator

 Carol J. Jorgensen

 Director 

American Indian Environment Office 

Enclosure 

cc: Indian Program Policy Council 

National Tribal Caucus 

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Tribal Information Access:

EPA responses to Tribal comments regarding

Tribal Leaders letter and conference presentations

September 2005

EPA’s American Indian Environmental Office received written comments from five 

tribes and evaluated feedback at two meetings in response to the May 11, 2005, draft 

tribal leaders letter on Tribal Information Access from Carol Jorgensen, Director of 

EPA’s American Indian Environmental Office. EPA had provided a copy of this draft 

letter to the Tribal Caucus of EPA’s Tribal Operations Committee for wider distribution 

to tribal leaders for comment prior to the letter being finalized. Additionally, these issues 

were also discussed with tribes in June at the National Tribal Environmental Management 

Conference in Traverse City, Michigan, and prior to that in May at the River Network’s 

2005 River Rally in Keystone, Colorado. The comments are summarized and combined 

by topic from all comments received. All attempts were made to use the original 

commenting language. 

STORET/Other Data Systems 

Tribal Comment: STORET is a cumbersome and excessively time-consuming and nonuserfriendly database. Also, using the program is incredibly labor-intensive and will take 

away from time and grant money that could be used for more beneficial programs. Tribes 

find it unreasonable of EPA to require the use of this program to store data. 

EPA Response: EPA is aware of the challenges involved in the use of STORET by tribal 

Clean Water Act Section 106 grant recipients and we have been working with tribes in 

several Regions to help facilitate submittal of tribal water quality monitoring data to 

EPA. Our Region 8 office has been working with tribes to load data into a copy of 

STORET hosted by an EPA contractor. Region 5 has been working with tribes on 

development of a simple Excel spreadsheet for use by tribes that can provide data in a 

consistent format that is readily accessible to STORET through the STORET Input 

Module (SIM) tool. EPA is currently embarking on the development of a new data 

management system (Water Quality Exchange, or WQX) that will free tribes and states 

from the burden of maintaining a local copy of STORET in order to submit their data to 

EPA. The Wind River Reservation is currently partnering with EPA in this effort. As we 

implement the Clean Water Act Section 106 tribal grant guidance, we will continue to 

work with tribes to implement better tools to manage water quality data and to submit 

that data to EPA. 

Tribal Comment: The tribe is willing to use STORET if EPA is willing to input the data 

into the database for tribes. 

EPA Response: In addition to the steps outlined in EPA’s response above, some EPA 

Regional programs are exploring the feasibility of developing tools to facilitate the entry 

of entering tribal Clean Water Act Section 106 information into STORET in order to ease 

the resource burden on the tribes and EPA. 

Tribal Comment: The tribe would be willing to use a workable database provided by EPA 

to replace STORET. The tribe opposes use of other databases (SDWIS, AQS, or any 

other) that operate similarly to STORET and take time and resources away from tribal 

priorities. 

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EPA Response: EPA is working to ensure that any data and information system used by 

tribal funding award recipients meets the needs of tribes as well as EPA. EPA recognizes 

that there may exist significant challenges to requiring tribal use of some EPA systems 

that were designed for input by non-tribal recipients and users. EPA is currently working 

with tribes to modify systems, such as the Air Quality System, to create a more tribal user 

friendly platform. EPA will continue to work with tribes to ensure that these challenges 

are recognized and resolved and that the need for data and information does not 

negatively impact tribes’ ability to conduct other activities under the EPA award. 

Tribal Comment: If issues regarding EPA positions on tribal data and information are not 

addressed, and data reporting becomes too costly and burdensome, then the tribe will 

have to consider pursuing other funding sources to implement its water quality program 

in a way that is consistent with tribal needs, goals, and priorities. 

EPA Response: It is EPA’s desire to strengthen its tribal program and tribal 

environmental programs to ensure the highest level of protection of human health and the 

environment in Indian country. To maintain and grow programs, EPA has identified a 

need for information that allows EPA to examine the effectiveness of its programs. At a 

time when all federal programs are being required to show results and positive benefits 

for the tax dollars spent, combined with decreasing federal resources for domestic 

programs, such self-examination is occurring in all federal programs. EPA is committed 

to working with the tribes to minimize the burden on the data providers as they implement the 

Clean Water Act Section 106 tribal guidance. 

Consultation and Coordination by EPA with Tribes 

Tribal Comment: Direct consultation needs to occur between EPA and tribal leaders 

before positions can be taken on general data and information issues and before a 

finalized Clean Water Act Section 106 tribal guidance is released. 

EPA Response: EPA takes seriously its government-to-government relationship with 

tribes and its consultation and coordination obligations. The release of the May 11, 2005, 

draft tribal leaders letter on Tribal Information Access from Carol Jorgensen, Director of 

EPA’s American Indian Environmental Office, is part of EPA’s effort to consult and 

coordinate. These efforts will continue to occur. Related actions, such as finalization of 

the Clean Water Act Section 106 tribal guidance, will also receive the proper level of 

coordination and consultation. 

Tribal Comment: The tribe questions the statement that there is a lack of tribal 

information regarding environmental quality in Indian country available to EPA. Tribes 

submit reports to Regional offices. 

EPA Response: EPA lacks comprehensive national information in a number of media 

areas for Indian country. EPA Regional offices have worked very hard with tribes to 

develop the information necessary to allow EPA Regional Programs to operate and 

continue funding. There is an additional need for EPA to have an ability to make 

comprehensive national statements regarding the environment in Indian country in order 

to support and maintain the current program levels. With the exceptions of limited 

circumstances, this is not occurring. The information submitted, in various manners and 

forms, to EPA Regional offices is not able to be combined in such a way as to present a 

national picture of need, nor of the effectiveness of the work being performed in Indian 

country under EPA funding. A number of EPA programs are expected develop national 

data systems for their programs in the coming years. Tribal leaders can expect to see 

additional EPA activity regarding tribal data. This activity is likely to take the form of 

requiring information that can be used on a national level. 

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Legal Issues 

Tribal Comment: There was no citation to the laws cited in the draft letter regarding 

access to data and information. 

EPA Response: As a general matter a grant of federal funds subject to conditions which 

must be met by the grantee, creates a type of contract between the United States and the 

grantee. See, McGee v. Mathis, 71 U.S. (4 Wall.) 143, 155 (1866); Pennhurst State 

School and Hosp. V. Halderman, 451 U.S. 1, 17 (1981); Bennett v. New Jersey, 470 U.S. 

632, 638 (1985). In carrying out its statutory grant authority, an agency is permitted to 

impose conditions on grantees who receive federal funds. Virginia Dep’t of Educ. v. 

Riley, 23 F.3d 80, 87 (4th Cir. 1994). For example, EPA can impose grant conditions 

under the Clean Water Act which are related to the water quality goals of the Act. Shanty 

Town Associates Limited Partnership v. EPA, 843 F. 2d 782 (4th Cir. 1988). 

Grant conditions not only include specific terms and conditions and applicable regulatory 

requirements, but also commitments made in a grant work plan. For example, EPA’s 

tribal environmental program grant regulations provide that a complete grant application 

must meet the requirements in 40 CFR Part 31 and include a proposed work plan. 40 

CFR 35.505. The work plan is negotiated between a tribe and the Regional 

Administrator and reflects consideration of national, regional, and tribal environmental 

and programmatic needs and priorities. 40 CFR 35.507(a). The work plan is “the basis 

for the management and evaluation of performance under the grant agreement” and must 

include “the work plan components to be funded under the grant” and the “commitments 

for each work plan component, and a time frame for their accomplishment.” 40 CFR 

35.507(b). Thus, if EPA is awarding a Clean Water Act Section 106 grant to a tribe for 

purposes of assessing tribal water quality, EPA has the authority to require in the work 

plan a commitment that the tribe submits to EPA water quality data collected under the 

grant. 

Tribal Comment: To ensure the appropriateness of EPA policies regarding access to data 

collected by tribes under federal assistance agreements, EPA should consider all existing 

Federal statutes, some of which prohibit public disclosure of information. Limitations can 

be found in the Freedom of Information Act and the National Historic Preservation Act. 

The limitations should be utilized as much as possible to protect tribal information. 

EPA Response: Under the Freedom of Information Act, a person may request any 

Agency record, including ones provided to EPA as part of a Federal assistance 

agreement. The requested record must be disclosed unless it is protected by one or more 

of the nine FOIA exemptions. Although FOIA does not contain a specific exemption to 

protect tribal-related information, such information may be protected under existing 

FOIA exemptions. Although several comments were received listing specific statutes that 

provide limitations on the disclosure of information under FOIA, most of these statutes 

have not been litigated, so their status as “Exemption 3” statutes is uncertain. Also, some 

of these laws appear to apply to information within specific agencies other than EPA. 

Tribal Comment: STORET is a data warehouse that is available to the public. For such 

data systems EPA must enter into a Memorandum of Agreement (MOA) or a Plan of 

Action (POA) with each tribe in each Region to address issues regarding sensitive data. 

EPA Response: The negotiated grant work plan contains any agreement regarding 

information requirements and data systems to be used under the funding award. No 

further agreement is required. EPA believes the issues of tribally-determined sensitive 

and cultural information warrants further discussion as these situations arise. 

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Tribal Comment: EPA’s rights to access records of grantees under 40 CFR 31.42 

(retention and access requirements for records), states in Section (f) that grantees do not 

have to allow public access and dissemination of records unless required by law. 

EPA Response: The regulation cited, 40 CFR 31.42, provides EPA and the Comptroller 

General with the right of access to any pertinent books, documents, papers, or other 

records of the grantees and subgrantees which are pertinent to the grant, in order to make 

audits, examinations, excerpts, and transcripts. Under Section (f), a grantee is not 

required to give the public the same right of access to these financial and programmatic 

records, unless otherwise required by law. This right of access is in addition in any other 

rights provided to EPA by the grant agreement itself, such as the requirement that a 

recipient submit water quality or other environmental data to EPA. Nothing in this 

regulation limits EPA’s authority to collect information through workplan commitments, 

as discussed above. 

AIEO’s Role in the Process 

Tribal Comment: What role does AIEO play in this process? 

EPA Response: AIEO plays an important role in developing EPA Tribal Program policies 

and in working with individual EPA Headquarters and Regional Offices on their 

activities with tribes. AIEO will continue to work with media specific offices - such as 

the Office of Water’s Office of Wastewater Management on the incorporation of 

STORET use into tribal Clean Water Act Section 106 grants - to ensure respect for the 

government-to-government relationship and adherence to EPA’s 1984 Indian Policy and 

its trust responsibility. AIEO has already begun discussions with EPA offices regarding 

the sensitivity of some tribal information and EPA’s obligation to work with tribes to 

develop mutually beneficial solutions to any challenges. Through these efforts, AIEO 

promotes the concept of seeking holistic solutions across tribal-state political boundaries 

by including tribal concerns in national level discussions. 

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Appendix D: Bibliography

Chapter 1 

General Resources 

The Federal Water Pollution Control Act (Clean Water Act). Available online at http://www.epa.gov/region5/ 

water/cwa.htm. 

The Code of Federal Regulations. Available online at http://www.gpoaccess.gov/cfr/index.html. 

U.S. EPA. EPA 2006 - 2011 Strategic Plan: Charting our Course. 2006. Available online at http:// 

www.epa.gov/cfo/plan/06strat_plan.pdf. 

Chapter 3 

General Resources 

Reed, A. and Dates, G. 2003. Listening to Watersheds: A Community-based Approach to Watershed 

Protection. Portland, OR. Available online at http://www.rivernetwork.org/ltw/. 

U.S. EPA Regional Office Web site. Available online at http://www.epa.gov/ow/region.html. 

U.S. EPA. Water Management Solutions: A Guide for Indian Tribes (EPA 908-K-93-001). 1993. Denver, 

CO. Available online at http://epa.gov/waterscience/tribes/wms.pdf. 

Funding Resources 

The Catalog of Federal Domestic Assistance. Available online at http://12.46.245.173/cfda/cfda.html. 

U.S. Department of Agriculture Natural Resources Conservation Service. 2005. Conservation Partnership 

Initiative. Available online at http://www.nrcs.usda.gov/programs/cpi/index.html. 

U.S. Department of Health and Human Services Web site. Available online at http://www.acf.dhhs.gov/ 

programs/ana/programs/annsumm.html. 

Obtaining Hard Copies of Electronic Resources 

Throughout this guidance you will find links to online technical documents, policies, and other guidances. 

If you wish to obtain a hard copy of any of these documents, you should contact your EPA regional 

office or the EPA Water Resource Center using the contact information provided below: 

United States EPA 

Water Resource Center (PC-4100) Phone: (202) 566-1729 

1200 Pennsylvania Ave., NW Fax: (202) 566-1736 

Washington, D.C. 20460 

D-1 
U.S. EPA. 2005. EPA Order 5700.7. Available online at http://www.epa.gov/ogd/grants/award/5700.7.pdf. 

U.S. EPA. 2005. Wetland Program Development Grants. Available online at http://www.epa.gov/owow/ 

wetlands/grantguidelines/. 

U.S. EPA. 1998. Interim Guidance for Cost Sharing/Match Requirement on the Award of Grants to 

Indian Tribes. Available online at http://www.epa.gov/owm/rmes/tribalcwas106_app-d.pdf. 

U.S. EPA American Indian Environmental Office. Related Links. Available online http://www.epa.gov/indian/ 

links.htm. 

U.S. EPA American Indian Environmental Office Web site. Available online at http://www.epa.gov/indian/ 

tgrant.htm. 

U.S. EPA Environmental Information and Exchange Network and Grant Program Web site. Available online 

at http://www.epa.gov/neengprg/. 

U.S. EPA Office of Grants and Debarment Web site. Available online at http://www.epa.gov/ogd/index.htm. 

U.S. Office of Management and Budget. Grants Management Web site. Available online at http:// 

www.whitehouse.gov/omb/financial/fin_grants_expanded.html#admin. 

Geographical Resources 

U.S. Department of Agriculture Natural Resources Conservation Service Web site. Available online at http:// 

www.nrcs.usda.gov/. 

U.S. EPA. 2005. EPA Reach File References. Available online at http://www.epa.gov/waters/doc/ 

rfindex.html. 

U.S. Geological Survey Web site. Available online at http://www.usgs.gov/. 

U.S. Geological Survey. National Hydrography Dataset. Available online at http://nhd.usgs.gov/. 

Training and Capacity Development Resources 

U.S. EPA American Indian Environmental Office. Training And Education. Available online at http:// 

www.epa.gov/indian/training.htm. 

U.S. EPA Office of Wastewater Management. Training Opportunities. Available online at http:// 

www.epa.gov/owm/mab/indian/training.htm. 

U.S. EPA Office of Wetlands, Oceans, and Watersheds. Online Training in Watershed Management. 

Available online at http://epa.gov/watertrain/. 

Outreach and Community Education Resources 

U.S. EPA. Environmental Education Web site. Available online at http://www.epa.gov/enviroed/index.html. 

U.S. EPA. Volunteer in Your Watershed. Available online at http://www.epa.gov/owow/volunteer.html. 

U.S. EPA. What Can You Do? Available online at http://www.epa.gov/water/citizen.html. 

D-2 
Program Review 

U.S. EPA. Program Evaluation Information Resources Web site. Available online at http://www.epa.gov/ 

evaluate/links.htm. 

Chapter 4 

Monitoring and Reporting 

American Public Health Association. 2005. Standard Methods for the Examination of Water and 

Wastewater. 21st edition. Washington, D.C.: American Public Health Association. 

Barbour, M.T., J. Gerritsen, B.D. Snyder, and J.B. Stribling. 1999. Rapid Bioassessment Protocols for Use 

in Streams and Wadeable Rivers: Periphyton, Benthic Macroinvertebrates, and Fish, Second Edition 

(EPA 841-B-99-002). Available online at http://www.epa.gov/owow/monitoring/rbp/. 

McCafferty, W. P. 1981. Aquatic Entomology: The Fishermen’s and Ecologists’ illustrated Guide to 

Insects and their Relatives. Boston, MA: Science Books International. 

Microbiological & Chemical Exposure Assessment Research Division of the National Exposure Research 

Laboratory. 2005. The EPA Microbiology Website. Available online at http://www.epa.gov/nerlcwww. 

U.S. EPA. 2004. Ecological Condition of Western Cascades Ecoregion Streams (EPA 910-R-04-005). 

Seattle, WA. Available online at http://www.epa.gov/emap/remap/html/docs/wcs.html. 

U.S. EPA. 2003. Elements of a State Water Monitoring and Assessment Program (EPA 841-B-03-003). 

Available online at http://www.epa.gov/owow/monitoring/repguid.html. 

U.S. EPA. 2002. Consolidated Assessment Listing Methodology (CALM) Guidance Document. Available 

online at http://www.epa.gov/owow/monitoring/calm.html. 

U.S. EPA. 2000. Guidance for the Data Quality Objectives Process (EPA 600/R-96/055). Available online 

at http://www.epa.gov/quality/qs-docs/g4-final.pdf. 

U.S. EPA. 1996. Volunteer Monitor’s Guide to QAPPs. Available online at http://www.epa.gov/owow/ 

monitoring/volunteer/qappcovr.htm. 

U.S. EPA. Knowing Our Waters: Tribal Reporting under Section 305(b). Available online at http:// 

www.epa.gov/volunteer/305btribal.pdf. 

U.S. EPA. Monitoring and Assessing Water Quality — Volunteer Monitoring. Available online at http:// 

www.epa.gov/owow/monitoring/volunteer/. 

U.S. EPA. Volunteer Monitoring Guidances. Available online at http://www.epa.gov/owow/monitoring/ 

vol.html. 

U.S. EPA Region 8 Water Management Division. Integrating Quality Assurance Into Tribal Water 

Programs. Undated. 

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U.S. EPA Region 9. 2004. Wetlands Quality Assurance Project Plan Guidance. Available online at http:// 

www.epa.gov/Region9/qa/pdfs/wetlandsqapp-04.pdf. 

Voshell, J. R. 2002. A Guide to Common Freshwater Invertebrates of North America. Blackburg, VA: The 

McDonald & Woodward Publishing Company. 

Data Management Tools 

STORET Web site. Available online at http://www.epa.gov/storet/. 

Water Quality Databases 

U.S. EPA. 305(b) Water Quality Report Database. Available online at http://www.epa.gov/305b/. 

U.S. EPA. Databases and Mapping. Available online at http://www.epa.gov/owow/data.html. 

Water Quality Problems 

U.S. EPA. 1997. Volunteer Stream Monitoring: A Methods Manual. Available online at http:// 

www.epa.gov/owow/monitoring/volunteer/stream/. 

U.S. EPA. Agriculture 101: Pathogens. Available online at http://www.epa.gov/agriculture/ag101/ 

impactpathogens.html. 

U.S. EPA. Alterations to Hydrology. Available online at http://www.epa.gov/bioindicators/aquatic/ 

hydrology.html. 

U.S. EPA. Animal Feeding Operations. Available online http://cfpub1.epa.gov/npdes/ 

home.cfm?program_id=7. 

U.S. EPA. Channelization and Chanel Modification. Available online at http://www.epa.gov/owow/nps/ 

MMGI/Chapter6/ch6-2a.html. 

U.S. EPA. Forestry. Available online at http://www.epa.gov/owow/nps/forestry.html. 

U.S. EPA. How Excessive Water Use Affects Water Quality. Available online at http://www.epa.gov/ow/ 

you/chap2.html. 

U.S. EPA. Land Disposal Restrictions. Available online at http://www.epa.gov/epaoswer/hazwaste/ldr/ 

snapshot.htm. 

U.S. EPA. Nonpoint Source Pollution From Agriculture. Available online at http://www.epa.gov/region08/ 

water/nps/npsag.html. 

U.S. EPA. Office of Prevention, Pesticides, and Toxic Substances Web site. Available online at http:// 

www.epa.gov/oppts/. 

U.S. EPA. Office of Waste Water Management Web site. Available online at http://www.epa.gov/owm/. 

U.S. EPA. Pollution. Available online at http://www.epa.gov/bioindicators/aquatic/pollution.html. 

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U.S. EPA. Salty Water. Available online at http://www.epa.gov/watrhome/you/salty.html. 

U.S. EPA. Sedimentation. Available online at http://www.epa.gov/bioindicators/aquatic/sediment.html. 

U.S. EPA. What is Acid Mine Drainage? Available online at http://www.epa.gov/region3/acidification/ 

what_is_amd.htm. 

Chapter 5 

Nonpoint Source Management Program Resources 

Center for Watershed Protection Web site. Available online at http://www.cwp.org. 

Michigan Department of Environmental Quality. 2000. Developing a Watershed Management Plan for 

Water Quality: An Introductory Guide. Available online at http://www.deq.state.mi.us/documents/deq-swqnps-Watershe.pdf. 

U.S. EPA. 2005. Community-based Watershed Management Handbook (EPA 842-B-05-003). Available 

online at http://www.epa.gov/owow/estuaries/nepprimer/handbook.htm. 

U.S. EPA. 2000. Watershed Analysis and Management (WAM) Guide for Tribes. Available online at http:// 

www.epa.gov/owow/watershed/wacademy/wam/. 

U.S. EPA. 1997. Tribal Nonpoint Source Planning Handbook (EPA 841-B-97-004). Available for order 

online at http://yosemite.epa.gov/water/owrccatalog.nsf/. 

U.S. EPA. Clean Water Act, Section 319. Available online at http://www.epa.gov/owow/nps/cwact.html. 

U.S. EPA. Publications and Information Resources. Available online at http://www.epa.gov/owow/nps/ 

pubs.html. 

U.S. EPA. Watersheds. Available online at http://www.epa.gov/owow/watershed/. 

Outreach 

U.S. EPA. 2003. Getting in Step: A Guide for Conducting Watershed Outreach Campaigns. Available 

online at http://www.epa.gov/owow/watershed/outreach/documents/getnstep.pdf. 

U.S. EPA. Non Point Source Outreach Digital Toolbox. Available online at http://www.epa.gov/owow/nps/ 

toolbox.html. 

Grants 

U.S. EPA. Tribal Information Page. Available online at http://www.epa.gov/owow/nps/tribal.html. 

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Chapter 7 

Water Quality Standards Resources 

U.S. EPA. 2001. Water Quality Standards and the Endangered Species Act. Available online at http:// 

www.epa.gov/ost/standards/esa.html. 

U.S. EPA. 1994. Water Quality Standards Handbook. Available online at http://www.epa.gov/ 

waterscience/standards/handbook/. 

U.S. EPA. 1990. Reference Guide to Water Quality Standards for Indian Tribes. Available for purchase at 

http://yosemite.epa.gov/water/owrccatalog.nsf/0/64f92e619e6f11df85256b0600724bcd?OpenDocument. 

U.S. EPA. 1990. Water Quality Standards for Wetlands. Available online at http://www.epa.gov/owow/ 

wetlands/regs/quality.html. 

U.S. EPA. 1988. CERCLA Compliance with Other Laws Manual, EPA/540/G-89/006, Interim Final. 

Available online at http://www.epa.gov/superfund/resources/remedy/pdf/540g-89006-s.pdf. 

U.S. EPA. 1983. Technical Support Manual for Conducting Use Attainability Analyses (EPA 440-486­

038). Available online at http://www.epa.gov/waterscience/library/wqstandards/uaavol123.pdf. 

U.S. EPA. Current National Recommended Water Quality Criteria. Available online at http:// 

www.epa.gov/waterscience/criteria/wqcriteria.html. 

U.S. EPA. Tribal Water Quality Standards Approved by EPA. Available online at http://www.epa.gov/ 

waterscience/standards/wqslibrary/tribes.html. 

U.S. EPA. Water Quality Standards: Trainings, Meetings, and Educational Materials. Available online at 

http://www.epa.gov/waterscience/standards/training.htm. 

Section 401 Certification 

U.S. EPA. 1989. Wetlands and 401 Certification: Opportunities and Guidelines for States and Eligible 

Indian Tribes. Available online through the Office of Water’s Online Publication Web site, http:// 

yosemite.epa.gov/water/owrccatalog.nsf. 

U.S. EPA. Clean Water Act Section 401 Certification. Available online at http://www.epa.gov/OWOW/ 

wetlands/regs/sec401.html. 

Section 404 Permitting 

U.S. EPA. Section 404 of the Clean Water Act: An Overview. Available online at http://www.epa.gov/ 

owow/wetlands/pdf/reg_authority_pr.pdf. 

U.S. EPA. State or Tribal Assumption of the Section 404 Permit Program. Available online at http:// 

www.epa.gov/owow/wetlands/facts/fact23.html. 

D-6 
NPDES 

U.S. EPA. 1996. NPDES Permit Writer’s Manual (EPA 833-B-96-003). Available online at http:// 

cfpub.epa.gov/npdes/writermanual.cfm?program_id=45. 

U.S. EPA. 1994. NPDES and Sewage Sludge Program Authority, a Handbook for Federally 

Recognized Indian Tribes (EPA 833-B-94-004). Available online at http://www.epa.gov/owm/rmes/ 

tribalcwas106_app-e.pdf. 

U.S. EPA. NPDES Web site. Available online at http://cfpub.epa.gov/npdes/index.cfm. 

U.S. EPA. NPDES Publications. Available online at http://cfpub.epa.gov/npdes/pubs.cfm?program_id=0.

 U.S. EPA. NPDES Training Courses and Workshops. Available online at http://cfpub.epa.gov/npdes/ 

outreach.cfm?program_id=0&otype=1. 

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