United States

Environmental Protection Agency

Water Quality Research Program 

Multi-Year Plan

Office of Research and Development

Version: 2003 Update

Date last peer reviewed: October 2001
The Office of Research and Development’s (ORD) multi-year plans (MYPs) present ORD’s

proposed research (assuming constant funding) in a variety of areas over the next 5-8 years. The

MYPs serve three principal purposes: to describe where our research programs are going, to

present the significant outputs of the research, and to communicate our research plans within

ORD and with others. Multi-year planning permits ORD to consider the strategic directions of

the Agency and how research can evolve to best contribute to the Agency’s mission of protecting

human health and the environment.

MYPs are considered to be “living documents.” ORD intends to update the MYPs on a regular

basis to reflect the current state of the science, resource availability, and Agency priorities. ORD

will update or modify future performance information contained within this planning document

as needed. These documents will also be submitted for external peer review.
PREFACE

The Water Quality Multi-Year Plan was developed and reviewed by the following individuals

representing the Office of Research and Development, the Office of Water and EPA Regions.

Writing Team

Lee Mulkey, NRMRL, ORD (Lead Author) Cynthia Nolt-Helms, NCER, ORD

Ben Blaney, NRMRL, ORD Lynn Papa, NCEA, ORD

Mimi Dannel, OSP, ORD Robert Spehar, NHEERL, ORD

Bruce Mintz, NERL, ORD

Review and Evaluation Team

Laura Gabanski, OWOW, OW

Roland Hemmett, Region 2

Renee Morris, OGWDW, OW

Laura Phillips, OWM, OW

Mary Reiley, OST, OW

Rita Schoeny, OST, OW

Barbara Walton, NHEERL, ORD

Molly Whitworth, OSP, ORD
Table of Contents

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

Scope of the Plan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Long Term Goals and Science Questions ........................................8

Setting Priorities and Science Questions ......................................8

Annual Performance Goals and Measures: The General Roadmap and Challenges . . . 11

Long Term Goal 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Summary of Research Questions and Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Expected Impact and Outcomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Long Term Goal 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Summary of Research Questions and Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Expected Impact and Outcomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Long Term Goal 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Summary of Research Questions and Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Expected Impact and Outcomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Long Term Goal 4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Summary of Research Questions and Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Expected Impact and Outcomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Resource Allocation Among the Long Term Goals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Summary of the Non-EPA research supportive of the LTGs . . . . . . . . . . . . . . . . . . . . . 20

Concluding Notations for Current Resource Base . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Unfunded Priorities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Appendix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

List of Tables

Table 1. Long Term Goals and Priority Science Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Table 2. Relative Resource Trends Among the Long Term Goals . . . . . . . . . . . . . . . . . . . . . . . 20

Table 3. Long Term Goal 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Table 4. Long Term Goal 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Table 5. Long Term Goal 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Table 6. Long Term Goal 4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

List of Figures

Figure 1. Goal 2 Context for Water Quality Multi-year Plan ............................3

Figure 2. Water Quality Framework ..............................................4

Figure 3. Relationship of OW Programs and Science Needs to ORD Research Areas . . . . 9

Figure 4. Setting Priorities for the Water Quality Multi-year Plan . . . . . . . . . . . . . . . . . . . . . 10

Figure 5. Long Term Goal 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Figure 6. Long Term Goal 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

Figure 7. Long Term Goal 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

Figure 8. Long Term Goal 4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
1

TEXT BOX 1

Water Quality Long Term Research Goals

LTG 1: Provide the approaches and methods to develop and apply criteria for habitat

alteration, nutrients, suspended and bedded sediments, pathogens and toxic chemicals

that will support designated uses for aquatic systems

LTG 2: Provide the tools to assess and diagnose the causes and pollutant sources of

impairment in aquatic systems 

LTG 3: Provide the tools to restore and protect impaired aquatic systems and to forecast

the ecological, economic, and human health benefits of alternative approaches to attain

water quality standards

LTG 4: Provide the approaches, methods and tools to assess the exposures and reduce

the human health risks from biosolids contaminants for use by OW, States and others in

updating biosolids guidance and regulations

Introduction

The Water Quality Multi-year Plan (MYP) is one of 16 MYPs developed by the Office of

Research and Development. The purpose of the MYPs is to aid ORD as a planning and

communication tool. Multi-year planning allows ORD to consider the future strategic direction

of the Agency, as described in the EPA and ORD Strategic Plans, and determine where scientific

discovery can contribute. MYPs also help ensure the relevance, quality, and performance of our

research program. 

The primary client for the Water Quality MYP is the U.S. EPA’s Office of Water. The research

to support the Office of Water’s Goals under the Clean Water Act (CWA) is described, or

referenced, in this document. The Long Term Goals (LTGs) guiding research for the next 5-8

years are given in the text box below. By design, the long term research goals and the interim

steps and planned accomplishments proposed here are directed specifically to enhance the

science and engineering content of EPA, State, and local action programs. Accordingly, ORD

envisions this research as the “application and demonstration vehicle ” for both its relevant

science programs described in Goal 4 (Healthy Communities and Ecosystems) and the

fundamental and applied science needed to underpin the strategic goals for the Agency Goal 2

(Clean and Safe Water) programs. Consistent with this approach, many of the annual goals and

planned products are phrased as “providing tools and data for...” or as “ demonstrating the

application to achieve....” where the specific goals or products correspond to one or more of the

major logical steps required to meet the Nation’s water quality goals. 
2

The level of resources for Water Quality research in Fiscal Year (FY) 2003 is approximately $45

Million including 225 full time equivalent (FTE) personnel.

Background

The conceptual and logical description of the EPA’s Water Quality programs are provided in

Figures 1 and 2. Included in Figure 1 are the relevant Agency policy instruments on the leftmost column; included as the right-most columns are the typical research topics from both this

plan and relevant topics from ORD’s core research program in Goal 4. Figure 2 illustrates the

same support and cross-connection keyed to a recent description of the Agency’s watershed

approach as provided by the Office of Water. In addition to the Agency’s mandates to guide and

enhance our meeting “fishable and swimmable” clean water goals, a number of specific and

technology-based components of the Act require periodic or stake-holder driven increased

attention. This plan also includes the specific issue of generation, treatment, and use/disposal of

biosolids. Biosolids are sewage sludge that have been treated in accordance with 40 CFR Part

503 (the “Part 503 rule”). Land application is one of several management options for biosolids

and disposal of biosolids. In this case, the EPA commissioned a review of current practices and

regulations for land application of biosolids by the National Research Council (NRC) which has

recommended research issues that should be addressed. Accordingly this Plan includes ORD’s

response to that study. The Long Term Goals for this Multi-Year Plan included in Text Box 1

reflect both the logical construct of the Agency’s programs and the current priority among a

much broader programmatic effort. 

The programmatic processes outlined in Figures 1 and 2 are not entirely new. The details of each

of the programmatic and policy-level programs will not be repeated here; such information is

available from the Agency’s Office of Water’s Strategic Plan and other web-site materials

available from the OW (http://www.epa.gov/ow). While the programs are varied and seemingly

complex, the major drivers for this research plan are the Agency’s watershed approach, specific

regulatory and guidance “tracks”, and the Total Maximum Daily Load (TMDL) program. A

TMDL is a calculation of the maximum amount of a pollutant that a waterbody can receive and

still meet water quality standards, and an allocation of that amount to the pollutant’s sources. 

Analysis and implementation are via watershed management, water quality restoration and

protection. 

ORD has been engaged in supporting the science needs of various aspects of the relevant

portions of the CWA for a number of years. Particularly, ORD has developed and defended

chemical water quality criteria, conducted dose-response experiments and developed causeeffect models, provided hydrologically-based modeling frameworks and models for TMDL

modeling, investigated the performance and costs of treatment technologies, developed and

evaluated best management practices, and provided indicators for assessing biological condition.

A number of 

environmental and institutional trends have emerged from application and use of previously

developed science and technology.
Goal 2 Instruments: Policy Guidance,

Regulations, and Program Initiatives

Steps Required to Meet Water Quality Goals Research products required 

sound scientific basis for imp

Goal 2 

R

M o n ito rin g fo r

C o n d itio n &

A t ta in m e n t o f W Q

S ta n d a r d s

D ia g no s tic

A sses sm ents

F o r m u la tin g A l te r n a tiv e S o lut io n s a nd

F o re ca stin g O u tco m es

D ev e lo p in g a n d E v a lu a t in g C o s ts ,

E f f e c t iv e n es s , a n d I m p le m e n ta t io n

S tra t e g ie s

Im p le m e n t in g W a t e rs h e d P r o te c tio n

R e sto ratio n a n d M a n a ge m e n t

M e as u rin g P ro g res s a n d E n su rin g

L o n g-te rm S u cc e ss

I ssu in g C rit e riat o S u p p o r t U s e

D e s ig n a tio n s

A p p lyin g

D e s ig n a te d U s e ,

W Q C riteri a,

a n d O th e r L istin g

C rit e ria

C o m m u n ity &

st a ke h o ld e r p ro b le mfo rm u la tio n a n d g o a l

s e tt in g f o r

d e sg in a t e d u se s Criteria development methods

Stressor-response ModelsHabitat and water body classification

Indicator development:microbial, chemical, IBI’s

SIE, Diagnostic methods & models, site-

watershed threshold approaches, eco-ri

approaches, eco-risk characterization

Load allocation modeling,

NPS Loading models & data, 

BMP design methods, landscape methods, restoration and treatmtechnologies

Cost effectiveness data, integrated case studies for waand watersheds

Near-Lab pilot stuand State Pilots

Water Quality Criteria and Designated Use Guidance

305(b), 303(d) Reporting

TMDL’s, 319 Program,

Stormwater Reg’s, WRAS’,

Beach Bill

NPDES,CWAP 106 Grants

Community and watershed actiongroupsNational Estuary ProgramWetlands Program

Figure 1. Goal 2 Context for Water Quality Multi-Year Plan
TMDL Minimum Elements

Identify Watershed

Identify and locate pollutant sources

Estimate existing pollutant loading

Determine assimilative capacity

Point Source 

NPDES Permits

Control 

Nonpoint Sources

List Impaired Waters

Monitor/Assess WQS Attainment

Water Quality Standards

Integrated 

Watershed

Process

Ref. O

Figure 2. The “Problem,” a.k.a. Water Quality Framework
5

Among the major trends that present remaining challenges are:

< over 20,000 waters identified by States as impaired due to one or more pollutants

< a shift from point source discharges as the major source of pollutants to nonpoint sources

< an increasing use of biological indicators and metrics as the preferred method for

determining the condition of aquatic ecosystems

< an increasing awareness of the importance of landscape- and watershed- scale processes

and activities as determinants of water quality

< an increasing awareness of the role of atmospheric deposition and multimedia sources as

determinants of water quality

< an increasing awareness of the role of habitat alteration as a cause of aquatic ecosystem

impairment 

< an increase in human-health risks from apparent ecosystem responses to stressors,

particularly pathogens 

< pressures to increase the efficiency and cost-effectiveness of implementation 

< an increase in the role of citizen stakeholders in setting watershed management goals and

in implementing action programs at the local and watershed levels

< increasing calls for more efficient, more nearly accurate models and methods, and more

explicit representation of uncertainties in decision-making processes used by EPA and

State Agencies (NRC, 2001)

< lack of systematic and statistically-robust evidence that best management practices

(BMP’s) for non-point source controls are working

< increasing calls for outcome-based implementation and accountability

< increasing calls for documentation of the economic benefits derived from Agency

approaches to meet Water Quality Standards and Goals

< an increasing awareness of the role of invasive species as a cause of aquatic ecosystem

impairment

< integrated assessments for allocation of restoration resources to support water quality

standards attainment within the context of socioeconomic factors
6

< recycling of biosolids through field application is the preferred method for biosolids

management, but there is increasing public concern that biosolids land application

practices may be causing adverse health effects in nearby residents 

< the NRC and others have called for an update of the scientific basis for the Part 503 rule,

particularly for Class B biosolids - those that are treated to reduce pathogens but still

contain detectable levels of them and consequently are restricted in their use. 

The trends and challenges cited above drive the current research agenda and help set the

priorities laid out in this multi-year plan. In particular, previously developed and current science

and technologies are apparently inadequate to meet the challenges for the following reasons:

< BMP’s and other nonpoint source control measures have rarely been evaluated for their

effectiveness in achieving improved water quality (particularly biological condition),

rather only for pollutant load or concentration reduction

< previous focus on chemical and pollutant-specific determinants of water quality does not

fully address biological condition

< the data, analysis tools, and assessment methodologies for landscape and regional scale

processes are leading edge research areas not yet exploited to solve problems

< atmospheric deposition of nutrients (e.g., nitrogen) and toxic substances (e.g., mercury)

have not been integrated into watershed management science 

< biological indicators and measurements of habitat alterations, particularly related to flow

and sediment, have only recently emerged as issues 

< the causes and control of increasing hazardous algal blooms (HAB’s), Pfiesteria, and

pathogens are not fully known

< ecological risk assessment guidelines, public awareness tools, and risk communication

programs are largely new and rarely applied 

< free market based and economically robust risk management systems and frameworks are

limited in scope and application

< many models and decision-support tools are often cumbersome to apply, require data all

too often unavailable, and fail to explicitly address uncertainty

< guidance for setting action and management priorities to achieve outcome-based goals

remains problematic
7

< water quality management solutions that also lead to sustainable ecosystems and related

economies are desirable; the ability to design and implement such solutions is lacking, in

large part because of scientific limitations.

< economic valuation of water quality benefits cannot yet be applied to action programs

and regulatory activities

< assessing exposures and risks of critical pathways and contaminants are limited by the

lack of improved scientific information and tools to identify hazards of biosolids

application.

< there are limited tools for analyzing pathogens and emerging chemicals in biosolids

< there are limited data on the appropriate use of existing or emerging biosolids

management techniques to minimize human health risks.

Scope of the Plan

Note that the long-term goals in Text Box 1 follow the logical construct of the steps in Figures 1

and 2. Simply stated, ORD envisions a logical progression in meeting water quality goals by: 1)

setting water quality criteria that are logically connected to specific designated uses; 2)

monitoring for the condition of designated water bodies and listing those having impairment; 3)

applying relevant criteria and stakeholder input to evaluate if action programs are needed to

either protect high quality systems or to restore impaired waters; 4) diagnosing the causes of

observed impairment (stressors) and determining the sources of the stressors; 5) developing an

array of technologies, management, and restoration actions that can be deployed to protect high

quality habitats, restore degraded systems to desired designated uses, and protect public health;

and 6) deploying institutional, implementation, and monitoring systems to ensure that long-term

and sustainable success is achieved. The geographical scope of the problem is national and both

freshwater and coastal systems are included. Critical habitats, particularly wetlands and riparian

zones, are included, largely as a part of the surface water network subject to the processes in

Figures 1 and 2. While other specific and perhaps critical or unique habitats and features of the

landscape are of interest to the Office of Water, ORD has made a strategic decision to limit the

scope of our research so that we can focus on high priority issues presented by TMDL’s and

related processes identified in Figure 1. In a later section of this Plan, ORD will identify areas of

needed emphasis should additional resources become available. 

The plan described in this document includes pathogens as a priority stressor. Pathogens are

regulated via both the Clean Water Act (CWA) and the Safe Drinking Water Act (SDWA). Only

the CWA is considered here, with logical references to the Safe Drinking Water Act. 

Accordingly, the scope of this plan for pathogens includes: TMDL-driven issues (i.e., setting and

meeting limits on loadings of pathogens from point and nonpoint sources); the role of aquatic

ecosystems in the survival and proliferation of human and ecological pathogens; ecosystem-
8

derived harmful microorganisms (e.g., hazardous algal blooms (HAB’s)); and development of

human exposure and effects data for risks in recreational water use designations.

ORD will support the specific steps illustrated in Figure 1 by providing data, methods, models,

and experimental protocols. ORD will also investigate innovative approaches that could

transform currently configured complex processes (e.g., TMDL’s) into profoundly simpler and

more cost-effective ways to meet water quality goals. Accordingly, ORD envisions interactive

partnerships with both the Office of Water and the State, interstate, and local agencies charged

under the Clean Water Act to design and implement action programs.

Long Term Goals and Science Questions

Setting Priorities and Formulating Science Questions

Resource materials that inform the content and priorities of this plan are derived in the most part

from the body of information jointly developed by ORD and the Office of Water through the

Strategic Planning and Research Coordination (SPRC) workshops held during 1999 - 2002. The

purpose of these workshops was to establish joint goals and strategic research directions in OW

program areas related to water quality and aquatic ecology. Figure 3 was used as a coordinative

guide to relate the OW program and science needs to the ongoing ORD research areas. While

this figure is somewhat dated, having been developed in 1999, it is instructive to modify the

figure by adding the right-most column as a means to inter-relate current ORD Multi-Year Plans. 

This figure shows that research planned and budgeted in Goals 4 (Healthy People, Communities

and Ecosystem - Ecological Research ), 5 (Compliance and Environmental Stewardship -

Pollution Prevention Research), and in Goal 3 (Land) also support the Long Term Goals

identified in this Plan.

Observations from the Regions and States on the condition of U.S. waters were heavily weighted

in the SPRC workshops and in development of this plan. ORD attended a National meeting of

the EPA Regional coordinators for nonpoint sources, monitoring, and TMDL’s and used a

questionnaire to query the group on the contents of this MYP. The response was remarkably

positive and supportive with notable requests for more integrated products and technical support

for monitoring and modeling.

The SPRC workshops resulted in the development of comprehensive “research needs” and 

“program needs” statements. ORD subsequently followed up with detailed in-house planning

activities. Notable among these efforts is NHEERL’s science planning for aquatic stressors

(Aquatic Stressors: A Framework and Implementation Plan for Effects Research 2002, EPA

600/R-02-074). Another notable effort was the generation and publication of five white papers

on the risk management of sediments, nutrients, toxics, flow, and pathogens by NRMRL.

Science planning documented in MYP’s must be sufficient to enable and guide the detailed

project planning steps at the Division and Investigator levels. This MYP is intended to provide 
OW

GOALS

OW

PROGRAMS

OW 

SCIENCE NEEDS

ORD 

MYP

Water Qu

Wetlands/Critical Habitats

Wet Weather Flow, Sediments,

Ecological Restoration,

Watershed Management

Ecologi

Drinkin

Biocriteria,

Monitoring, W/S classification 

Modeling: development and 

support 

Nutrient Criteria

Chemical-Specific Criteria

Wildlife Criteria

Assessment Research

Trading, C:B

Economics, CSO’s, ETV

CAFO’s

WQ

Eco

Ec

W

WQ

WQ, 

Contamin

WQ

-Eco

Eco

W

Ec

Water Safe to Drink

Fish and ShellfishSafe to Eat

Water Safe for Swimming

Protect and Improve WQ on Watershed BasisImprove Coastal and Ocean Waters

Source Water 

Protection

303(d) Listing

TMDL’s

Microbial Strategy

Beach Action Plan &

Fish Advisories

Criteria 

Development

319 NPS

Wetlands, NEP, ....

Invasive Species

Figure 3. Relationship of Office of Water Program and Science Needs to ORD Research Are
10

IncreasingUncertainty 

Increasing Sensitivity or 

Magnitude of Impact

high priority

medium 

priority

low 

priority

medium

priority

Figure 4. Setting Priorities for the Water Quality Multi-Year Plan

the “top down” priorities and expectations for detailed water quality science planning at the

bench and field level within and among the ORD Laboratories and Centers. While the science

questions included in this plan are projected to be appropriate and the related outputs and goals 

the “right” milestones, the reader should understand that detailed implementation planning is not

the intent nor the content.

 

Priorities within this plan were selected by “weighing” the combination of the reported reasons

for listing U.S. waters as impaired and the levels of uncertainty the Agency and States face in

using the steps in Figures 1 and 2 to achieve water quality goals, i.e. restoring the impaired

waters and maintaining designated uses. Conceptually the priority-setting approach is illustrated

in Figure 4. An elaboration on priorities is useful here because the priorities identified in this

plan imply changes in the content and pace of ORD’s research. It is also true that ORD envisions

this as an ongoing process that will require reconsideration of the current plan on a biennial 

basis.

Consider, for example, nutrients, pathogens and suspended and bedded sediments, which are the

most-cited stressors reported by the States as the reasons for listing U.S. waters as impaired.

Recall that such listings set in motion many of the policy and regulatory steps depicted in

Figures 1 and 2, including requirements for setting and implementing TMDL’s. Accordingly,

nutrients, pathogens and suspended and bedded sediments would occupy a “high” position on the

x-axis of Figure 4. That is, the listing process is demonstrably “sensitive” to these stressors and

their impact on water quality is judged to be substantial. From an uncertainty perspective, (the
11

y-axis of Figure 4) the ability to reliably measure pathogens and to infer their sources within

watersheds is very limited and the quantitative dose-response data for suspended and bedded

sediments are virtually non-existent. Clearly, in these cases, uncertainty is also “high”. This

uncertainty is a major, if not an absolute, limiting factor in the ability of the Agency and States

to successfully implement the steps (Figures 1 and 2) needed to meet water quality goals. And, a

high priority “weight” is now attached to these problems. This process is, of course, somewhat

qualitative but it is also believed to be reasonably objective. (Actually, it is also akin to the

concepts of “analysis of the value of data” and first-order error analyses, both representing

formal analytical and mathematical procedures.) 

Another perspective on the use of Figure 4 is application to the four LTGs. (See Text Box 1.) 

While meeting all the goals is critical to Agency programs and success, the recent NRC study

calls for increased attention to the “listing problem” and for more explicit “adaptative

management” approaches for implementing TMDL requirements. Accordingly, this MYP has

proposed relative increases in resources for LTGs 2 and 3, within an overall level-resource

environment. 

Table 1 provides specific research questions and topics under each LTG. Approximate time

frame for their completion is in the figures and tables to follow. The content as expressed in

annual performance goals and measures and their respective timing reflect the priorities as

judged by the above process.

Note that the questions in Table 1 are informed by additional specific information. For example,

the order and specificity of the major stressors (suspended and bedded sediments, pathogens,

nutrients, etc.) reflect the outcomes and priorities of the ORD-OW workshops. This does not

mean that all ORD resources will be deployed in a simple sequential fashion in order to answer

the questions, rather that the detailed science planning at the Division and investigator levels

should reflect the topics in a balanced and sufficiently focused manner so that the questions can

be answered in a timely fashion. The importance of this principle cannot be overstated –

projected resource levels simply do not accommodate relevant but lower priority research. 

Annual Performance Goals and Measures: The General Roadmap and Challenge for Meeting

Agency Long Term Goals 

Meeting the Agency long term goals and their related research goals by answering the associated

research questions summarized in Table 1, will enable OW, the Regions, the States, and

watershed stakeholders to develop and apply creative and robust approaches to meet Clean

Water Act requirements. The steps illustrated in Figure 1, while straight-forward in form, operate

in a challenging institutional environment of multiple interests, diverse constituencies,

overlapping jurisdictional boundaries, and calls for accelerated time frames. Such operational

complexities produce pressures for “faster, cheaper, more accurate” solutions. The overriding

public interest is in the outcome – clean water on a sustained and sustainable basis. 
12

The annual performance goals and measures outlined in this plan are designed to provide a

product stream of data, methods, models, and tools that both recognize the operational

complexities of Figure 1 and that support the specific steps taken by the various entities charged

with clean water action programs (of course, all entities respond to the Agency’s policy

development and guidance). All stakeholders serve the interest to protect high quality aquatic

systems and to restore U.S. waters currently listed as impaired.

Stakeholders and resource managers need to be able to set criteria or goals and monitor for

condition, to identify and list impaired waters for action, to diagnose the causes and sources of

current and future problems, and to formulate and implement cost-effective prevention and

restoration solutions. Some stakeholders need support in making local decisions and

implementing action programs while others need support in formulating policies that integrate

multi-objective interests while providing improved water quality outcomes. 

Operational time-lines among States and other stakeholders are variable with some depending on

rotation cycles among river basins or watersheds within a given jurisdiction, while others are

following a litigation-based schedule mandated by the Courts. The problem remains to provide

the science necessary to inform decision-making and document outcomes across this range of

needs. A specific time-frame from FY03 through FY08 has been adopted for this plan. The

cyclical and ongoing nature of the Clean Water Act will require both operational and research

support beyond the FY08 target. 
Table 1. Long Term Goals and Priority Science Questions

Long Term Goal 1: Provide the approaches and methods to develop and apply criteria for

habitat alteration, nutrients, suspended and bedded sediments, pathogens and toxic chemicals

that will support designated uses for aquatic systems

P What are the quantitative and causal relationships between varying levels of stressors, alone and in

combination, and the biological response of aquatic ecosystems and the resulting services such systems

provide? For habitat alteration? For nutrients? For suspended and bedded sediments? For pathogens? 

For toxic chemicals?

P What are the best ways to classify ecosystems, landscapes, and watersheds to enable efficient and

scientifically sound development and application of indicators, biocriteria, listing criteria, and water

quality criteria?

P How can stressor levels, biological-response relationships, classification schemes, bioassessment

methods, ecological risk assessments, and indicators be applied across U.S. surface waters to set criteria

for identifying/restoring impaired waters and maintaining designated uses?

Long Term Goal 2: Provide the tools to assess and diagnose the causes and pollutant sources of

impairment in aquatic systems

P How can multiple and possibly related causes of biological impairment be inferred from indicator and

other observations, and cause-effect modeling? For habitat alteration? For nutrients? For suspended

and bedded sediments? For pathogens? For toxic chemicals?

P How can the sources and source strengths of stressors be inferred from in situ measurements? From

stressor measurements? From biological indicators? From remotely-sensed observations and watershed

properties?

P How does one determine the most appropriate and efficient scale for application of diagnostic methods

within the TMDL and 303(d) process?

Long Term Goal 3: Provide the tools to restore and protect impaired aquatic systems and to

forecast the ecological, economic, and human health benefits of alternative approaches to attain

water quality standards

P What additions to models are most needed for the TMDL process? For habitat alteration? For nutrients? 

For suspended and bedded sediments? For pathogens? For toxic chemicals?

P What BMP’s treatment systems and restoration technologies remain as uncertain options for watershed

management? For mixed land use watersheds? For habitat alteration? For nutrients? For suspended

and bedded sediments? For pathogens? For toxic chemicals?

P How can classification schemes, modeling scenario analyses, landscape classification, and economic

projections be applied to provide alternatives for meeting water quality goals efficiently at multiple

scales? What are the economic benefits of watershed management?

Long Term Goal 4: Provide the approaches, methods and tools to assess the exposures and

reduce the human health risks from biosolids contaminants for use by OW, States and others in

updating biosolids guidance and regulations

P Do contaminants in biosolids pose a significant health risk to the public when applied in compliance

with current regulations?

P What additional models, tools and methods are needed to identify, measure and assess aggregate

exposure pathways and risks?

P What improved analytical techniques can be developed to adequately determine pathogen and priority

toxic chemicals in or released from biosolids?

P What is the current state of management practices for biosolids production and application, and how can

those be made more effective? 
14

Consider in detail the first Long Term Goal.

Long Term Goal 1. Provide the approaches and methods to develop and apply criteria for

habitat alteration, nutrients, suspended and bedded sediments, pathogens and toxic

chemicals that will support designated uses for aquatic systems

Summary of Research Questions and Approaches 

# What are the quantitative and casual relationships between varying levels of stressors,

alone and in combination, and the biological response of aquatic ecosystems and the

resulting services such systems provide? For habitat alteration? For nutrients? For

suspended and bedded sediments? For pathogens? For toxic chemicals?

# What are the best ways to classify ecosystems, landscapes, and watersheds to enable

efficient and scientifically sound development and application of indicators, biocriteria,

monitoring and assessment methodologies, and water quality criteria?

# How can stressor levels, biological-response relationships, classification schemes,

bioassessment methods, ecological risk assessments and indicators be applied across U.S.

surface waters to set criteria for identifying /restoring impaired waters and maintaining

designated uses? 

ORD envisions an approach to meeting the first Long Term Goal that develops and integrates

indicators, classification schemes, stressor-response relationships and modeling, and

bioassessment methods into generally applicable ways to set criteria for a wide array of

designated uses. ORD’s role does not currently extend to deriving criteria, rather to provide the

science to develop improved or new criteria. The recent National Research Council (NRC) study

on TMDL’s has recommended that more comprehensive and flexible consideration be given to

listing impaired waters. While this recommendation may be directed to policy constructs within

TMDL and Agency monitoring guidance, the related scientific issue includes the rationale for

relating designated use to water quality criteria. 

Table 2 arrays the APG’s and APM’s proposed to meet this goal. Figure 5 shows the linkage and

timing of the proposed Annual Performance Goals for this Long Term goal. Note that the

structure of the APG’s illustrated in Figure 5 implies both the provision of relevant and

necessary science and the application, or, demonstration, of the science. The structure and

choice of wording were deliberate; ORD needs to both produce peer-reviewed science and to

demonstrate via application and case studies that the research can be used to satisfy the

requirements shown in Figure 1. 

Priorities include increased stressor-specific efforts for sediments, nutrients, pathogens, and

highly persistent bioaccumulative toxic chemicals (PBT’s) for the protection of wildlife

populations. Bioassessment research is proposed to continue as a field-oriented approach to
15

setting biocriteria as the basis for relating designated uses to biological condition in streams and

rivers.

Research for this long term goal builds on a longstanding program having already “plucked the

low-hanging fruit.” Much of the remaining work will focus on aquatic populations and

communities and will specifically address multiple stressors. In the case of nutrients, a strategic

decision has been made to focus on coastal and Great Lakes systems with an expectation that the

knowledge gained will address national priorities (hypoxia in coastal systems) that can be

extrapolated across a wide array of geographical systems (e.g., streams, rivers, lakes and

wetlands). In the case of suspended and bedded sediments, this MYP sets near term goals but

defers projection of expected research products pending a state of the science assessment on the

topic and the integration of these results with research being conducted under the Goal 4

Ecological Research MYP.

Research progression over time is envisioned as moving from laboratory and conceptual

approaches of increasing complexity to watershed and regional demonstrations as part of

interactive partnerships with Regions and States. The Logic Flow Diagram of Figure 5 illustrates

the cumulative progress over time for the major stressor categories (habitat alteration, nutrients,

suspended and bedded sediments, pathogens, and toxic chemicals). 

Expected Impact and Outcomes

Currently, the States operate from a mixture of narrative and numerical water quality criteria.

The major causes of impairment (nutrients, pathogens, and suspended and bedded sediments)

often reflect nonattainment of narrative criteria caused in many cases by episodic events and that

will require, over time, numerically-based reductions in loads and monitoring of the outcomes. If

successful, the research outlined for this goal will enable the Agency and States to avoid over-or

under- managing stressors and their related costs. National, regional, and watershed-based

management strategies for stressors discussed in the plan (e.g. nutrients, pathogens, etc.) that are

based on criteria thresholds and quantitative targets will emerge. While ORD has not set targets

for the number and extent of States and other organizations that develop water quality criteria or

standards based on products in Table 2, such statistics will best document the outcomes of this

research. 

Now, consider Long Term Goal 2 in more detail.

Long Term Goal 2. Provide the tools to assess and diagnose the causes and pollutant

sources of impairment in aquatic systems

Summary of Research Questions and Approaches 

P How can multiple and possibly related causes of biological impairment be inferred from

indicator and other observations, and cause-effect modeling ? For habitat alteration? 
16

For nutrients? For suspended and bedded sediments? For pathogens? For toxic

chemicals?

P How can the sources and source strengths of stressors be inferred from in situ

measurements? From stressor measurements? From biological indicators? From

remotely-sensed observations and watershed properties?

P How does one determine the most appropriate and efficient scale for application of 

diagnostic methods within the TMDL and 303(d) process?

Once an impaired water body is listed for restoration, it is rarely the case that the exact causes of

the impairment and the stressor sources are known. Indeed, the NRC report (June 2001) suggests

that the process of listing impaired waters in the first place (the CWA as amended, 303(d) listing

process) may have identified waters that should be further analyzed before TMDL and

restoration actions are required. While such recommendations are policy-related, an important

science issue is clearly raised: what is the most robust and practical approach for identifying

impaired waters for further analysis and actions? Accordingly, ORD has developed a diagnostic

research program having two dimensions. First, ORD is developing approaches and diagnostic

methods that encompass the analysis of watershed, land use, hydrological properties, biological

outcomes, and other features that are most likely to lead to impaired waters. Such methods, when

integrated into probability or other monitoring designs, should specifically enable EPA and the

States to address the NRC recommendation. 

ORD envisions the second dimension as one of diagnostic analysis to solve the “inverse

problem”. That is, given evidence of biological or physicochemical impairment in surface

waters, how does one infer the causes (stressor or suite of stressors) and the sources (e.g., current

or historical discharges, point or nonpoint sources, anthropogenic or natural)? For example, if

the observed benthic invertebrate indicators suggest aquatic impairment, what are the specific

stressors and their related sources? And, given evidence of stressors in surface water, how does

one infer the sources and their magnitudes? For example, if nitrogen levels exceed nutrient

criteria, how does one infer the sources, their magnitudes, and transport pathways leading to the

observed levels? 

An array of data and tools will be investigated as approaches for both dimensions of the problem.

Included among the approaches are water body and ecosystem classification schemes, landscape

characterization, cause-effect modeling and experimental watershed analysis methods including

gradient studies. Table 3 arrays the APG’s and APM’s proposed to meet this goal. Figure 6

shows the linkage and timing of the proposed Annual Performance Goals for this Long Term

Goal. Note, again, that the structure of the APG’s illustrated in Figure 6 implies both the

provision of relevant and necessary science and the application, or demonstration of the science. 

A major, and perhaps overriding, challenge for this entire body of work is to provide robust

methods that can be implemented by watershed managers and State Agencies within the

expected operational constraints of limited data sets and analysis time frames.
17

Priorities include continued development of the science from this plan (e.g., stressor-response

relationships and diagnostic indicators) and from other multi-year plans (e.g., Goal 4 Ecology

Research) to support OW Stressor Identification Guidance. The expectation is that such

guidance will be supported by an ongoing product stream of increasing complexity and

robustness.

Progression over time is envisioned as moving from empirical methods that embed limited

causality to robust and field-capable methods and models that provide robust causality and

unambiguous source identification. ORD also envisions, pending resource availability,

watershed demonstrations as part of interactive partnerships with EPA Regions and States.

Expected Impact and Outcomes

A notable and potentially powerful outcome of research proposed to meet this long term goal is

the prospect of inventing alternative but efficient and economical ways to implement major steps

in the TMDL development process, especially in the listing and assessment phases (e.g., use of

extrapolation techniques such as classification schemes). Because this goal speaks both to the

NRC report on 303(d) listing decisions and to existing and proposed TMDL guidance on

problem and source identification, reasonable expectations for outcomes include efficient,

precise, and robust prescriptions for intervening to restore impaired waters, i.e., we can cure the

patient only when we have diagnosed the illness. 

Now, consider Long Term Goal 3 in more detail.

Long Term Goal 3. Provide the tools to restore and protect impaired aquatic systems and

to forecast the ecological, economic, and human health benefits of alternative approaches

to attain water quality standards 

Summary of Research Questions and Approaches 

P What additions to models are most needed for the TMDL process? For habitat alteration? 

For nutrients? For suspended and bedded sediments? For pathogens? For toxic

chemicals?

P What BMP’s, treatment systems and restoration technologies remain as uncertain options

for watershed management? For mixed land use watersheds? For habitat alteration? For

nutrients? For suspended and bedded sediments? For pathogens? For toxic chemicals?

P How can classification schemes, modeling, scenario analyses, landscape classification,

and economic projections be applied to provide alternatives for meeting water quality

goals efficiently at multiple scales? What are the economic benefits of watershed

management? 
18

ORD envisions an approach for meeting the third long-term goal that also builds on prior work

in both modeling and technology development but that shifts the focus of research from

“pollutant loading and load reduction” to pollution prevention, multimedia modeling, and

restoration approaches for watershed management. Priorities are proposed for “performancebased” technologies, increasing use of and anticipation for market-based risk management

frameworks, and more efficient and cost-effective forecasting and modeling. Another feature of

the proposed research is integration of economic data into watershed planning and

implementation that will lead to a better understanding of both the costs and benefits of

alternative ways to achieve water quality.

Table 4 arrays the APG’s and APM’s proposed to meet this goal. Figure 7 shows the linkage and

timing of the proposed Annual Performance Goals for this Long Term Goal. Note, again, that

the structure of the APG’s illustrated in Figure 7 implies both the provision of relevant and

necessary science and the application, or, demonstration, of the science. 

Priorities include the stressor-specific emphases common to Long Term Goals 1, 2, and 3 for

habitat alteration, nutrients, suspended and bedded sediments, and pathogens, and toxic

chemicals, while working to resolve remaining uncertainties for PBT’s and metals. The proposed

priority sources and watershed types are intended to reflect both the weights illustrated in Figure

4 and in ORD’s understanding of the non-EPA research being conducted by other Federal and

State agencies responding to other constituencies.

The recent TMDL NRC (June 2001) study also specifically challenged the Agency to address

science needs in both the modeling and implementation strategies currently being deployed for

topics under this long term goal. Adaptive management (watershed scale hypothesis-driven

research with feedback monitoring) and increased use of uncertainty analysis in modeling and

decision-making are notable and appropriate challenges. 

Expected Impact and Outcomes

The public rightly holds EPA accountable for the outcome of our collective efforts in research

and operational activities to be measured as improvements in water quality. Simply put, the

expectation is the formulation and implementation of solutions that work, are affordable, and that

are sustainable in social, economic, and ecological terms. This outcome-based expectation

provides the focus for research under this long-term goal.

If successful, the results from this research will enable States and watershed stakeholders to be

more efficient in meeting process requirements (e.g., load allocations, implementation plans,

load reductions, etc.) and, more importantly perhaps, develop linked socioeconomic and water

quality management and policy strategies that lead to sustainable and sustained improvements in

both environmental and economic well being. 
19

Expected outcomes include moving from technology-based to performance-based approaches,

full integration of biological and physicochemical factors, and decision-making that is fully

informed by inherent variability and uncertainties.

Finally, consider the Long Term Goal 4 in more detail.

Long Term Goal 4. Provide the approaches, methods and tools to assess the exposures and

reduce the human health risks from biosolids contaminants for use by OW, States and

others in updating biosolids guidance and regulations

Summary of Research Questions and Approaches 

P Do contaminants in biosolids pose a significant health risk to the public when applied in

compliance with current regulations?

P What additional models, tools and methods are needed to identify, measure and assess

aggregate exposure pathways and risks?

P What improved analytical techniques can be developed to adequately determine pathogen

and priority toxic chemicals in or released from biosolids?

P What is the current state of management practices for biosolids production and

application, and how can those be made more effective? 

ORD envisions a program that addresses key issues identified in the 2002 NRC report:

“Biosolids Applied to Land: Advancing Standards and Practices.” The key finding of that report

was that the scientific basis for protecting human health needs to be updated. The science

questions listed above are key to addressing this finding.

As dictated by the large number of uncertainties associated with the science questions, ORD is

conducting several studies in FY03 and FY04 to better formulate the problem, including

screening level risk assessments and field studies of biosolids composition, management

techniques and releases to the environment. These initial studies will be used to better define

research gaps and will support others in EPA in addressing the NRC findings.

Based on work in FY03 and FY04, ORD plans to identify more specific research that is needed

to address the science questions. This research in FY04 and beyond may address the

improvement of assessment methods and their application, analytical technique development,

and further evaluation and/or development of biosolids management techniques. The biosolids

research APGs and APMs beyond FY04 that are listed at the end of this plan are current ORD

proposals and subject to change (see Table 5 and Figure 8). 

 

Expected Impact and Outcomes

If successful, the results of this research will lead to a reduction of uncertainties about the

impacts on the public near biosolids sites and provide alternatives for reduction of any health

risks posed by biosolids land application. The research can support EPA and others in
20

Table 2. Relative Resource Trends

Among the Long Term Goals

Goal FY03 Base FY10 Base

 % of total % of total 

LTG 1 53 40

LTG 2 16 20

LTG 3 31 40

LTG 4 TBD TBD

determining if there are significant risks associated with current management of biosolids

application. The research also supports decisions on what improved management techniques

might be chosen.

Resource Allocation Among the Long Term Goals

Table 2 illustrates the relative resource allocation among the Plan’s Long Term Goals. This table

was constructed by including all relevant resources including intramural accounting (personnel

and related costs) and extramural accounting (funding for grants, cooperative agreements, and

contracts). 

The proposed resource shifts shown are modest,

project trends to reflect priorities, and are

consistent with the principle embedded in Figure

3. Precise and annual allocation of limited

resources among essential components of the

research will remain difficult and are subject to

Agency priorities and contingencies; the guidance

in the Table should inform the annual processes. 

Summary of the non-EPA research supportive

of the LTG’s

The process illustrated in Figure 1 is EPA and

“State-centric” in that it describes the Agency’s

mandate under the Clean Water Act, as widely,

but not exclusively, implemented by the States. It

also invites interest from multiple groups and institutions, especially those serving 

constituencies with real or perceived liabilities for the action programs implemented by EPA and

the States. Such groups advocate and support research programs in both the public and private

sector. Among Federal natural resource management agencies, research programs are responsive

to Department priorities, which are relevant to, if not overlapping with, ORD research. For

example, the U.S. Department of Agriculture (USDA) has both natural resource management

and Clean Water Act responsibilities (e.g., the U.S. Forest Service’s multiple-use management of

the National Forests). Also, the USDA responds to constituencies (e.g., animal producers and

row-crop commodity groups) who advocate research to enable appropriate and effective

responses to Clean Water Act programs. The U.S. Geological Survey (USGS) and National

Oceanic and Atmospheric Administration (NOAA) are federal agencies charged with providing

data and public information on surface water resources and marine fisheries. These agencies

often view EPA as clients within the federal community and ORD often partners with them to

leverage our respective missions, interests, and resources (e.g., coastal monitoring, surface water

monitoring as part of field research projects, joint solicitations for competitive grants on HAB’s

and algal toxins). While common interests with the non-EPA research community are varied,

and opportunities for meaningful and effective partnerships are acknowledged (and often
21

implemented within Labs and Centers), the scope and intensity of such research has been

implicitly integrated into the content and priorities of this proposed plan. Formal coordination is

provided via standing and ad hoc working groups and committees within the prevailing

Administration research coordinative mechanisms (e.g., the Committee on the Environment and

Natural Resources (CENR) as configured by the White House Office of Science and Technology

Policy). 

A summary of how knowledge of the non-EPA research was factored into the proposed APG’s

and APM’s is summarized below:

‚ ORD’s National Center for Environmental Research (NCER) issues joint solicitations

with NOAA, USDA, the Centers for Disease Control (CDC), and the National Science

Foundation (NSF) on topics related to HAB’s, pathogens in recreational waters, and

CAFO’s

‚ field and laboratory experimental work in pursuit of LTG’s 1-4 are supplemented by

Interagency Agreements with USGS, NOAA, TVA, USDA, and the U.S. Army Corps of

Engineers.

‚ for LTG 3, ORD has set a priority on reducing uncertainties for urban and mixed landuse watersheds, and watersheds in transition from development pressures; completely

forested and agricultural watersheds are largely the domain of USDA

‚ ORD will (and has to date) coordinate if not negotiate with relevant federal research and

funding agencies in order to avoid unnecessary duplication

‚ a limited number of cooperative agreements with research universities are issued as part

of the ORD Laboratory or Center research portfolio across the long term goals 

‚ ORD proposes to integrate research from other Agencies and the academic community as

a means to provide leadership in advice to the OW, Regions, States, and local agencies; a

renewed interest in technology transfer is expected to focus on the long term goals as

well

‚ Due to its long term involvement in biosolids research, ORD has a strong with a strong

understanding of current biosolids research in the Office of Water and outside EPA.

Outside research is being further evaluated by EPA to determine critical research needs.

In addition, ORD is conducting collaborative research with USDA, States and others.

Concluding Notations for Current Resource Base
22

EPA’s mission to protect human health and the environment via the Clean Water Act is among

the most mature and longstanding mandates entrusted to the Agency. Progress over the last thirty

years is notable, even commendable. Much remains to be done; public support is strong, direct

stakeholder interest and participation are growing, and the watershed approach is firmly

established. Our continued progress and success depend on the continued dedication of ORD’s

and the Nation’s researchers to resolve the increasingly complex and interacting factors that

determine both biogeophysical response and human behavior in watersheds. The multi-year plan

described herein is proposed as a framework for achieving the research components required to

achieve measurable and measured improvement in water quality. Desirable, overall outcomes

are as follows:

< impaired waters are accurately and efficiently identified and characterized

< causes and sources of stressors leading to impairments are made readily apparent

< all interested stakeholders will have robust and efficient tools at their disposal to assess

the restoration requirements, evaluate their costs and feasibility, and project their

optimum deployment

< locally developed and implemented systems to regulate or motivate actions are available 

< water quality improvements from action programs are fully documented at reasonable

costs

< water quality is sustained and maintained in a balanced fashion that reflects legislative

mandates, reflects public and stakeholder interests, and that provides ecosystem and

public health services for future generations. 

Unfunded Priorities

The decisions leading to the research described in this plan are intended to be largely strategic

and to reflect the highest priorities with consideration for ORD workforce skills and Office of

Water programmatic priorities. The challenges presented by the long term goals are daunting and

merit a sustained research program. That said, a number of emerging issues and policy-relevant

questions remain under- studied and must be integrated into the resource allocation process.

Accordingly, this section of the Plan identifies a number of research areas and questions that

remain largely unaddressed. As such, this section is intended to describe areas for which

additional funding is needed.

In some cases, this section will also identify alternative priorities beyond those embedded in the

research program that should be carefully weighed as annual budgets are developed. Progress in

some areas should enable a different resource allocation than is now in force and hence these

priorities are also candidates to displace lower priorities within the base program.
23

Issue 1 – economic benefits from water quality programs and rule-making

What are the economic benefits of meeting water quality goals and standards? What is the

cost-effectiveness of the programs and approaches designed to achieve the goals and

standards?

The 305(b) reports and the 303(d) listed waters are evidence that failure to attain water quality

goals and standards is widespread. From the perspective of an economist, it must be true that the

benefits of achieving water quality goals are less than the costs and hence the lack of attainment.

The reasons for this apparent condition are no doubt manifold and complex. Among the reasons

must be the difficulty in assigning monetary benefits to “ecosystem conditions” that are

typically not part of market transactions. Other reasons include uncertainties in the connection

and relationship between management or program variables (e.g., nutrients reduction, BMP’s for

nonpoint source controls, permit conditions for CAFO’s, among many others) and the water

quality condition indicators (e.g., IBI’s, coastal hypoxia, fish abundance and species richness,

among many others). Research is needed on non-market valuation methods, on cost-benefit

methodologies, and on the translation of control/programmatic variables into benefits measures.

This issue is made all the more urgent when one considers the nascent EPA Report on the

Environment, which is expected to serve as the baseline for a sustained public communication of

the EPA’s progress in achieving our mission. 

 

Issue 2 – BMP effectiveness 

What is the effectiveness of Best Management Practices as the conceptual and

programmatic solution to meeting water quality goals? 

BMP’s were invented circa 1974 and have stood as the EPA policy to achieve nonpoint source

pollutant control. Over this time period, the BMP research and implementation communities

have provided an array of BMP’s, design and operational procedures, and models that are

intended to implement EPA policies. The context and “design parameters” for BMP’s have not

changed. 

Since 1974, the measures and indicators of ambient water quality have evolved to accommodate

more complex and biologically-based outcomes. Non-attainment of water quality goals is often 

 attributed to failure to meet these more relevant indicators of ecosystem health. This trend has

resulted in less ability to know or estimate the effectiveness of the BMP policy and the

cumulative investments in that policy. 

Research is needed to develop new approaches to empirically documenting the effectiveness of

BMP’s in meeting biologically-derived water quality goals. New models are urgently needed to

forecast outcomes from BMP’s at different scales. 

Issue 3 – use attainability and adaptive management
24

What additional knowledge is needed to engage in adaptive management of the waters of

the U.S. as an outcome-oriented approach to achieving Clean Water Act goals? 

Water quality standards, when properly constructed and met, ensure that the waters of the U.S.

provide the ecosystem goods and services required to achieve the designated use. The

“designated use” decisions reflect long-standing public expectations and regulatory bodies at the

State and Federal level have been reluctant to call for “use attainability” as a scientific issue. 

Arguably, if the scientific and policy communities respond to the call for “increased use of

adaptive management” as expressed in the NRC study on TMDL’s, then the interaction among

standards, designated uses, and the “attainability” of both must be better understood. 

Research is needed to provide more focus on this use attainability issue so that the scientific

basis for possible policy developments will exist.

Issue 4 – ecological and human health links

What are the scientific links and interactions among ecological and human health

endpoints and benefits vis-a-vis the Clean Water Act? 

 

The reality that the Nation often fails to meet the water quality goals of the Clean Water Act

begs many questions. Arguably, one science issue is the lack of understanding available that

links human health benefits to ecological health and biological integrity and sustainability. That

said, it is very clear that much of the early success in water pollution control came from actions

driven by public health goals, particularly reduction in water-bourne diseases.

There is a need to re-visit this vital link between water quality to protect ecosystems and public

health and well-being. 
25

TABLE 3

LONG TERM GOAL 1: Provide the approaches and methods to develop and apply criteria for

habitat alteration, nutrients, suspended and bedded sediments, pathogens and toxic chemicals

that will support designated uses for aquatic ecosystems

ANNUAL PERFORMANCE GOALS AND MEASURES YEAR LAB/

CENTER

HABITAT ALTERATION

APG 8 (GPRA) - Provide demonstration stressor-response

relationships and/or models linking loss and alteration of

habitat to selected fish, shellfish, and wildlife endpoints.

2006 ORD

APM Report on Penaeid shrimp dependence on seagrass habitat 2003 NHEERL

APM Report on finfish dependence on seagrass and oyster reef

habitats

2003 NHEERL

APM Prototype watershed-stream network model for Pacific

Salmon

2004 NHEERL

APM Report characterizing relationships between multiple

habitat types and economically valuable fish at the scale

of an estuarine shoreline

2004 NHEERL

APM Report characterizing the relationship between habitat in

stream networks and salmon-native fish for coastal

Oregon watersheds

2005 NHEERL

APM Report characterizing the relationship between alteration

of vegetated habitats and nekton use of those habitats

2006 NHEERL

APM

58

GPRA

Report characterizing relationships between abundance,

quality, and arrangement of various habitat types and

selected biotic assessment endpoints in coastal systems

2006 NHEERL

APG - Provide stressor-response relationships and/or models

linking loss and alteration of habitat to selected fish, shellfish,

and wildlife endpoints

2006 ORD

APM Report on habitat suitability indices to support population

models for projecting relative risks of multiple stressors

including toxic chemicals and habitat alteration to

common loons 

2004 NHEERL
26

APM Report on indices of watershed integrity based on land

use/land cover and relationships to fish (e.g., salmon,

pike, and/or others)

2005 NHEERL

APM Reports characterizing the relationship between

landscape-scale habitat mosaics and native fish by

wetland type in the Great Lakes

2005 NHEERL

APM Final report characterizing relationships between

abundance, quality, and arrangement of various habitat

types and selected biotic assessment endpoints in coastal

systems 

2006 NHEERL

APG - Provide suites of habitat alteration - biological response

relationships and generalization/extrapolation schemes suitable

for developing broad-scale habitat criteria for streams and

coastal systems, and provide approaches for evaluating

combined effects of habitat alteration and other stressors

2008 ORD

APM Report on the ecological consequences of marine derived

nutrients and nutrient enrichment for aquatic biota and

stream habitat quality, with an emphasis on salmon and

native fish

2004 NHEERL

APM Initial report on food web-mediated vs. habitat-based

alteration of fish communities from field studies across a

representative group of Great Lakes coastal wetlands

2006 NHEERL

APM Report on estimating the feasibility of restoring currently

at-risk wild salmon habitat through use of replacing lost

marine derived nutrients and the likely ecological side

effects of such additions

2006 NHEERL

APM Regional models of landscape influence of salmon/native

fish in the Pacific Northwest and native fish in Great Lake

coastal wetlands

2007 NHEERL

APM Empirical and model-based evaluation of effectiveness of

habitat and nutrient criteria as protective of the health of

aquatic life in Great Lakes coastal wetlands

2008 NHEERL

APM Report on the interactions between stream nutrients and

habitat alteration on water quality and aquatic life 

2008 NHEERL

APM Synthesized quantitative species-habitat relationships

suitable for developing regional habitat-based biocriteria

for shorelines, lakes, and estuaries

2008 NHEERL
27

NUTRIENTS

APG 15 GPRA) - Complete the framework for including

dissolved oxygen and other receiving water thresholds into

watershed management for nutrients

2003 ORD

APM

201

GPRA

Report on the effects of nutrient enrichment on coastal

phytoplankton communities 

2003 NHEERL

APM Propose classification scheme for predicting sensitivity of

coastal receiving waters to effects of nutrients on DO

2003 NHEERL

APM Provide minimum dissolved oxygen requirements for a

suite of the important marine organisms in the Atlantic,

Pacific, and Gulf of Mexico coastal waters of the U.S. 

2003 NHEERL

APG - Provide the scientific foundation for establishing sitespecific nutrient threshold criteria to protect estuarine SAVs

and freshwater organisms 

2007

ORD

APM Report on the correlation of water quality with SAV

change

2003 NHEERL

APM Report on environmental requirements of three main

species of seagrasses

2004 NHEERL

APM Development of stress-response model for Zostera

marina in Pacific Northwest and validation of stressresponse model for Thalassia testudinum.

2004 NHEERL

APM Development of empirical load-response models for

Zostera marina in NE U.S.

2004 NHEERL

APM Report on a spatial approach to assessing nutrients and

nutrient criteria at landscape and watershed scales

2005 NCEA

APM Report on an approach to refining regional nutrient

criteria on the basis of adverse effects to faunal

assemblages.

2005 NCEA

APM Development of load-response models for estuaries of

Pacific Northwest and Gulf Coast, and validation of

stress-response model for Zostera marina in NE U.S.

2005 NHEERL

APM Propose classification scheme for predicting sensitivity of

coastal receiving waters to the effects of nutrients on

SAV

2005 NHEERL
28

APM Report on the empirical and numeric models for SAV 2006 NHEERL

APM Report on a classification scheme for grouping coastal

receiving waters based on sensitivity to nutrients

2007 NHEERL

APG - Provide scientific foundation for development and

application of quantitative measures of food web attributes that

are sensitive to ecological changes associated with nutrient

enrichment

2007 ORD

APM Report on the sensitivity of food web responses to

nutrient loading in coastal systems

2004 NHEERL

APM Propose classification scheme for coastal receiving waters

based on food web sensitivity to nutrients

2005 NHEERL

APM Report on coastal wetlands of the Great Lakes:

Discrimination of trends in food web response as a

function of nutrient loading and ecosystem classification

factors

2005 NHEERL

APM Report on empirical and numeric models for food webs 2006 NHEERL

APM Report on the parameterization of food web models 2007 NHEERL

APM Report on classification scheme for grouping coastal or

lake receiving waters based on sensitivity to food web

alterations

2007 NHEERL

APM Final report on Great Lake coastal wetlands to define

food web-nutrient response thresholds

2007 NHEERL

APG - Provide the scientific foundation and information for the

development of a water quality model of the Gulf of Mexico

hypoxic zone

2008 ORD

APM Field cruise report for 2002-2004 for hypoxia surveys in

the Gulf of Mexico

2005 NHEERL

APM Report on the conditions and seasonal trends of water

quality in the Gulf of Mexico hypoxic zone

2006 NHEERL

APM Report on the database of environmental information

necessary to develop the water quality model of the Gulf

of Mexico hypoxic zone

2007 NHEERL
29

BIOCRITERIA/BIOASSESSMENT

APG - Demonstrate bioassessment methods to establish

biocriteria for a range of designated uses in freshwater systems

within Eastern US rivers 

2004 ORD

APM Report on newly developed and review of existing

biocriteria and bioassessment tools for rivers and streams

in MidAtlantic 

2004 NERL

EERD

APM Report on newly developed and review of existing

bioassessment tools and biocriteria for New England

2004 NERL

EERD

APM Statistical/analytical guidance, including case studies, to

help states choose scientifically sound methods for setting

biocriteria in the eastern U.S.

2004 NERL

EERD

APG - Demonstrate bioassessment methods to establish

biocriteria for a range of designated uses in freshwater systems

within Mid-Western U.S. rivers 

2006 ORD

APM Report comparing differences among invertebrate data

collected using EMAP, NAWQA and OEPA methods in

large rivers 

2003 NERL

EERD

APM Report on the association among invertebrates and habitat

indicators for large rivers in the midwest 

2004 NERL

EERD

APM Report on prototype indicators of condition for deep river

fish assemblages

2004 NERL

EERD

APM Guidance Document on the Bioassessment of Large

Rivers: Concepts, Approaches and Theory

2005 NERL

EERD

APM Report on the field and laboratory performance

characteristics of a new sampling method for riverine

macroinvertebrate assemblages

2005 NERL

EERD

APM Report on the comparison of random site selection and

systematic site selection for assessment of 305(b)

reporting segments of the Ohio River 

2006 NERL

EERD

NEW

APM

Report that compares aquatic life criteria , direct bioassay

results and bioassessments of macroinvertebrates or fish

assemblages; to examine the protectiveness of chemical

criteria in streams and estuaries

2006 NCEA
30

PATHOGENS/INDICATORS OF FECAL CONTAMINATION

APG Provide a rapid means of measuring recreational water

quality and an assessment of the health risks associated with

swimming in waters of varying quality

2007 ORD

APM Report on faster, simpler indicator method for fecal

contamination

2003 NERL

MCEARD

APM Produce a report on the pilot studies and preliminary

statistical analyses used to evaluate the beaches

epidemiological data

2003 NHEERL/

NERL

APM Report on the evaluation of water quality indicators and

health outcomes for beaches evaluated in FY03

2004 NHEERL/

NERL

APM Report on determination of exposure characteristics(e.g.,

activity patterns, ingestion rates) for recreational users 2004

NERL

MCEARD

APM Report on fecal indicator monitoring protocols for

different types of recreational waters 

2004 NERL

MCEARD

APM An evaluation of alternative indicators of recreational

water safety for tropical regions

2004 NCER

APM An evaluation of the risk posed by exposure to pathogens

in the swash zones (sand/water interface regions) of

recreational beaches

2004 NCER

APM Report on the evaluation of water quality indicators and

health outcomes for beaches evaluated in FY04

2005 NHEERL/

NERL

APM Report on the evaluation of water quality indicators and

health outcomes for beaches evaluated in FY05

2006 NHEERL/

NERL

APM Deliver a rapid method (less than 2 hours to results) for

monitoring beach water quality that provides the best

relationship to the frequency of swimming-associated

illness

2007 NERL/

NHEERL

APM Report describing swimming associated illness and the

quality of water measured using a rapid indicator method

2007 NHEERL/

NERL

TOXIC CHEMICALS

APG - Provide a summary of the available methods to set riskbased water and sediment quality criteria for toxic chemicals

 2003 ORD
31

APM Describe a framework for water quality criteria for

nonbioaccumulative chemicals based on risks to aquatic

organisms

2003 NHEERL

APG - Provide methods for extrapolating chemical toxicity data

across exposure conditions and across endpoints, life stages, and

species which can support assessment of risks to aquatic life and

aquatic-dependent wildlife for chemicals with limited data

2006 ORD

APM Acute-to-chronic estimation (ACE) user guide and

software

2003 NHEERL

APM PBTK/TD model for predicting individual effects on birds

from chronic mercury exposure to facilitate cross-species

extrapolation of toxicity responses

2005 NHEERL

APM Report on evaluating importance of dietary route of

exposures to aquatic risk assessments for metals

2006 NHEERL

APG - Provide approaches for evaluating the relative and

cumulative risks from toxic chemicals, with respect to risks

from nonchemical stressors, on populations of aquatic life and

aquatic-dependent wildlife at various spatial scales

2008 ORD

APM Report regarding assessment of risks to aquatic organisms

from combined exposure to polycyclic aromatic

hydrocarbon mixtures and ultraviolet radiation in natural

systems

2005 NHEERL

APM Benthic Macroinvertebrate indicators of pesticides in

stream water and sediment

2006 NERL

EERD

APM Develop and test an approach for assessing risks of

multiple stressors to wildlife populations in spatiallydiverse landscapes

2008 NHEERL

MULTIPLE STRESSORS

APG 111 (GPRA) - Provide methods for characterizing

population-level risks of multiple stressors to aquatic life and

aquatic-dependent wildlife for use in developing improved

criteria to protect water quality

2005 ORD

APM Two final reports (and a database) comparing and

analyzing the quantitative dose-response relationship

form recently published studies of aquatic and aquaticassociated wildlife

2003 NCEA
32

APM

59

GPRA

Develop and test simple population models that project

the relative risks of multiple stressors (toxics, habitat

alterations) to piscivorous birds

2004 NHEERL

APM Methods for characterizing the exposure and response of

sensitive ecosystems components to pesticides or nutrient

stress using biomonitors and stable isotope ratios of

nitrogen

2005 NCEA

OTHER STRESSORS

APG Data and analysis are made available to help OW

characterize the potential risk of PPCPs to impair waterbodies

and evaluate the need for human health and ecological criteria

(i.e., MCLs and AWQC)

2006 ORD

APM Toward a green pharmacy - Cradle to cradle stewardship

of drugs for minimizing their environmental disposition

while promoting human health

2004 NERL

APM

281 

Concentration, detection and measurement of four

widely-prescribed pharmaceuticals at three municipal

wastewater treatment plants using POCIS and LC/MS. 

2005 NERL

APM

282 

Levels of synthetic musks in municipal wastewater for

estimating biota exposure in receiving waters

2005 NERL

APM

283 

Closed-loop stripping of synthetic musk compounds from

fish tissues and analysis by GC/MS/SIM. 

2005 NERL

APM "Virtual” Symposium: State of the Science — PPCPs as

Environmental Pollutants

2005 NERL

APM Review of Environmental forensic techniques (e.g., high

resolution MS and ICE software) over the last decade. 

Review article.

2005 NERL

APM Sensitive Hemoglobin Adduct Methodology Applied to

the Terminal Valine Proteins in Carp as an Indicator of

Environmental Exposure. Journal article. 

2005 NERL

APM Applications of Advanced Mass Spectrometric

Techniques to Defining Environmental Exposures.

Internal report. 

2006 NERL
33

APM Improved detection methods for, and occurrence levels of,

pharmaceuticals and personal care products in effluents,

surface waters, treated drinking water and groundwaters

[Brownawell, Graham, Weinberg, Roberts]

2006 NCER

APM An evaluation of how effective wastewater treatment

practices are at decreasing levels of pharmaceuticals and

antiseptics in drinking water [Brownawell Graham,

Roberts] 

2006 NCER

APM An evaluation of conferred antibiotic resistance in

microbial communities resulting from pharmaceuticals

and personal care products in the water [Weinberg,

Graham]

2006 NCER

APM An evaluation of the influence of amphiphiles on the fate

and transport of pharmaceuticals in the environment. 

[Kibbey]

2006 NCER

APM An evaluation of the ecotoxicity of seclective serotonin

reuptake inhibitors (SSRIs) in wasteaters, effluents, &

surface waters & the ecotixicity of fluoroquinolone

antibiotics via lab- & field-scale systems [Armbrust,

Graham]

2006 NCER
34

TABLE 4

 

LONG TERM GOAL 2: Provide the tools to assess and diagnose sources and causes of

impairment in aquatic systems.

ANNUAL PERFORMANCE GOALS AND MEASURES YEAR LAB/

CENTER

APG 16 (GPRA) - Provide the scientific foundation and

information management scheme for the 303(d) listing process

including a classification framework for surface waters,

watersheds, and regions to guide problem formulation 

2003 ORD

APM

202

GPR

A

Classification frameworks for geographic regions and at the

watershed, water body and habitat scale 

2003 NHEERL

APG - Provide first generation diagnostic methods, including

stressor identification (SI) methods, for causal linkage of

observed major classes of single stressors and biological

indicators to stressors in freshwater and marine systems; scale

the methods to States and watershed organizations

2005 ORD

APM Develop molecular diagnostic techniques to identify

Pfiesteria complex organisms and better delineate their

distribution. And identify, purify, and chemically

characterize their toxins (R82-6791; R82-7084; & R82-

6655)

2003 NCER

APM Develop a method for cryopreserving strains of Pfiesteria

complex organisms and establish over 50 culture isolates to

be available to the scientific community (R82-6793)

2003 NCER

APM Model of the biophysical interactions Gymnodinium breve

red tides with its chemical and physical habitat and

determine the production, occurrence, fate and effects of

brevetoxins in the environment during and after blooms. 

(82-6792 & 82-7085)

2003 NCER

APM Guidance on whole sediment Toxicity Identification

Evaluation (TIE) procedures

2003 NHEERL
35

APM Publication of the newly identified mechanisms of lesion

initiation and the contributory environmental and

biological conditions required for lesion development &

progression in fish following exposure to PCO (Pfiesteria

complex organisms) (R82-8224 & Shields)

2004 NCER

APM Landscape Atlas for pesticides, nutrients and sediments for

streams in the Mid-Atlantic coastal plain

2004 NERL

ESD

APM Application of coastal watershed and estuarine/lacustuary

classification schemes to predict probability of impairment

based on Great Lakes and Gulf of Mexico regional case

studies

2005 NHEERL

APM Guidance on and user-friendly interfaces for derivation of

diagnostic indicators for individual stressors

2005 NHEERL

Equip EPA Regions, States and Tribes with knowledge, skills

and tools to determine the causes of impairments for freshwater

and coastal systems required in various regulations

2008 ORD

APM Case study implementation plans for multivariate

approaches to community data analysis to apportion cause

among stressors in coastal ecosystems

2003 NHEERL

APM Case study demonstrating the Stressor Identification

Process that identifies the causes of biological impairment

in the nation’s waterbodies

2003 NERL/

NCEA

APM Evaluate the efficacy of AFLP technology as a fast and

reproducible molecular tool to discriminate among species

of enterococci

2004 NERL

APM Report on methods/indicators for determining when

biological impairments of rivers and streams are due to

sediment loads

2004 NERL

EERD/

NCEA

APM Report on potential of swine CAFOs to contribute

pathogens, EDCs and other contaminants of concern to

ground water (Also included in LTG 3 2007 APG on

CAFOs)

2004 NRMRL

GWERD

APM Determine the nature and concentration of aquatic stressors

released from animal agriculture operations in the form of

aerosols (Also included in LTG 3 2007 APG on CAFOs)

2005 NRMRL

LRPCD
36

APM Application and evaluation of molecular methods (AFLP

and others) to discriminate between human and non-human

sources of fecal indicator bacteria

2005 NERL

APM Report on methods/indicators for determining when

biological impairments of rivers and streams are due to

toxics

2005 NERL

EERD/

NCEA

APM Training and problem solving workshop: determining the

causes of biological impairment, the scientific basis, tools

and applications applied to state-listed 303(d) streams

2005 NERL/

NCEA

APM Produce landcover/landuse digital database for watersheds

in southwest US

2005 NERL

ESD

APM Make landcover/landuse digital database for watersheds in

southwest US publically available thru website 

2006 NERL

ESD

APM Produce landscape atlas for pesticides and nutrients in

Midwest streams

2006 NERL

ESD

APM Implementation plans for extension of case studies from

coastal ecosystems into their watersheds

2006 NHEERL

APM Report on the importance of subsurface transport in the

release of nutrients, pathogens, and antibiotics into the

watershed (Also included in LTG 3 2007 APG on CAFOs)

2006 NRMRL

GWERD

APM Case study determining the causes of biological impairment

in an urban setting with non-point source impacts so that

states and tribes will have prototypes to facilitate

completion of TMDL’s.

2006 NERL/

NCEA

APM Watershed Academy website training for causal analysis 2006 NERL/

NCEA

APM Publication of an in situ method for determining growth

rates of natural populations of Karenia brevis (formerly G.

breve), utilizing radiolabeling of the biomarker pigment

gyroxanthin (R82-9369)

2006 NCER

APM Publication of a behavioral model for G. breve based on a

characterization of the chemotaxis of the organism obtained

by using G. breve Population Mimics (GBPMs) as

Lagrangian drifters (R82-9370)

2006 NCER

APM Publication presenting the influence of grazing pressure and

viral activity on the dynamics of blooms caused by harmful

dinoflagellates and algae (R82-9366 & R82-9367)

2006 NCER
37

APM Publication of an evaluation of 38-year Narragansett Bay

Time Series (NBTS) data to discern long-term patterns and

variability in blooms of representative HAB species due to

the effects of meteorological, climatic, physical, chemical

and biological parameters (R82-9368)

2006 NCER

APM Publication presenting a suite of microsatellite markers for

use as tools to link diversity and structure of isolates of K.

brevis with the physiological and ecological bases of bloom

formation (R830413)

2007 NCER

APM Publication of an assay to identify a nitrogen-regulated

enzyme in Alexandrium for use as a new tool for

identifying and monitoring nitrogen nutrition in field

populations of harmful algae (R83-0415)

2007 NCER

APM Publication of an evaluation of the physiology and ecology

of macroalgae to identify different combinations of factors

that lead to bloom formation and the potential for

herbivores to control these blooms (R83-0414) 

2007 NCER

APM Simulation of key stressor interactions with generic

ecosystem models using sensitivity analysis to define the

range of stressors and stressor combinations under which

nonadditive interactive effects will occur

2007 NHEERL

APM Evaluate the DNA-based technology in impaired

watersheds impacted by fecal contamination from diverse

sources under a range of temporal (different flow dynamics,

after strong rain episodes)and spatial (distance from the

source, water vs. sediment)variability 

2007 NERL

APM Produce landscape atlas for pesticides and nutrients in

California streams

2007 NERL

ESD

APM Collection of case studies determining the causes of

biological impairment, the scientific basis, tools and

applications toward improving stream quality.

2007 NERL/

NCEA

APM Report on methods/indicators for diagnosing when

biological impairments of rivers and streams are due to

stressors associated with habitat alteration

2007 NCEA/

NERL

APM Case study focusing on the special needs to perform causal

analysis in biologically impaired large rivers.

2008 NERL/

NCEA
38

TABLE 5

LONG TERM GOAL 3: Provide the tools to restore and protect aquatic systems and to forecast

the ecological, economic, and human health outcomes of alternative solutions

ANNUAL GOALS AND PERFORMANCE MEASURES YEAR LAB/

CENTER

APG Provide updated models for stormwater management, and for

allocating suspended solids and sediment loads, and related

uncertainties for mixed land use watersheds.

2003 ORD

APM Report on GSTARS predictive model for sediment transport

for use in TMDL watershed assessments for protecting aquatic

ecosystems from siltation

2003 NERL

ERD

APM

172

Provide States and watershed managers a document on

managing pathogen contamination in the urban watersheds

with information on health effects, detection methods and best

management practices to meet TMDL requirements

2003 NRMRL

WSWRD

APM 

173

Update Storm Water Management Model (SWMM) for use by

states, utilities and consulting firms in allocating pollutants in

urban watersheds to meet TMDL requirements

2003 NRMRL

WSWRD 

APM Develop and verify a numerical model for sediment oxygen

demand exerted by organic material in the sediments and

nitrogen and methane production under aerobic and anaerobic

conditions at the sediment-water interface

2003 NRMRL

LRPCD

APG Provide indicators, monitoring strategies, and guidance for

determining the effectiveness of Best Management Practices

(BMP's) in meeting water quality goals.

2004 ORD

APM

144

Develop a strategy to evaluate BMP performance via

molecular based methods in watersheds impaired by fecal

contamination

2004 NRMRL

WSWRD/

LRPCD

APM Provide guidance on indicator selection and monitoring

strategies for evaluating effectiveness of BMPs

2004 NRMRL

WSWRD

APM

142

Report to the states, regions and program offices on methods

to evaluate wet pond design effectiveness to control sediments

and nutrients

2004 NRMRL

WSWRD

APM Develop an innovative BMP filter fence for sediment control

to address inefficiencies with current practices at construction

sites

2004 NRMRL

WSWRD
39

APM

148

Report on microbial source tracking and its utilization to

identify sources and measure the effectiveness of mitigation

measures in waters impaired due to microbiological

contamination

2004 NRMRL

WSWRD

APM Report on BMP performance data for controlling nutrients,

suspended solids and sediments, and flow variations within 

urban watersheds and identifying information/research gaps

2004 NRMRL

WSWRD

APG Complete at least three (3) demonstrations of updated models

for stormwater management, suspended solids, sediment, and

nutrients to meet water quality objectives.

2005 ORD

APM

137

Decision support tool for a lake/reservoir based on system

assimilative capacity

Linkage to Goal 4 Ecological Research

2004 NRMRL

GWERD

APM

 175

Prepare a document for use by states to assist in modeling risk

management options and restoration measures in water bodies

impaired due to suspended solids and sediment 

2004 NRMRL

LRPCD

APM New sediment modeling protocol for instream processes 2004 NERL

ERD

APM Report demonstrating the effectiveness of applying stormwater

structural BMPs as a tool to address sediment TMDL’s

2005 NRMRL

WSWRD

APM Report to states, regions, and program offices demonstrating

the use of time series analysis to identify non-point source

impacts

2005 NRMRL

LRPCD

APM Report to states and program offices on the performance of 

models (risk management options and restoration measures) to

meet water quality objectives for nutrients and sediments 

2005 NRMRL

LRPCD

APM Report on the application of the updated Storm Water

Management Model (SWMM) to predict drainage from

alternative systems as a tool to assist in meeting TMDL

requirements

2005 NRMRL

WSWRD 

APM Technical outreach for new spatial grids of storm erosive

power (R-factor and EI-30) for use in innovative landscape

indicator development and the Revised Universal Soil Loss

Equation 

2005 NERL

ESD

APM Report describing processes controlling oxidation state in

subsurface environments and related controls on nitrogen fate 

2005 NERL

ERD
40

APM Report describing factors and processes controlling the fate of

nutrients in streams 

2005 NERL

ERD

APM Documentation of linked TMDL modeling system for

nutrients

2005 NERL

ERD

APG Provide at least six (6) reports of performance data and

information for controlling nutrients, suspended solids, sediments,

pathogens, toxic chemicals (metals and PBTs), and flow variations

urban and rural watersheds. 

2006 ORD

APM Determine effectiveness of field application of clays to

mitigate HABs NCER & NHEERL (CR-82-7091)

2003 NCER

APM

(EDC177)

Report on the stressor reduction (pathogen, EDC, antibiotic,

and airborne nitrogen, particulate and pathogens) achievable

using existing manure management practices at CAFOs

 2004 NRMRL

LRPCD

APM Provide a method to identify areas within mixed-use

watersheds most susceptible to channel instability and erosion

as a tool to drive restoration prioritization for waterbodies

impaired due to suspended solids and sediments

2004 NRMRL

WSWRD

APM

146

Guidance document on Best Management Practices (BMP) 

for sewer solids management

2004 NRMRL

WSWRD

APM Report on BMP performance (including effectiveness/cost of

constructed wetlands) for controlling nutrients, suspended

solids and sediments, within mixed land-use watersheds

2006 NRMRL

LRPCD

APM Report on placement of BMP’s in urban watersheds to meet

water quality goals

2006 NRMRL

WSWRD

APM Evaluation of the effectiveness of watershed management for

suspended solids and sediments in controlling excess turbidity

and the resulting biotic degradation in receiving waters

2006 NRMRL

LRPCD

APG – Provide State of the Science Synthesis and Application

Approaches for Managing Risks from CAFO’s

2007 ORD

APM Report on potential of swine CAFOs to contribute pathogens,

EDCs and other contaminants of concern to ground water

(Also included in LTG 2 2008 APG)

2004 NRMRL

GWERD

APM Determine the nature and concentration of aquatic stressors

released from animal agriculture operations in the form of

aerosols (Also included in LTG 2 2008 APG)

2005 NRMRL

LRPCD
41

APM Report on the importance of subsurface transport in the release

of nutrients, pathogens and antibiotics into the watershed (Also

included in LTG 2 2008 APG)

2006 NRMRL

GWERD

APM Report on CAFO pollution prevention opportunities and a

framework for successful implementation

2006 NRMRL

STD

APM Report on lifecycle assessment/sustainability evaluations of

CAFOs including thresholds at which animal density begins to

impair watersheds

2006 NRMRL

STD 

APM Capstone report on the use of natural and constructed wetlands

for the management of environmental stressors

 2007 NRMRL

LRPCD

APM Capstone report on methods to reduce environmental risk from

synthetic and natural hormones, pathogens and nutrients from

CAFO manure management practices

2007 NRMRL 

LRPCD

APG Provide at least seven (7) key reports. updated models, and

data bases for allocating and managing suspended solids, sediment,

pathogen, nutrients, and toxic chemical (metals and PBTs) loads

among all sources in mixed land-use watersheds.

2007 ORD

APM TMDL database for sediments, nutrients, & organic carbon in

the South Fork Broad River

2003 NERL

ERD

APM Database on pathogen indicators in the South Fork Broad

River

2004 NERL

ERD

APM Visual Beach Model adapted to coastal, riverine, and lake

systems

2005 NERL

APM Report to states and program offices on the performance of 

models (risk management options and restoration measures) to

meet water quality objectives for nutrients, sediments,

pathogens and toxic chemicals

2007 NRMRL

LRPCD

APM Report on the field validation of the updated Stormwater

Management Model to predict pollutant loadings to meet

TMDL requirements

2007 NRMRL

WSWRD 

APM Report on a state-of-the-science meeting on progress made in

the restoration of water bodies impaired by key stressors

2007 NRMRL

LRPCD
42

APM Report that outlines improvements made to existing models to

predict reductions of key stressors (nutrients, pathogens, toxics

and clean sediments) in water bodies and improvement in

biological integrity in mixed land-use watersheds and identify 

research gaps

2007 NRMRL

LRPCD

APG Demonstrate the application of innovative wet weather flow

technologies in urban watersheds regulated under the National

CSO Control Policy and SSO Programs

2007 ORD

APM Report demonstrating a Real Time Control system to

maximize storage of wet weather flows in an urban sewer

system to minimize CSOs/SSOs and meet the National CSO

Policy

2005 NRMRL

WSWRD

APM Report on using/demonstrating CSO pollution control

methods/concepts for urban stormwater pollution control

2005 NRMRL

WSWRD

APM Report on emerging engineering practices applying CSO

pollution control methods/concepts for SSO pollution control

2005 NRMRL

WSWRD

APM Report on computer tools for predicting rainfall dependent

infiltration/inflow in sanitary sewer systems and SWMM

EXTRAN modeling analysis for SSO control planning

2006 NRMRL

WSWRD

APM Report on emerging engineering practices for the application

of urban stormwater management techniques for CSO

pollution control

2006 NRMRL

WSWRD

APM Report demonstrating a vacuum flushing system to remove

sediments in an urban combined sewerage system

2007 NRMRL

WSWRD

APM Develop a manual on new sewer design methodology for

preventing sewer solids deposition during dry-weather lowflow periods in combined and sanitary sewerage systems

2007 NRMRL

WSWRD

APG Demonstrate the application of models, landscape

characterization methods, and economic analyses to formulate

alternative approaches for protecting and restoring water quality

and critical habitats and to forecast the ecological, economic, and

human health outcomes of the alternatives

2008 ORD

APM Report on selected methods for integrating ecological risk

assessment and economics to support watershed decision

making

2003 NCEA
43

APM GIS and landscape models to evaluate effectiveness of BMPs

(case studies)

2006 NERL

ESD

APM Final methods for integrating ecological risk assessment and

economics to support water body uses, water quality

standards, and TMDL’s 

2007 NCEA

APM Economic analysis of changes to human and ecological risk 

due to specific management alternatives

2008 NCEA

APM Produce landscape indicator “tool box” to forecast impacts

from pesticide use strategies

2008 NERL

ESD

APM Provide to the regions a framework for evaluating whether a

TMDL restoration will be effective to restore water quality in

the urban watershed.

2008 NERL/

NRMRL

WSWRD

APG Demonstrate proof-of-concept integrated assessments for

allocation of restoration resources to support water quality

standards attainment within the context of relevant socioeconomic

factors and ecological integrity.

2010

ORD

APM Develop and deliver a methodology for economic evaluation of

West Virginia watershed ecological restoration including

market and non-market costs and benefits

Linkage to Goal 5 Pollution Prevention and New Technologies

MYP

2005 NRMRL

STD

APM Ecological evaluation of West Virginia watershed restoration as

a basis for environmental decision making

2005 NHEERL

APM Evaluation of watershed-based classification and assessment

for State of West Virginia as a framework for watershed

restoration decisions

2005 NHEERL

APM Report on the use of ecological and economic evaluation as a

basis for environmental decision making in West Virginia

watershed ecological restoration.

2008 NHEERL

Lead

NRMRL,

Support

STD

APM Report on the demonstration of ecological analysis/cost-benefit

analysis as an approach to make more integrated resource

management decisions in watershed ecological restoration in

West Virginia to meet water quality standards

2010 NHEERL,

Lead

NRMRL,

Support

STD
44

TABLE 5

LONG TERM GOAL 4: Provide the approaches, methods and tools to assess the exposures and

reduce the human health risks from biosolids contaminants for use by OW, States and others in

updating biosolids guidance and regulations.

ANNUAL GOALS AND PERFORMANCE MEASURES YEAR LAB/

CENTER

APG Provide the EPA Program Offices, EPA Regions, States,

utilities and others with improved tools for characterizing

pathogens in biosolids

2004 ORD

APM Development and validation of methods for enumeration of

fecal coliforms in biosolids to develop a draft EPA Method

1680 entitled “Fecal Coliforms in Biosolids by Multiple-Tube

Fermentation Procedures”

2004 NRMRL

APM Development and validation of methods for enumeration of

salmonellae in biosolids to develop a draft EPA Method 1682

entitled “Salmonella in Biosolids by Enrichment, Selection and

Biochemical Characterization”

2004 NRMRL

APG Provide the EPA Program Offices, EPA Regions, States and

others with study findings that improve the understanding

of the effectiveness of current biosolids practices and of the

significance of human health risks to support decisions on

biosolids management and research

2005 ORD

APM

147

Report on the evaluation of contaminant concentrations and on

the reduction of biosolids contaminants achieved by current

biosolids management practices at field application sites

2005 NRMRL

APM Risk Assessment Analysis Plan that defines needs for biosolids

research to support NRC recommendations and 503(b) listings

2005 NCEA

APG Provide the EPA Program Offices, EPA Regions, States and

others with improved data, tools, and methods for the

analysis of risks, and for selection of more effective

management options

2007 ORD

APM Methods for selected pharmaceutical and personal care

products (PPCPs) (e.g., antibiotics and musks) adapted for solid

materials

2005 NERL
45

APM Reports on case studies of up to 7 biosolids production and/or

application sites providing data on contaminant occurrence,

treatment and application process cost-effectiveness and

contaminant transport and fate for selected biosolids

contaminants

2006 NRMRL 

APM An optimized method for measuring enteric viruses in biosolids 2006 NERL

APM Improved risk assessment methodologies and assessment of

key contaminants for land application of biosolids in support of

503 listings

2006 NCEA

APM Improved pathogens risk assessment methodologies for

regulatory decisions

2007 NCEA

APM An optimized method for measuring helminth ova in biosolids 2007 NERL

APM Report on small pilot survey to identify pharmaceutical and

personal care products (PPCPs) in biosolids

2007 NERL
Complete the framework

for including dissolved

oxygen and other

receiving water

thresholds into

watershed management

for nutrients

Extrapolate chemical toxicity across

exposure conditions, endpoints,

lifestages, and species for aquatic lifeand wildlife for chemicals with limited

data

Water quality criteria for

population-level risks of

multiple stressors to

aquatic life and aquaticdependent wildlife

Site-specific nutrient

threshold criteria to protect

estuarine SAVs and

freshwater organisms

Link loss and alteration of habitat

to fish, shellfish, and wildlife

endpoints. Application of food web attributes sensitive to

ecological changes

associated with nutrient

enrichment

FY03 FY04 FY05 FY06 FY07 F

LONG TERM GOAL 1. Provide the approaches and methods to develop and apply criteria for habitat alteration,nutrients, suspended and bedded sediments, pathogens and toxic chemicals that will support designated uses

for aquatic ecosystems

Provide a summary ofthe available methods

to set risk-based water

and sediment quality

criteria for toxic

chemicals

Biocriteria for

designated uses in

Eastern rivers

Biocriteria for designated uses in

Mid-Western Rivers

Risk of PPCPs to impair

waterbodies and need for

human health and ecological

criteria

Provide a rapid means of

measuring recreational waterquality and an assessment of

the health risks associatedwith swmming in waters of

varying quality

Provide t

foundation an

the develop

quality mod

Mexico h

Habitat alte

respons

suitable for criteria for s

systems, a

evaluating c

habitat alt

s

Relative an

from tox

nonchem

populations 

aquatic-de

various 

Relationships

and/or models

linking loss and

alteration of

habitat to

selected fish,shellfish, and

wildlife

endpoints.

Figure 5. Long Term Goal 1
Provide the scientific

foundation and

information

management scheme

for the 303(d) listing

process including a

classification

framework for surface

waters, watersheds, and

regions to guide

problem formulation

Provide first generation

diagnostic methods,

including stressor

identification (SI)

methods, for causal

linkage of observed

major classes of single

stressors and biological

indicators to stressors

in freshwater and

marine systems; scale

the methods to States

and watershed

organizations

Equip EPA R

States and Tri

knowledge, s

tools to deter

causes of imp

for freshwat

coastal sys

required in v

regulatio

FY03 FY04 FY05 FY06 FY07 FY0

Long Term Goal 2: Provide the tools to assess and diagnose sources and causes of

impairment in aquatic systems.

Figure 6. Long Term Goal 2
Provide updated

models for

stormwater

management, and

for allocating

suspended solids

and sediment

loads, and related

uncertainties for

mixed land use

watersheds.

Complete at least three (3)

demonstrations of updated

models for stormwater

management, suspended

solids, sediment, and

nutrients to meet water

quality objectives.

Provide State of the Science

Synthesis and Application

Approaches for Managing

Risks from CAFO's

Provide at least

six (6) reports of

performance data

and information

for controlling

nutrients,

suspended

solids,

sediments,

pathogens, toxic

chemicals (metals

and PBTs), and

flow variations

urban and rural

watersheds.

 Provide at least seven

(7) key reports. updated

models, and data bases

for allocating and

managing suspended

solids, sediment,

pathogen, nutrients, and

toxic chemical (metals

and PBTs) loads among

all sources in mixed landuse watersheds

FY03 FY04 FY05 FY06 FY07 FY08

Long Term Goal 3. Provide the tools to restore and protect aquatic systems and

to forecast the ecological, economic, and human health outcomes of alternative

solutions

Forecasting Outcomes

Provide

indicators,

monitoring

strategies, and

guidance for

determining theeffectiveness of

Best Management

Practices (BMP's)

in meeting water

quality goals.

Demonstrate the application

of innovative wet weather

flow technologies in urban

watersheds regulated under

the National CSO Control

Policy and SSO Programs. Demonstrate the

application of models,

landscape

characterization

methods, and economic

analyses to formulate

alternative approaches

for protecting and

restoring water quality

and critical habitats and

to forecast the

ecological, economic,

and human health

outcomes of the

alternatives.

Dem

c

alloc

res

wat

att

c

soc

and 

BMP's &

Watershed

Management

Figure 7. Long Term Goal 3
Provide the EPA

Program Offices, EPA

Regions, States, utilities

and others with

improved tools for

characterizing

pathogens in biosolids.

Provide the EPA

Program Offices, EPA

Regions, States and

others with study

findings that improve

the understanding of

the effectiveness of

current biosolids

practices and of the

significance of humanhealth risks to supportdecisions on biosolids

management and

research.

FY03 FY04 FY05 FY06 FY07 

Long Term Goal 4. Provide the approaches, methods and tools to assess the

exposures and reduce the human health risks from biosolids contaminants for use by

OW, States and others in updating biosolids guidance and regulations

Provide the EPA

Program Offices, EPA

Regions, States and

others with improved

data, tools, and

methods for the

analysis of risks, andfor selection of more

effective management

options.

Figure 8. Long Term Goal 4
APPENDIX

52

EPA Strategic Plan Goals and Related ORD MYPs

Goal MYP

Goal 1: Clean Air Particulate Matter

Air Toxics

Tropospheric Ozone

Goal 2: Clean and Safe Water Drinking Water

Water Quality

Goal 3: Protect and Restore the Land Resource Conservation and Recovery Act

(RCRA)

Contaminated Sites

Goal 4: Healthy Communities and

Ecosystems

Mercury

Global Change

Ecological Research

Human Health Risk Assessment

Endocrine Disruptors

Safe Pesticides/Safe Products

Safe Food

Goal 5: Compliance and Environmental

Stewardship

Economics and Decision Sciences

Pollution Prevention and New Technologies

for Environmental Protection
53

LIST OF ACRONYMS

ACE Acute-to-Chronic Estimation

AFLP Amplified Fragment Length Polymorphisms

APG Annual Performance Goal

APM Annual Performance Measure

AWQC Ambient Water Quality Criteria

BMP Best Management Practice

CAFO Confined Animal Feeding Operation

CDC Centers for Disease Control

CFR Code of Federal Regulations

CSO Combined Sewer Overflow

CWA Clean Water Act

DO Dissolved Oxygen

EDC Endocrine Disrupting Chemicals

EMAP Environmental Monitoring and Assessment Program

EPA Environmental Protection Agency

ERD Ecosystems Research Division of NERL

ESD Environmental Sciences Division of NERL

ETV Environmental Technology Verification

EXTRAN Extended Transport Module in Storm Water Management Model

FTE Full Time Equivalent

GC/MS/SIM Gas Chromatography/Mass Spectrometry - Selective Ion Monitoring

GIS Geographic Information System

GPRA Government Performance and Results Act

GSTARS Generalized Stream Tube model for Alluvial River Simulation

GWERD Ground Water and Ecological Restoration Division of NRMRL

HAB Hazardous Algal Bloom

IBI Index of Biotic Integrity

ICE Ion Composition Elucidation

LC/MS Liquid Chromatography/Mass Spectrometry

LRPCD Land Remediation and Pollution Control Division of NRMRL

LTG Long Term Goal

MCL Maximum Contaminant Level

MS Mass Spectrometry

MYP Multi-year Plan

NAS National Academy of Science

NAWQA National Ambient Water Quality Assessment (within USGS)

NCEA National Center for Exposure Assessment within EPA’s Office of Research

and Development

NCER National Center for Environmental Research within EPA’s Office of Research

and Development

NEP National Estuary Program

NERL National Exposure Risk Laboratory within EPA’s Office of Research and

Development
54

NHEERL National Health and Ecological Effects Research Laboratory within EPA’s

Office of Research and Development

NOAA National Oceanic and Atmospheric Administration

NPS Nonpoint Source

NRC National Research Council of the National Academies

NRMRL National Risk Management Laboratory within EPA’s Office of Research and

Development

NSF National Science Foundation

OEPA Ohio Environmental Protection Agency

OGWDW Office of Ground Water and Drinking Water within EPA’s Office of Water

ORD Office of Research and Development

OSP Office of Science Policy within EPA’s Office of Research and Development

OST Office of Science and Technology withing EPA’s Office of Water

OW Office of Water

OWM Office of Wastewater Management within EPA’s Office of Water

OWOW Office of Wetlands, Oceans and Watersheds within EPA’s Office of Water

P2 Pollution Prevention

PBT Persistent Bioaccumulative Toxic

PBTK/TD Physiologically-Based Toxicokinetic/Toxicodynamic

PCO Pfisteria Complex Organisms

POCIS Polar Organic Chemical Integrative Sampler

PPCP Pharmaceuticals and Personal Care Products

SAV Submerged Aquatic Vegetation

SI Stressor Identification

SDWA Safe Drinking Water Act

SPRC Strategic Planning and Research Coordination

SSO Storm Sewer Overflow

SSRI Selective Serotonin Reuptake Inhibitors

STD Sustainable Technology Division of NRMRL

SWMM Storm Water Management Model

TIE Toxicity Identification Evaluation

TMDL Total Maximum Daily Load

TVA Tennessee Valley Authority

USDA United States Department of Agriculture

USGS United States Geological Survey

WSWRD Water Supply and Water Resources Division of NRMRL

WWT Waste Water Treatment
55

References

National Research Council (NRC), 2001. Assessing the TMDL Approach to Water Quality

Management. Washington, DC: National Academy Press.

National Research Council (NRC), 2002. Biosolids Applied to Land: Advancing Standards and

Practices. Washington, DC: The National Academies Press.

USEPA,1999. Action Plan for Beaches and Recreational Waters. EPA/600/R-98/079.

Office of Research and Development and Office of Water, Washington, DC.

USEPA, 2002. Aquatic Stressors: A Framework and Implementation Plan for Effects Research

2002. EPA 600/R-02-074. U.S. Environmental Protection Agency, Office of Research and

Development, National Health and Ecological Effects Research Laboratory, Research Triangle

Park, NC.

USEPA, 2002. Draft Strategy for Microbial Waterborne Disease Control. U.S. Environmental

Protection Agency, Office of Water, Washington, DC.

USEPA, 2002. Strategic Planning and Research Coordination (SPRC) Action Plan for Aquatic

Ecology and Water Quality. (Unpublished internal planning document) U.S. Environmental

Protection Agency, Office of Research and Development and Office of Water, Washington, DC.

USEPA, 2002. The Twenty Needs Report: How Research Can Improve the TMDL Program.

EPA 841-B-02-002. U.S. Environmental Protection Agency, Office of Water, Washington, DC.

USEPA, 2003. Draft 2003 Strategic Plan. U.S. Environmental Protection Agency, Office of the

Chief Financial Officer, Washington, DC.

USEPA,2003. Ecological Research Multi-Year Plan. FY2005 Planning - Final Version, April

25, 2003. U.S. Environmental Protection Agency, Office of Research and Development,

Washington, DC.