U.S. Environmental Protection Agency

Region 1, New England

Boston, MA

Phosphorus TMDLs for 

Vermont Segments of 

Lake Champlain

June 17, 2016
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TABLE OF CONTENTS

Table of Contents .................................................................................................................................................................................. i

CHAPTER 1. BACKGROUND ................................................................................................................................................. 1

1.1 Lake Champlain TMDL History: VT 2002 Lake Champlain TMDL ......................................................................... 4

1.2 Legal History ................................................................................................................................................................................ 4

1.3 Why EPA is Establishing These TMDLs............................................................................................................................. 5

1.4 TMDL Process, Partner Coordination and Responsibilities ..................................................................................... 5

CHAPTER 2: WATER QUALITY STANDARDS ................................................................................................................ 7

CHAPTER 3: WATERSHED AND IMPAIRMENT DESCRIPTION .........................................................................10

3.1. General Watershed Setting ................................................................................................................................................10

3.2. Pollutant of Concern .............................................................................................................................................................12

3.3 303(d) Listings .........................................................................................................................................................................13

CHAPTER 4: SOURCES OF PHOSPHORUS LOADING TO LAKE CHAMPLAIN & SEGMENTS ...................16

4.1 Pollutant Source Sector Contributions ...........................................................................................................................19

CHAPTER 5: ESTABLISHING LAKE SEGMENT LOADING CAPACITIES .........................................................20

5.1 Modeling Methods ....................................................................................................................................................................20

5.1.1 BATHTUB Model Revision ................................................................................................................................................20

5.1.2 SWAT Model Development ...............................................................................................................................................21

5.1.3 The BMP Scenario Tool ......................................................................................................................................................22

5.1.4 Quality Assurance for Model Development ...............................................................................................................22

5.2 Development and Application of the Lake Spreadsheet Model for TMDL Load Reduction Analysis ....23

5.3 Seasonal Variation ...................................................................................................................................................................25

5.4 Consideration of Climate Change ......................................................................................................................................26

CHAPTER 6: ESTABLISHING ALLOCATIONS ...........................................................................................................27

6.1 Wasteload Allocation - General Approach ....................................................................................................................27

6.1.1 Wastewater Treatment Facilities Wasteload Allocations...................................................................................27

6.1.1.1 Segment-Specific WWTF Allocations ......................................................................................................................30

6.1.1.2 Future Growth in Wastewater Loads .......................................................................................................................32

6.1.2 Developed Land Wasteload Allocations .....................................................................................................................32

6.1.2.1 Setting the WLA Levels for Developed Land ..........................................................................................................36

6.1.2.2 Future Growth From Developed Land ....................................................................................................................37

6.2 Load Allocation .......................................................................................................................................................................38

6.2.1 Internal Sediment Considerations – St. Albans Bay and Missisquoi Bay ......................................................39

6.3 Margin of Safety ......................................................................................................................................................................41
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6.4 TMDL Allocation Summary ................................................................................................................................................43

CHAPTER 7: REASONABLE ASSURANCE & ACCOUNTABILITY FRAMEWORK .........................................49

7.1 Reasonable Assurance – Background ...............................................................................................................................49

7.2 Reasonable Assurance – General Approach ...................................................................................................................50

7.2.1 Reasonable Assurance – Missisquoi Bay .....................................................................................................................52

7.2.2 Reasonable Assurance – South Lake B ........................................................................................................................54

7.3 Accountability Framework ..................................................................................................................................................54

7.3.1 Accountability Framework Through 2017 .................................................................................................................55

7.3.2 Accountability Framework Beyond 2017 ...................................................................................................................57

CHAPTER 8: IMPLEMENTATION ..................................................................................................................................60

CHAPTER 9: PUBLIC PARTICIPATION .......................................................................................................................64

CHAPTER 10: REFERENCES ...........................................................................................................................................66

CHAPTER 11: ABBREVIATIONS AND ACRONYMS ................................................................................................71

APPENDICES ............................................................................................................................................................................72

APPENDIX A ........................................................................................................................................................................................72

APPENDIX B ........................................................................................................................................................................................72
CHAPTER 1. BACKGROUND 

Section 303(c) of the Clean Water Act (CWA) requires states to establish water quality standards 

(WQS) that identify each waterbody’s designated uses and the criteria needed to support those uses. 

Such WQS must be sufficient to ensure, wherever attainable, a level of water quality that provides for 

the protection and propagation of fish, shellfish, and wildlife and recreation in and on the water. 

Section 303(d) of the CWA requires states to develop lists of impaired waters that fail to meet Water 

Quality Standards (WQS) set by jurisdictions even after implementing technology-based and other 

pollution controls. The Environmental Protection Agency’s (EPA) regulations for implementing CWA 

section 303(d) are codified in the Water Quality Planning and Management Regulations at 40 CFR Part 

130. The law requires that states establish priority rankings and develop Total Maximum Daily Loads 

(TMDLs) for waters on the lists of impaired waters (40 CFR 130.7). 

A TMDL specifies the maximum amount of a pollutant that a waterbody can receive and still meet 

applicable WQS. A mathematical definition of a TMDL is written as the sum of the individual 

wasteload allocations (WLAs) for point sources, the load allocation (LAs) for nonpoint sources and 

natural background, and a margin of safety (MOS)[CWA 303(d)(1)(C)]: 

TMDL = ΣWLA + ΣLA + MOS 

Where: 

WLA = wasteload allocation, or the portion of the TMDL allocated to existing and/or future point 

sources. 

LA = load allocation, or the portion of the TMDL attributed to existing and/or future nonpoint 

sources and natural background. 

MOS = margin of safety, or the portion of the TMDL that accounts for any lack of knowledge 

concerning the relationship between effluent limitations and water quality, such as uncertainty 

about the relationship between pollutant loads and receiving water quality, which can be 

provided implicitly by applying conservative analytical assumptions or explicitly by reserving a 

portion of loading capacity. 

The process of calculating and documenting a TMDL involves a number of tasks and—especially for a 

large, complex, and multijurisdictional waterbody with multiple impairments—can require substantial 

effort and resources. Major tasks involved in the TMDL development process include the following: 

 characterizing the impaired waterbody and its watershed; 

 identifying and inventorying the relevant pollutant source sectors; 

 applying the appropriate WQS; 

 calculating the loading capacity using appropriate modeling analyses to link pollutant loads to 

water quality; and 

 identifying the required source allocations.

Phosphorus concentrations in Lake Champlain typically exceed Vermont’s water quality standards. 

This TMDL report presents the results of numerous analyses and model simulations designed to 

calculate Lake Champlain’s phosphorus loading capacity and documents the informational elements 
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described above. Although Lake Champlain is bordered by Vermont, New York, and the Province of 

Quebec, the TMDLs established in this report address the 12 lake segments to which Vermont sources 

discharge and are affected by Vermont sources (hereafter referred to as the “Vermont portion of Lake 

Champlain” or “Vermont segments”) for reasons explained in Sections 1.1 – 1.2. Five of these 

segments are exclusively within VT waters, the remainder are shared with New York and/or Quebec. 

As described in detail in Chapter 5, the modeling and analyses to determine base loads and loading 

capacity covered the full extent of the Lake Champlain watershed. 

Lake Champlain is divided into thirteen segments for phosphorus management purposes, and 12 of these 

segments (all except Cumberland Bay) are influenced at least in part by discharges of phosphorus from 

sources in Vermont (Figure 1). The Lake is impaired due to excess phosphorus loadings, which have 

resulted in severe eutrophication in many lake segments. Consistent with the approach taken in the 2002 

Lake Champlain Phosphorus TMDL (see TMDL history section below), TMDLs have been developed 

for all 12 of the Vermont segments (see Table 1). This approach recognizes that the lake functions as a 

set of hydrodynamically interconnected segments that extensively influence each other. 

The TMDLs set allocations for Vermont sources of phosphorus, including permitted point sources such 

as wastewater treatment facilities, and municipal and transportation stormwater sources, and diffuse 

sources such as runoff from agriculture and forests, and stream bank erosion. 

Table 1. Waterbodies Addressed by the Lake Champlain Phosphorus TMDLs 

Waterbody ID Number Waterbody Name

VT04-02L01 South Lake A

VT04-02L01 South Lake B

VT04-01L02 Port Henry

VT04-01L01 Otter Creek

VT05-10L02 Main Lake

VT05-11L01 Shelburne Bay

VT05-10L01 Burlington Bay

VT05-09L01 Malletts Bay

VT05-04L01 Northeast Arm

VT05-07L01 St. Albans Bay

VT05-01L01 Missisquoi Bay

VT05-04L02 Isle LaMotte
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1.1 LAKE CHAMPLAIN TMDL HISTORY: VT 2002 LAKE CHAMPLAIN TMDL

The Vermont Department of Environmental Conservation (DEC) began preparing a set of Lake 

Champlain phosphorus TMDLs in the late 1990s, following the development and approval by 

Vermont, New York, and EPA of the Lake Champlain Management Conference plan entitled 

“Opportunities for Action” in 1996, and the completion of a multi-year Lake Champlain diagnosticfeasibility study in 1997. Drafts of the TMDL document were circulated for public comment in 2001 

and 2002, and provided to EPA for comment as well.

DEC submitted the final Lake Champlain Phosphorus TMDLs to EPA Region 1 for review and approval 

under Section 303(d) of the Act on September 25, 2002. The submittal addressed the nine segments of 

Lake Champlain that were at that time identified on Vermont’s Clean Water Act Section 303(d) list of 

impaired waters as being impaired by phosphorus. At the same time, the New York State Department of 

Environmental Conservation submitted TMDLs to EPA Region 2 for the seven impaired segments 

identified on New York’s Section 303(d) list of impaired waters (most of which overlapped with the 

Vermont segments). Following a review of the final TMDL package, including DEC’s response to 

public comments, the Region approved Vermont’s TMDLs on November 4, 2002. EPA Region 2 

approved New York’s portion of the Lake Champlain TMDLs on September 30, 2002. 

1.2 LEGAL HISTORY

On October 28, 2008, the Conservation Law Foundation (CLF) filed suit in federal district court against 

EPA seeking to set aside the Region’s November 4, 2002 approval of Vermont’s Lake Champlain 

Phosphorus TMDLs and seeking establishment by EPA of new TMDLs. (CLF did not challenge Region 

2’s approval of New York’s portion of the TMDLs.) The complaint alleged that EPA’s approval was 

arbitrary, capricious, and not in accordance with law under the Clean Water Act and the Administrative 

Procedure Act, 5 U.S.C. § 706(2). Specifically, the complaint asserted that the 2002 TMDLs contained 

a variety of flaws, including insufficiently stringent wasteload allocations coupled with a lack of 

reasonable assurances that nonpoint source reductions would occur; an inadequate margin of safety; 

inadequate specificity of the stormwater component of the wasteload allocations; and failure to consider 

water resources effects associated with documented and predicted climate change. The State of Vermont 

intervened in the case. 

In April 2010, CLF and EPA signed a settlement agreement, and EPA filed a motion with the court 

seeking a voluntary remand to allow the Region to reconsider its 2002 TMDL approval decision and a 

stay of the litigation. The State objected to EPA’s motion and moved the court to deny the request for 

remand and dismiss the case. On August 25, 2010, the court granted EPA’s motion for voluntary remand 

and stayed the case for 180 days. In the settlement agreement with CLF, EPA agreed to complete its 

reconsideration of the 2002 TMDLs no later than 120 days from the court’s order granting the remand. 

That date was December 24, 2010. On December 14, 2010, EPA received a 30-day extension from CLF 

of the date by which EPA must issue its decision, i.e., no later than January 23, 2011. 

Following the judge’s order, the Region reviewed the 2002 Lake Champlain TMDLs and the 

administrative record in light of applicable statutory and regulatory provisions and EPA guidance 

available at the time of the original approval. The Region’s task was to determine, after a fresh look at 

these materials and consideration of the allegations in CLF’s complaint, whether the TMDLs were 

consistent with Section 303(d) of the Act and its implementing regulations. The Region focused its 
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reevaluation on the four major contested areas of the TMDLs: margin of safety, stringency of WLAs in 

light of reasonable assurance that sufficient load reductions would occur, aggregation of stormwater 

WLAs, and climate change considerations associated with the loading capacity and hydrologic base 

year. 

Upon reconsideration of the four contested elements of the 2002 Vermont Lake Champlain 

Phosphorus TMDLs, the Region concluded that two of the elements were consistent with EPA 

regulations and guidance available at the time of TMDL approval, and two elements were not. 

The aggregate expression of the stormwater component of the wasteload allocation was found to be 

consistent with EPA’s regulations and 2002 guidance on this topic. The calculation of the loading 

capacity and phosphorus allocations using the 1991 hydrologic base year was also found consistent with 

EPA guidance and regulations, and based on sound science. However, the portions of the TMDLs 

addressing the margin of safety and the establishment of wasteload allocations based on assumptions 

that nonpoint source reductions would be achieved were found inadequate and inconsistent with EPA 

regulations and guidance. Accordingly, on January 24, 2011, the Region withdrew its November 4, 2002 

approval of the Vermont portions of the Lake Champlain Phosphorus TMDLs and disapproved the 

Vermont portions of the TMDLs (USEPA 2011a, b).

1.3 WHY EPA IS ESTABLISHING THESE TMDLS

Pursuant to Section 303(d)(2) of the Act and 40 C.F.R. § 130.7(d)(2), upon disapproval of a TMDL, 

EPA must establish a new TMDL as determined to be necessary to implement applicable water quality 

standards. Accordingly, the Region commenced development of new phosphorus TMDLs for the 

segments in the Vermont portion of Lake Champlain. The Region will issue a public notice of the 

completion of these new TMDLs and will seek public comment. After considering public comments and 

making any appropriate revisions in response to such comments, the Region will transmit the TMDLs to 

the State. 

1.4 TMDL PROCESS, PARTNER COORDINATION AND RESPONSIBILITIES

At the time of the disapproval of the 2002 TMDLs, EPA indicated that the new phosphorus TMDLs for 

the Vermont portion of Lake Champlain would be based on an evaluation of all available current 

information as well as any applicable updated EPA guidance. The Region anticipated there would be 

refinements of several aspects of the new TMDLs, not just the two components that the disapproval 

determined were inadequate. While EPA is responsible for establishing the new TMDLs, the Region 

made it clear from the outset that it intended to work collaboratively with Vermont in developing the 

TMDLs. In EPA’s view, long-term implementation of the TMDLs will have the greatest chance of 

achieving the necessary phosphorus reductions through programs developed and embraced by the State. 

Throughout the development of the TMDLs, EPA has considered and, in many instances, incorporated 

the Vermont DEC’s and Agency of Agriculture’s scientific, technical and policy approaches.

The new TMDLs were developed in three phases. In the first phase, the scientific foundation for the 

TMDLs was established and public input was invited on policies and programs. In the second phase, the 

State developed its approach to reducing phosphorus inputs to the lake and its tributaries. In the final 

phase, EPA built upon the first two in developing the wasteload and load allocations and an 

Accountability Framework that tracks implementation actions, assesses progress and determines the 
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need for alternative management actions, to ensure the allocations and ultimately, water quality 

standards, are met. Each phase is described in further detail below. 

EPA quickly set to work on the scientific and technical foundation for the new TMDLs. In 2011, EPA 

hired a contractor (Tetra Tech) to provide modeling support, and established technical workgroups to 

provide input on modeling approaches and available data both for the in-lake processes and watershed 

dynamics. The workgroups were co-lead by scientists from EPA and DEC. Parallel to the technical 

workgroup process, nine stakeholder outreach sessions were held across the basin in the fall of 2011, cohosted jointly by EPA, DEC and the VT Agency of Agriculture. This phase culminated in the 

completion of the in-lake and watershed models. 

In the second phase, the State developed a suite of programs to achieve the phosphorus reductions that 

early iterations of the models indicated were necessary to achieve the water quality targets in the lake. 

Throughout this phase, meetings were held with representatives from EPA, DEC and the Agency of 

Agriculture at the staff and management levels to develop policies and programs. The State agencies 

were also gathering input and feedback from regulated entities. In the fall of 2013, EPA, DEC and the 

Agency of Agriculture hosted six public outreach sessions to solicit input on an outline of measures the 

State had under consideration. EPA then asked the State for a formal plan containing the set of 

measures Vermont was committed to implement. This phase culminated in Governor Shumlin 

submitting the “Vermont Lake Champlain Phosphorus TMDL Phase 1 Implementation Plan” (Vermont, 

2014) to EPA in May, 2014. 

In the final phase, EPA evaluated the measures contained in the Phase 1 Implementation Plan using 

updated versions of the TMDL models. EPA then prepared preliminary allocations for each of the lake 

segments. EPA’s preliminary allocations and the associated reductions necessary to achieve them were 

the subject of five public outreach meetings conducted jointly by EPA, DEC and the Agency of 

Agriculture in December, 2014. In May, 2015, the Vermont General Assembly passed H.35, “An act 

relating to improving the quality of state waters.” The law provides statutory authorities and deadlines 

for many of the key programs contained in the Phase 1 Implementation Plan and establishes a “Clean 

Water Fund” to support implementation. H.35, subsequently designated as Act 64, was signed into law 

by Governor Shumlin on June 16, 2015. The State then revised the Phase 1 Implementation Plan 

(Vermont, 2015) to ensure consistency with the new law. Based on the feedback from the meetings, the 

new law, and the revised Phase 1 Implementation Plan, EPA made final adjustments to establish the 

allocations that constitute the new Phosphorus TMDLs for the 12 segments of Lake Champlain listed in 

Table 1. While EPA benefited greatly from policy and program input from the State throughout this 

phase, the final allocations were determined by EPA. 
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CHAPTER 2: WATER QUALITY STANDARDS

Water Quality Standards (WQS) are the foundation for a wide range of programs under the CWA. They 

serve multiple purposes including establishing the water quality goals for a specific waterbody, or 

portion thereof, and providing the regulatory basis for establishing water quality-based effluent limits 

beyond the technology-based levels of treatment required by CWA Sections 301(b) and 306. The water 

quality criteria within WQS serve as targets or endpoints for CWA restoration activities such as TMDLs. 

Water quality criteria define the chemical, physical and biological conditions which are needed to 

support and protect designated uses of surface waters. Most water quality criteria are numeric 

expressions with measurable parameters. Numeric criteria specify measurable levels of particular 

chemicals or conditions allowable in a water body. When pollutants cannot be precisely measured, 

narrative criteria are used to express a parameter in a qualitative form. 

Based on the Vermont Water Quality Standards (VT WQS), Lake Champlain segments are Class B 

waters (Vermont Water Resource Board, 2011). The designated uses associated with Class B waters 

include: 

1. Aquatic biota, wildlife and aquatic habitat 

2. Aesthetics 

3. Public water supply 

4. Irrigation of crops and other agricultural uses 

5. Swimming and other primary contact recreation 

6. Boating, fishing, and other recreational uses 

The pollutant of concern for these TMDLs is phosphorus because it is causing or contributing to 

excessive algal biomass in the lake, and monitoring data indicate phosphorus levels are elevated above 

established phosphorus criteria in the VT WQS. Section 3-04(B)(5)(b) of the VT WQS (Vermont ANR, 

2014) lists the numeric phosphorus criteria for each lake segment (see Table 2 below).

The numeric, in-lake total phosphorus concentration criteria were incorporated into the Vermont Water 

Quality Standards in 1991. The phosphorus criteria range from 0.010 to 0.054 mg/l as shown in Table 2. 

The 15 core lake stations are sampled approximately biweekly from May to early November each year. 

An effort is made to obtain up to 20 samples per year at each tributary site, including as high a 

proportion of samples as possible during high flow conditions in order to improve the precision of 

tributary annual mass loading estimates. 

A complete description of the monitoring program for Lake Champlain can be found in the Long Term 

Water Quality and Biological Monitoring Quality Assurance Project Plan (LCBP, 2013) and Long Term 

Biological and Water Quality Monitoring Report (LCPB, 2014) 

To assess attainment of annual mean total phosphorus criteria for Lake Champlain, VT DEC uses the 

total phosphorus concentrations obtained through the Long-Term Monitoring Program. A segment is 

determined to be in non-attainment/impaired when the annual mean total phosphorus concentrations in 

the euphotic zone in the lake segment consistently exceed the applicable total phosphorus concentration 

criterion in Section 3-04 B.5.b of the VT WQS (DEC, 2014b). Figure 5 shows the annual mean 
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concentrations for each segment from 1990 to 2014 in comparison to the applicable phosphorus 

criterion. 

Table 2. Vermont Phosphorus Criteria for Lake Champlain Segments 

Lake Segment Total Phosphorus Criterion (mg/l)*

Main Lake 0.010

Malletts Bay 0.010

Burlington Bay 0.014

Shelburne Bay 0.014

Northeast Arm 0.014

Isle LaMotte 0.014

Otter Creek 0.014

Port Henry 0.014

St. Albans Bay 0.017

Missisquoi Bay 0.025

South Lake A 0.025

South Lake B 0.054

*The Vermont Water Quality Standards specify that these criteria shall be achieved as the annual mean total phosphorus 

concentration in the photosynthetic depth (euphotic) zone in central, open water areas of each lake segment.
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Figure 2: Sampling stations in Lake Champlain and its tributaries. LCBP, 2013 
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CHAPTER 3: WATERSHED AND IMPAIRMENT DESCRIPTION

3.1. GENERAL WATERSHED SETTING

Lake Champlain is one of the largest lakes in North America, and is bordered by the States of Vermont 

and New York and the Province of Quebec. It is 120 miles long, with a surface area of 435 square miles 

and a maximum depth of 400 feet. The 8,234 square mile watershed drains nearly half the land area of 

Vermont (56% of the basin), as well as portions of northeastern New York (37% of the basin) and 

southern Quebec (7% of the basin). 

The Lake Champlain basin includes a large percentage of the Green Mountains in Vermont, parts of the 

Adirondack Mountains in New York, and the Pike River floodplain in Quebec. Sixty four percent of its 

land area is forested, 16% is agricultural, 10.3 % is open waters, 5.6% is developed, and 3.8% is 

wetlands (Figure 3). 
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3.2. POLLUTANT OF CONCERN

Lake Champlain is impaired by the nutrient phosphorus, which causes algal blooms and obnoxious 

odors, and leads to low dissolved oxygen concentrations, impaired aquatic life, and reduced recreational 

use. Phosphorus sources to the lake include agriculture, streambank erosion, developed land sources 

(including roads, parking lots, lawns, athletic fields, buildings, and industrial facilities), wastewater 

treatment plants, and forest harvesting operations and forest roads. The relative amounts of phosphorus 

loading from Vermont sources are shown in Figure 4. For some lake segments, internal sources of 

phosphorus from bottom sediments contribute a significant load. 

Total phosphorus concentrations vary greatly among the lake segments, as shown in Figure 5. Lake 

segments such as Malletts Bay and the Main Lake have phosphorus levels in the low-mesotrophic range 

of 0.009-0.012 milligrams per liter (mg/l). Eutrophic conditions exist in South Lake A and B, St. Albans 

Bay, and Missisquoi Bay, all segments where mean phosphorus concentrations are in the range of 0.024-

0.058 mg/l. While phosphorus concentrations vary among the segments, the interconnectedness of the 

segments (and the way each segment influences other segments) necessitates a lake-wide approach to 

TMDL development. Based on the 2002 TMDL approach, and the lake modeling that took into account 

all these interconnections, EPA has established TMDLs for all 12 segments in order to ensure that 

phosphorus targets are met throughout the lake. 

Phosphorus has long been regarded as the primary limiting nutrient for algal growth in freshwater lakes 

(Wetzel, 2001). For this reason, management efforts have historically focused on reducing phosphorus 

inputs as the primary means to control algal blooms and improve lake water quality. This is also why the 

Lake Champlain segments have been listed on Vermont’s Section 303(d) list as impaired for 

phosphorus, but not any other nutrient, such as nitrogen. In recent years, some scientists have postulated 

that it may also be important to control nitrogen inputs to freshwater systems to manage algae growth, 

but the role of nitrogen in lake restoration is still uncertain (Lewis et al., 2011; Sterner, 2008). In 

contrast, there is clear evidence from case histories and whole-ecosystem experiments that phosphorus 

reduction can successfully control algal growth (Schindler, 2012). Given the much stronger scientific 

basis for the importance of phosphorus in this context, these TMDLs establish allocations and reduction 

requirements only for phosphorus. Two additional factors reinforce the soundness of this approach: 1) 

nitrogen concentrations in Lake Champlain have actually been going down in recent decades, possibly 

due to decreasing atmospheric nitrogen deposition (Smeltzer et al., 2009), and 2) many of the best 

management practices (BMPs) that will be implemented to control phosphorus, also control nitrogen to 

some extent. These co-benefits should help continue the downward trend of nitrogen concentrations in 

the lake. 

Water quality monitoring can be used to identify whether waters are meeting designated uses, to identify 

specific pollutants and their sources, determine long term trends and to screen for impairment. As 

noted, numeric water quality criteria identify the concentration of a chemical pollutant that is allowable, 

yet protects designated uses. When chemical pollutants exceed maximum or fall below minimum 

allowable concentrations, waters may no longer be able to support the designated uses such as fishing, 

swimming and drinking. Water quality conditions and use attainment may be assessed by comparing the 

concentrations of chemical pollutants found in surface waters to the criteria in the State's standards. In 

this case, total phosphorus data collected for each lake segment by Lake Champlain’s long term water 

quality monitoring program were used to assess whether phosphorus criteria were being met and 

whether or not designated uses were supported. 
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The Lake Champlain Long-Term Water Quality and Biological Monitoring Program began in 1992 and 

has continued each year since then. A total of 37 monitoring stations are included in the sampling 

station network, which includes a core set of 15 lake stations and 22 tributary stations (Figure 2). 

Tributary stations are located as near to the river mouths as possible on rivers which have continuous 

flow gages operated by the U.S. Geological Survey (USGS) or the Quebec Ministry of Sustainable 

Development, Environment, and Parks. These lake and tributary stations have been sampled consistently 

during the entire monitoring period since 1992, with the exception of lake stations 9 and 16 which were 

added in 2001, and station 51 which was added in 2006. The sampling station on Rock River was added 

in 2007, and sites on Stevens Brook and Jewett Brook were added late in 2008. In 2010, a USGS gaging 

station was installed on the Mill River, bringing the total tributaries monitored to 22. Other lake stations 

listed in Vermont DEC and New York State DEC (VT and NY, 1997) have been sampled during shortterm surveys for a limited number of water quality measurements (LCBP, 2013).

3.3 303(D) LISTINGS

At the time of the original TMDLs’ development in 2002, these nine segments were on the Vermont 

303(d) list as impaired for phosphorus and were high priorities for TMDL development: 

South Lake A Otter Creek Northeast Arm 

South Lake B Main Lake St. Albans Bay 

Port Henry Shelburne Bay Missisquoi Bay 

These segments are still not consistently meeting the applicable phosphorus water quality criteria and, 

following EPA’s disapproval of the Lake Champlain TMDLs in 2011, they remain impaired and in need 

of TMDLs. Consistent with the 2002 TMDL approach, EPA is also establishing TMDLs for the other 

three Vermont segments due to the hydrodynamic connections among the segments and the way each 

segment affects the water quality of other segments. The lake modeling results indicate that phosphorus 

reductions are needed in all lake segments to ensure phosphorus criteria are met throughout the lake.1 

See Table 2 for a listing of all 12 segments covered by the TMDLs. 

 

1

 The frequent exceedances of phosphorus criteria and upward phosphorus concentration trends in Malletts Bay and Isle 

LaMotte, together with the occasional exceedances of the phosphorus criterion in Burlington Bay, underscore the importance 

of including all 12 segments in the TMDL group. 
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CHAPTER 4: SOURCES OF PHOSPHORUS LOADING TO LAKE CHAMPLAIN & SEGMENTS

Phosphorus enters Lake Champlain from multiple point and nonpoint sources in Vermont, New York, 

and Quebec. A total phosphorus budget, annual mass balance model, and load allocation strategy were 

developed by the Lake Champlain Diagnostic-Feasibility Study (Vermont DEC and New York State 

DEC 1997, Smeltzer and Quinn 1996, Smeltzer 1999). The budget and modeling was updated in 2012 

to support EPA’s establishment of new TMDLs. The updates included a revision of the original in-lake 

BATHTUB model and the development of a SWAT (Soil and Water Assessment Tool) model for the 

watershed that identified the magnitude of phosphorus loading from each lake segment watershed. Both 

of these modeling steps are described in more detail in Chapter 5. 

The total phosphorus load to Lake Champlain from all sources was estimated to be 922 metric tons per 

year (mt/yr) during the 2001-2010 modeling period. As shown in Figure 6, wastewater treatment plant 

sources in Vermont, New York, and Quebec accounted for 7% of the total load during the same time 

period, with the remainder coming from agriculture, developed land, forests, and unstable stream 

corridors, referred to below as “streambank erosion” – the categories that together make up the “nonWWTF” load in Figure 6.

Table 3 shows the break-out of the loads among each source category for the 2001-2010 modeling 

period, derived from the combination of BATHTUB and SWAT modeling results. The table also shows 

how these loads combine with the aggregate NY and Quebec loads to add up to the total of 

approximately 922 metric tons per year. 
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Table 3. Phosphorus loads to each lake segment during the 2001-2010 base period (Tetra Tech 2015a, 2015b).

2001-2010 Vermont Base Loads (mt/yr)

Total Total Total Total

Lake Segment Wastewater Developed Forest Stream Agriculture Vermont New York Quebec Basin

South Lake B 0.6 9.0 13.6 8.3 19.6 51.1 39.4 0.0 90.5

South Lake A 0.1 2.3 0.5 0.0 23.6 26.5 24.4 0.0 50.8

Port Henry 0.0 0.7 0.04 0.0 6.3 7.0 8.4 0.0 15.4

Otter Creek 4.5 20.2 24.0 23.0 68.9 140.5 0.4 0.0 140.9

Main Lake 11.7 35.1 32.5 50.2 32.7 162.2 65.0 0.0 227.0

Shelburne Bay 0.6 3.4 0.3 0.2 5.7 10.2 0.0 0.0 10.2

Burlington Bay 2.8 1.7 0.02 0.0 0.0 4.5 0.0 0.0 4.5

Cumberland Bay 0.0 0.0 0.0 0.0 0.0 0.0 42.0 0.0 42.0

Malletts Bay 1.9 17.2 7.6 6.5 23.2 56.4 0.0 0.0 56.4

Northeast Arm 0.0 3.9 1.8 0.0 12.1 17.8 0.0 0.5 18.3

St. Albans Bay 0.9 2.6 0.2 1.5 8.6 13.9 0.0 0.0 13.9

Missisquoi Bay 1.5 17.0 20.1 40.2 57.6 136.3 0.0 72.3 208.6

Isle LaMotte 0.0 0.9 0.1 0.0 3.1 4.1 34.2 4.6 42.9

TOTAL 24.6 113.9 100.7 129.9 261.5 630.6 213.8 77.4 921.6
4.1 POLLUTANT SOURCE SECTOR CONTRIBUTIONS

Overall, the largest source of phosphorus is the agricultural sector, followed by streambank erosion, 

developed land, and forests. However, the importance of each sector varies considerably by lake 

segment watershed: For example, while agricultural sources are dominant in watersheds such as Otter 

Creek and Missisquoi Bay, developed land and streambank erosion are the largest sources to the Main 

Lake segment (see Figure 4). Forest land contributes a relatively small amount of phosphorus per unit 

area (the loading rate) but because forest land covers such a huge amount of the basin (see Figure 3) it 

represents a fairly large source of phosphorus in some watersheds. Wastewater treatment plants 

generate a very small percentage of the overall Vermont phosphorus load to the lake (currently about 

3%) but they constitute a significantly higher percentage of the load to some lake segments, such as St. 

Albans Bay, particularly when the permitted load at the design capacity of a plant is considered. 

The major sources of phosphorus within each sector also vary by lake segment, but some general trends 

are clear from the modeling work completed by Tetra Tech (2015b and 2015c). Within the agricultural 

sector, cropland is by far the largest phosphorus source, followed by pasture and farmsteads. Within the 

developed land sector, back roads are the single largest source category in most lake segment 

watersheds, due primarily to erosion and sedimentation from poorly managed roadside ditches. 

Impervious surfaces in residential, commercial and industrial land use categories (as a group) represent 

the next largest developed land source in most watersheds. Highly eroding, unstable stream reaches 

account for the majority of the phosphorus inputs from stream corridors. Within the forest sector, the 

vast majority of the phosphorus load comes from erosion along forest roads and active harvest areas. 
Page | 20 

CHAPTER 5: ESTABLISHING LAKE SEGMENT LOADING CAPACITIES

5.1 MODELING METHODS

The establishment of phosphorus loading capacities is a fundamental part of the TMDL process because 

they identify the amount of phosphorus that each segment can receive and still meet the applicable 

phosphorus criteria. The load allocations to point and nonpoint sources must be set so as not to exceed 

the loading capacities of each segment. Loading capacities are typically derived by using water quality 

models that establish a relationship between the amount of the pollutant (in this case phosphorus) 

entering the lake and the pollutant concentrations in each segment. Note, however, that in this case the 

loading capacities were established using a somewhat different process from the simplified approach 

described above. This is because each individual segment of Lake Champlain (each with its own 

phosphorus criterion and therefore its own TMDL) affects the phosphorus levels in a number of other 

segments, especially the nearest segments. This means that the loading capacities for a particular 

segment must be set at a level that not only allows the phosphorus criterion in that segment to be met, 

but also allows phosphorus criteria to be met in all other segments within its sphere of influence. Given 

this situation, there is not just one mathematical loading capacity for each segment; there are multiple 

options for loading capacities that together result in all segment criteria being met. The modeling 

approach described in the remaining sections, particularly 5.1.1 and 5.2, allows for consideration of a 

variety of combinations of load reduction scenarios among the various lake segments that together allow 

all segment criteria to be met. 

5.1.1 BATHTUB MODEL REVISION

In the 1990s, a phosphorus mass balance model for Lake Champlain was developed by the Lake 

Champlain Diagnostic-Feasibility Study (Vermont DEC and New York State DEC 1997). This model 

was used to derive the loading capacities for the 2002 Lake Champlain TMDLs. The model considered 

the circulation patterns within the lake, and established a predictive link between the in-lake total 

phosphorus concentrations and the phosphorus loading from each lake segment watershed. 

The original Lake Champlain phosphorus model was based on a modified version of the U.S. Army 

Corps of Engineers BATHTUB program (Walker 1987). The model used an annual steady-state 

approach with spatial segmentation that accounted for diffusive exchange mixing and advective 

transport of water and phosphorus between 13 lake segments (Vermont DEC and New York State DEC 

1997, Smeltzer and Quinn 1996, Smeltzer 1999). The model was used to analyze alternative 

combinations of load reductions from each lake segment watershed in Vermont, Quebec, and New York, 

and to predict the load reductions required to attain the in-lake phosphorus criteria in each lake segment. 

The model was calibrated using chloride and total phosphorus concentrations from a two-year data set 

(1990-1992). 

For the new TMDLs, EPA contracted with Tetra Tech to update the original BATHTUB model, using 

monitoring data collected from 1991 through 2010 through the Lake Champlain Long-Term Monitoring 

Program (see program description in Chapter 3, and Vermont DEC and New York State DEC, 2015) . 

The set-up and calibration of this model is described in detail in a separate report (Tetra Tech 2015a), 

but the main steps included: 
Page | 21 

1) Generation of tributary nonpoint source and point source flows and water quality parameter loads, 

using the FLUX32 software and monitoring data collected between 1990 and 2011; 

2) Preparation of BATHTUB model input datasets for steady-state simulation of 2-year duration and 

other time periods between 1990 and 2011; and 

3) Calibration and validation of the resulting updated BATHTUB model, using lake monitoring data 

collected between 1990 and 2011. 

5.1.2 SWAT MODEL DEVELOPMENT

While most of the inputs used to run the BATHTUB model were based on monitoring data, monitoring 

data were not available for phosphorus inputs from some smaller tributaries and areas that drain directly 

into the lake rather than into a major river. For these areas, the load estimates from the watershed model 

SWAT (Soil and Water Assessment Tool) were used as inputs to BATHTUB. The SWAT model was 

set up primarily to estimate phosphorus loads from different source sectors within the basin (in support 

of the load and wasteload allocation process and the development of reasonable assurance), but a 

secondary use was to provide these estimates of phosphorus from direct drainage areas for use in the 

BATHTUB model. A brief discussion of the SWAT model and its set-up for the Lake Champlain Basin 

is provided below. 

SWAT was jointly developed by the U.S. Department of Agriculture’s Agricultural Research Service 

and Texas A&M University’s, AgriLife Research Division. SWAT is a basin-scale, continuous model 

that operates on a daily time step. It is designed to predict the impact of management on water, sediment 

and agricultural chemical yields in watersheds and is capable of predicting water quantity, water quality 

and sediment yields from large, complex watersheds with variable land uses, elevations and soils. The 

model is physically based, computationally efficient and capable of continuous simulation over long 

periods. 

In SWAT a watershed is divided into sub-basins, which are then further subdivided into hydrologic 

response units (HRUs) on the basis of unique combinations of land use, soil and slope class. Hydrology 

and water quality computations are performed at the level of each HRU. They are summed to the subbasin level and routed through channels, ponds, wetlands or lakes to the watershed outlet. Hydrology in 

SWAT is based on the water balance. Overland flow runoff volume is computed using the Natural 

Resources Conservation Service (NRCS) curve number method. Curve numbers are a function of 

hydrologic soil group, vegetation, land use, cultivation practice and antecedent moisture conditions. 

The Lake Champlain Basin is composed of eight 8-digit Hydrologic Unit Code (HUC8) watersheds. 

Tetra Tech developed a discrete SWAT model for each of these HUC8 watersheds, as well as for direct 

drainage areas to the lake. The watershed models were calibrated and validated for daily hydrology, as 

well as monthly sediment and phosphorus loadings.

The SWAT modeling results were used for three main purposes as part of TMDL development: 

1) To quantify annual phosphorus loads from existing land-use and watershed process sources –

this information is needed for the establishment of load and wasteload allocations; 

2) To support the estimates of phosphorus load reductions potentially achievable through 

implementation of a mix of BMPs – an important part of evaluating the level of “reasonable 

assurance” that allocations for nonpoint sources can be achieved; and
Page | 22 

3) To estimate phosphorus loads from unmonitored drainage areas for input to the lake model 

(BATHTUB). 

The calibrated SWAT model was also used to project potential changes in phosphorus loading to the 

lake due to climate change. To develop the projections, Tetra Tech ran the SWAT model using data for 

six regionally downscaled climate change scenarios (based on four underlying Global Climate Change 

models) from the National Center for Atmospheric Research (NCAR) North American Regional Climate 

Change Assessment Program (NARCCAP) project, representative of the future period 2040-2070 

(Mearns, 2009). The results from the six climate change scenarios were compared with the current 

conditions (baseline loads) to project potential changes in phosphorus inputs to the lake from each major 

tributary for the mid-century time period. 

For a much more detailed description of the set-up and calibration of the SWAT model, see Tetra Tech 

(2015b). For more information on the use of the model in evaluating potential effects of climate change, 

see Tetra Tech (2015d). 

5.1.3 THE BMP SCENARIO TOOL

The BMP (Best Management Practice) Scenario Tool is a spreadsheet-based modeling tool designed to 

estimate how much phosphorus reduction could potentially be achieved by various mixes of BMPs in 

each watershed. It uses SWAT-generated baseline loading rates for each land use sector together with 

BMP efficiency information to estimate the amount of phosphorus reduction potentially achievable from 

a wide variety of user-selected BMP scenarios in each lake segment watershed. EPA made extensive 

use of the Scenario Tool when evaluating whether there was sufficient reasonable assurance that load 

allocations could and would be met. The Scenario Tool also includes phosphorus loading amounts both 

at the source (e.g., at a field or parking lot at the upper end of a large sub-watershed) and at the mouths 

of the major tributaries to the Lake – referred to as the delivered loads. The delivered loads take into 

account attenuation (or phosphorus storage or loss on route to the lake) estimated by the SWAT model. 

More details on this tool are included in Tetra Tech (2015c). 

5.1.4 QUALITY ASSURANCE FOR MODEL DEVELOPMENT

A number of steps were taken to ensure that the modeling work in support of the TMDL was conducted 

in accordance with standard modeling practices, and that modeling uncertainty was within acceptable 

ranges for this type of application. These steps included: 1) the establishment of technical workgroups 

(as described in Chapter 1) to review and provide input on the modeling approach; 2) an evaluation of 

potential modeling approaches conducted by EPA’s contractor followed by its recommendations of the 

selected approaches with input from members of the technical workgroups and EPA (Tetra Tech, 2011 

and 2012a); 3) the preparation of a quality assurance project plan that addressed performance 

expectations for both the BATHTUB and SWAT models (Tetra Tech, 2012b); 4) Internal quality 

assurance reviews completed by the contractor following completion of the modeling work (Tetra Tech, 

2014a and 2014b); and 5) an outside technical review of the modeling work conducted by independent 

modeling experts unaffiliated with this project (WaterVision, 2015).
Page | 23 

5.2 DEVELOPMENT AND APPLICATION OF THE LAKE SPREADSHEET MODEL FOR 

TMDL LOAD REDUCTION ANALYSIS

The calibrated BATHTUB model (Tetra Tech, 2015a) was transferred into a spreadsheet format 

(Microsoft Excel®) in order to facilitate the analysis of TMDL load reduction policy options and 

scenarios. The spreadsheet lake model used the same lake segmentation scheme and mass balance 

equations on which the BATHTUB model for Lake Champlain was based, solving the mass balance 

equations using iterative calculation methods in Excel®. The spreadsheet model produced the same lake 

phosphorus concentration predictions when given the same input data, but without the prediction 

uncertainty estimates provided by BATHTUB. 

Model parameters for the exchange flows and net sedimentation rates were maintained in the 

spreadsheet model as calibrated by Tetra Tech (2015a), except for the following modifications for St. 

Albans Bay and Missisquoi Bay. The calibrated internal phosphorus loading rate of 4.2 mg/m2/d for St. 

Albans Bay was set to zero for the TMDL load reduction analysis to represent the expectation that 

excessive internal loading will be eliminated over time, possibly with a sediment phosphorus 

inactivation treatment as a final lake restoration step. The BATHTUB model formulation for Missisquoi 

Bay was replaced in the spreadsheet model by the predictions from a more mechanistic phosphorus 

model for the bay (LimnoTech, Inc., 2012) that considered internal sediment-water phosphorus transfers 

and their long-term response to reductions in external phosphorus loads from the bay’s watershed. The 

long-term response of phosphorus concentrations in Missisquoi Bay was modeled using the following 

equation derived from LimnoTech, Inc. (2012, 2015): 

Y = 53.74 – 47.04 X 

Where: 

Y = predicted bay annual average total phosphorus concentration (μg/L) 70 years after watershed load 

reduction is achieved 

X = percent (as decimal fraction) watershed phosphorus load reduction from base period rates 

Note that while this equation predicts phosphorous levels in the Bay out to 70 years after load reduction 

is achieved, phosphorous levels in the Bay are predicted to decline abruptly and get very close to the 

phosphorus criteria within 10 years of watershed load reduction. The modeling then indicates a very 

slight continual decrease in Bay phosphorus concentrations over the next 60 years, with the phosphorus 

criteria being met in the vicinity of year 20 or 30. The modeling indicates that the internal sediment load 

is what necessitates such a substantial reduction from watershed sources (64% overall), but once the 

watershed source reduction is achieved, the Bay response is projected to be fairly rapid. 

Refer to Section 6.2.1 for more information on internal phosphorus loading. 

The spreadsheet lake model was initialized with phosphorus loading and hydrologic input data for the 

2001-2010 base period, aggregated as totals for each lake segment watershed. The base period 

phosphorus loads were partitioned by state/province using estimates provided by Tetra Tech (2015a). 

The Vermont base period phosphorus loads were further partitioned into the source categories listed in 

Table 4 based on delivered load estimates obtained from the Lake Champlain TMDL Scenario Tool 

(Tetra Tech, 2015c). 
Page | 24 

Before using the spreadsheet model to analyze the Vermont segments’ loading capacities and load 

reduction scenarios, phosphorus loads to each of the six New York segments were set equal to the total 

loading capacities defined in the 2002 Lake Champlain Phosphorus TMDLs for those segments 

(Vermont DEC and New York State DEC, 2002). This ensured that the New York allocations and 

attendant/current obligations on discharges were preserved and accounted for. Early in the process, EPA 

asked New York State DEC whether it wanted to update its portion of the TMDL at the same time. NY 

DEC declined to reopen its TMDL. Still, EPA provided the opportunity for New York to participate in 

the technical effort to develop the models and provided occasional technical briefings. As a result, the 

loading capacities and allocations specified for New York segments in the original 2002 TMDLs remain 

unchanged. The Vermont TMDL load reduction analysis assumed that the new total loading capacity 

for Missisquoi Bay would be shared on a 60/40% basis between Vermont and Québec, consistent with 

the 2002 Agreement between the Gouvernement du Québec and the State of Vermont Concerning 

Phosphorus Reduction in Missisquoi Bay (Québec & Vermont, 2002). 

Table 4. Source categories for Vermont phosphorus loads.

Source categories included in the wasteload allocation

Wastewater discharges

Stormwater from Developed land, excluding back roads

Stormwater from Back roads

Treated combined sewer overflow (Burlington Main Facility)

Agriculture production areas

Source categories included in the load allocation

Forest land 

Stream channel instability/erosion

Agricultural land

The lake spreadsheet modeling tool provided the ability to select from a menu of policy scenarios for 

each of the wasteload allocation source categories listed in Table 4, along with the load allocation 

categories of forestland and streambanks (see Appendix B for further details). Once the allocations for 

these source categories were specified for each segment, the load reduction percentages applied to the 

agricultural load allocation category for each lake segment watershed were adjusted until the predicted 

lake phosphorus concentrations attained the in-lake water quality criteria in each lake segment, with 

allowances for a 5% margin of safety in each lake segment and for the allocations for future growth in 

stormwater loads specified in Tables 7 and 8 in Chapter 6. 

The following approaches were used when applying reductions to the nonpoint source load allocation 

categories. 

1. In keeping with Vermont’s desire to apply basic measures uniformly across the basin, a 

minimum reduction in agricultural source loads was applied to all lake segment watersheds 

except for Burlington Bay, where no reduction was applied since agricultural nonpoint sources 

are minimal. 

2. Additional agricultural source load reduction percentages were applied equally to the South Lake 

B and South Lake A watersheds since both watersheds have common characteristics and 

influence the loads that would achieve the phosphorus criterion in the South Lake A segment. 
Page | 25 

3. Additional agricultural source load reduction percentages were applied equally to the Otter Creek 

and Main Lake watersheds to ensure consistent treatment of agricultural lands in the central part 

of the lake when determining the loads that would achieve the phosphorus criterion in the Main 

Lake. 

4. As described in Section 6.2, more modest reductions to the forest category (and to some extent 

the streambank category) were specified in many segments, as there was sufficient capacity to 

achieve most of the reductions needed in the agricultural category. More stringent reductions 

were required for these categories in the South Lake B and Missisquoi Bay segments. 

The application of these approaches resulted in the identification of the lake segment loading capacities 

and percent reductions described in detail in Section 6.2 and shown in Tables 7 and 8. 

The loading capacities and wasteload and load allocations are expressed in terms of annual loads. EPA's 

November 15, 2006 guidance entitled "Establishing TMDL 'Daily' Loads in Light of the Decision by the 

U.S. Court of Appeals for the D.C. Circuit in Friends of the Earth, Inc. v. EPA, et al., No.05-5015, 

(April 25, 2006) and Implications for NPDES Permits," recommends that TMDLs express allocations in 

terms of daily time increments, consistent with the D.C. Circuit’s ruling. This guidance also 

acknowledges that the decision of the U.S. Court of Appeals for the Second Circuit, NRDC v. 

Muszynski, 268 F.3d 91 (2nd Cir. 2001), established the controlling legal precedent for cases brought in 

the Second Circuit, which includes Vermont. In this decision, the Court held that the Clean Water Act 

does not require TMDLs to be expressed in terms of daily loads, but on remand the Court required a 

reasoned explanation for the choice of any particular non-daily load. EPA believes there is a reasonable 

basis for not including daily loads in these TMDLs. In-lake concentrations of phosphorus in Lake 

Champlain are not affected by variations in daily inputs because the lake has a long residence time of 

about two years. In evaluating the best expression of loading, EPA determined that an annual load 

allocation is the most appropriate measure of how phosphorus affects Lake Champlain. Neither daily 

nor seasonal loads as accurately represent the effect of phosphorus loading to the lake. In addition, 

Vermont’s WQS express the applicable phosphorus criteria in terms of annual mean total phosphorus 

concentrations. The expression of the loading capacity and wasteload and load allocations on an annual 

basis is therefore a logical and effective approach in this case. 

5.3 SEASONAL VARIATION

The Clean Water Act and implementing regulations require that a TMDL be established with 

consideration of seasonal variations. 

For Lake Champlain, critical conditions occur during the summer season when algae growth is more 

likely to interfere with uses. However, water quality in the lake is generally not sensitive to seasonal or 

short term phosphorus loading. With a water residence time of about two years (Vermont DEC and 

New York State DEC, 1997), the lake generally responds to loadings that occur over longer periods of 

time (e.g., annual loads). Accordingly, the in-lake numeric phosphorus criteria are expressed as annual 

mean values (see Table 2) and were selected to be protective of uses during all seasons, including the 

summer season. As described in Section 5.1.1, the Lake Champlain TMDLs were developed using a 

steady-state modeling approach that supported the establishment of annual average phosphorus 

allocations designed to achieve the phosphorus criteria. Meeting the phosphorus criteria on an annual 

basis automatically addresses any concerns due to seasonal variation, given that the criteria were 

established to be protective during all seasons. 
Page | 26 

5.4 CONSIDERATION OF CLIMATE CHANGE

EPA considered climate change to the extent feasible. As described in Section 5.1.2, EPA’s contractor, 

Tetra Tech, used the calibrated Lake Champlain SWAT model to project mid-century potential changes 

to phosphorus loads to the lake with six different precipitation and temperature projections derived from 

global climate change models. The model runs projected a possible overall average increase in 

phosphorus loading of approximately 30% for the period 2040 – 2070, assuming other factors remain 

the same. However, there are a variety of reasons why the results of this approach to projecting climate 

change impacts should be viewed with caution. First, as discussed in Vermont’s Phase 1 Implementation 

Plan, this projected increase likely overestimates the potential effect of climate change on the lake, 

because it does not take into account the fact that under these future scenarios the loading capacity of the 

lake will be larger due to increased lake volume and flushing rates that will accompany the increased 

flows projected by the model. Once the mitigating factor of increased flow volume is considered (as 

indicated by flow-weighted average tributary inflow concentrations) DEC calculated that the projected 

climate change scenarios would likely increase the effective phosphorus loads by about 15%. However, 

even that estimate may be overstated, since the modeling is driven by one, pessimistic greenhouse gas 

emissions scenario (A2), so the full range of emission scenarios is not represented. This means that the 

modeling projections rely on only the more extreme end of the range of possible climatic changes. An 

additional concern is the time factor: the analyses project phosphorus loads for the average of the period 

2040-2070, which is beyond the timeframe for which TMDLs are typically designed to be applicable, 

and the path of change between now and that far off point is not included in the analyses so it is not 

known whether phosphorus load increases might occur gradually or ramp up more abruptly as the midcentury point nears. Lastly, the future effects of climate change on in-lake biological and chemical 

processes in each of the lake’s individual (and very different) segments are not well understood. More 

research, such as that now being conducted by the University of Vermont for at least some lake 

segments, is needed to factor in the effects of possible in-lake changes. 

However, recognizing that the tributary loading analysis suggests that climate change could cause at 

least a modest increase in phosphorus loads to the lake, the State included measures in its Phase 1 

Implementation Plan that will minimize the phosphorus increases projected by the modeling. Examples 

of these measures include: a focus on agricultural and stormwater practices that infiltrate water and 

therefore minimize phosphorus runoff even during large, high intensity rainfall events; new agricultural 

practice requirements to stabilize soil (such as the gully stabilization requirements specified in Act 64); 

and stream corridor policies (such as those included in Act 110) that call for managing rivers and 

streams to achieve naturally stable stream conditions – conditions that will still perform well and 

minimize streambank erosion even with a changing climate. 

As described in Section 6.3, EPA allocated a 5% margin of safety (MOS) for each segment, to account 

for any lack of knowledge concerning the relationship between load and wasteload allocations and water 

quality. EPA considered whether it was necessary to increase the MOS above 5% to account for 

uncertainties related to potential climate change effects. Given that: 1) any increases in tributary 

phosphorus loads to the lake due to climate change are likely to be modest (i.e., 15%), 2) the State’s 

implementation strategy includes measures that will minimize possible increases due to climate change, 

and 3) the information at this time on the effects of climate change on in-lake processes is too 

preliminary to justify an increase in the MOS, EPA determined that it was not necessary to increase the 

MOS above the 5% already identified to account for possible, far-term effects of climate change. 
Page | 27 

CHAPTER 6: ESTABLISHING ALLOCATIONS

As described earlier, a TMDL can be described as the sum of the individual wasteload allocations 

(WLAs) for point sources, the load allocation (LAs) for nonpoint sources and natural background, and a 

margin of safety (MOS). Under the regulatory definition of WLA at 40 C.F.R. § 130.2(h) and EPA’s 

longstanding interpretation, point sources that discharge pollutants to waters of the United States and are 

subject to the jurisdiction of the National Pollutant Discharge Elimination System (NPDES) permit 

program are required to be assigned to the WLA. All other sources – both point sources and nonpoint 

sources – are included in the load allocation. States (and EPA) have the discretion to include point 

sources that are not subject to the NPDES permit program in the WLA portion of a TMDL, but they are 

not required to do so. (Wayland and Hanlon, 2002). This chapter describes the allocations that are 

established and how EPA developed them. It first details the general approach EPA took when 

considering the whole Vermont portion of Lake Champlain. It then describes how the general approach 

was applied to the different lake segments. 

EPA developed the allocations in close consultation with the State. Given the predominant role of 

precipitation driven runoff from certain point and nonpoint sources, the initial focus of the state agencies 

was on policies and programs to address these sources. Vermont committed early in the process to a 

Lake Champlain basin-wide approach to measures to control loads from developed land, agricultural 

lands, forested land and stream banks. In the modeling and spreadsheet analyses, the proposed measures 

were applied to the relevant land use type in each of the lake segments. EPA focused on the Wastewater 

Treatment Facilities to determine what reductions might be necessary to achieve the water quality 

standards, both lake-wide and within each segment. The sections that follow describe in detail the 

general approach to each part of the allocation. 

6.1 WASTELOAD ALLOCATION - GENERAL APPROACH

The phosphorus wasteload allocations in the Lake Champlain TMDLs for Vermont point sources are 

divided into two groupings. The first includes the Vermont Wastewater Treatment Facilities (WWTFs) 

whose discharges are authorized by Vermont’s NPDES permits. The second contains stormwaterrelated phosphorus sources in the general category of developed land sources, which includes 

stormwater runoff from sources such as municipal and residential areas, construction sites, state 

highways and back roads. This developed land category incorporates stormwater sources that require 

state NPDES permits; stormwater sources that are subject to other, non-NPDES, state permits; and other 

stormwater runoff from developed land that may not be subject to either type of state permit (such as 

stormwater from small land areas below the State's permitting threshold). More information on the 

approach to the stormwater portion of the WLAs is included below in Section 6.1.2. Information on the 

WWTF portion of the WLAs is included immediately below in Section 6.1.1. 

6.1.1 WASTEWATER TREATMENT FACILITIES WASTELOAD ALLOCATIONS

As detailed in Chapter 4, wastewater treatment facilities are not the dominant source of phosphorus to 

Lake Champlain as a whole, nor to any of the individual impaired lake segments. As noted above, the 

initial focus of the state agencies was on policies and programs to address the other sources of 

phosphorus loadings. Vermont’s Phase 1 Implementation Plan contained an explicit policy preference 

to not allocate any additional phosphorus reductions to the WWTFs. However, recognizing that the 
Page | 28 

final allocations might include reductions to WWTFs, the State requested EPA to apply the following 

principles: 

 Reductions in wastewater allocations should be targeted only to facilities in those lake segment 

watersheds where the currently permitted wastewater load represents a significant proportion of 

the total phosphorus load from all Vermont sources, and where wastewater upgrades would 

meaningfully reduce the phosphorus reduction burden placed on non-wastewater sources. 

 TMDL-based discharge permit limits should be defined as annual average phosphorus loading 

rates, rather than as concentration limits, in order to allow operational flexibility in attaining the 

limits. 

 New permit requirements should be implemented through compliance schedules that allow 

sufficient time for planning, budgeting, and engineering, and that advantage of cost-efficient 

opportunities to couple phosphorus upgrades with other planned facility construction projects. 

 Other forms of flexibility should be available to achieve the wasteload allocation in an optimally 

cost-effective manner, including phosphorus trading and integrated permitting. 

For each lake segment, EPA considered both the relative contribution of the WWTFs and the degree of 

reduction required for developed land and nonpoint sources. EPA determined that a targeted approach is 

appropriate -- reductions in allowable WWTF phosphorus discharges are a necessary component of the 

wasteload allocation in some, but not all, lake segments. 

In determining any necessary reductions, EPA established a baseline by looking first at the allowable 

discharges from each WWTF, that is, the amount of phosphorus the facility is authorized to discharge at 

design flow rates under the current NPDES permit. These permits reflect the wasteload allocations made 

in the 2002 TMDLs. 

For the Port Henry, Otter Creek, Malletts Bay, Northeast Arm, and Isle LaMotte segments, where the 

combined WWTF permitted discharges comprised less than 10% of the total phosphorus base load, and 

the developed land and nonpoint reduction needed was 30% or less, EPA’s WLAs for the WWTFs are 

the same WLAs for those facilities as in the 2002 TMDLs. This is reasonable because the WWTFs’ 

contributions are relatively small, and reductions at the WWTFs would not meaningfully change the 

reductions needed from non-WWTF sources. 

In the Main Lake, Shelburne Bay, Burlington Bay and St. Albans segments, the loads allocated to the 

WWTFs in the 2002 TMDL range between 16 and 97% of the segments’ base loads. EPA considers 

these to be significant contributions and has determined that further WWTF load reductions are 

appropriate in these segments. 

In the South Lake A and B and Missisquoi Bay segments, although the loads allocated to the WWTFs in 

2002 TMDL are less than 5%, of the base loads, the needed load reductions from developed lands and 

nonpoint sources exceed 50%. This percent reduction was considered high enough that EPA included 

the WWTFs in consideration for further reductions. 

Having established the lake segments that require WWTF reductions, EPA then considered which 

factors should be used to determine how the allocations would be set. EPA evaluated the annual loading 

impacts of these facilities and subdivided them into three groups. The first group includes facilities with 

design flow capacities less than 0.10 million gallons per day (MGD). These small facilities typically 

have simple treatment systems and discharge very small phosphorus loads. The second group consists 
Page | 29 

of facilities with design flows between 0.10 and 0.20 MGD. The third group comprises facilities with 

design flows greater than 0.20 MGD. These facilities are generally the most technically sophisticated 

treatment plants, contribute the largest portion of the WWTF load, and provide the best opportunities to 

achieve significant reductions. 

EPA then considered a range of phosphorus loads for each of the three groups. Given the minor 

contribution of the small facilities, EPA determined that further reductions would have negligible 

impact. Thus, they were given the same allocations as in the 2002 TMDLs. EPA next considered the 

range of phosphorus concentration limits that are achieved in practice at facilities throughout New 

England. A phosphorus discharge limit of 0.10 milligram per liter (mg/l) is currently considered to 

represent very good treatment practices. A discharge limit of 0.20 mg/l is routinely achievable at 

facilities with flow greater than 0.20 MDG, while a limit of 0.8 mg/l is achieved widely and is already 

required of all facilities with flow greater than 0.20 MGD in Vermont. 

After further consideration of the contributions of the WWTFs within each affected segment, EPA made 

total segment WWTF wasteload allocations equivalent to setting the phosphorus limit at 0.2 mg/l at 

design flow for the facilities with flow greater than 0.20 MGD and at 0.8 mg/l at design flow for the 

WWTFs in the middle-sized group. EPA determined that extra reductions that could be achieved by 

requiring a WLA that reflects a limit of 0.1 mg/l at the facilities with flow greater than 0.20 MGD were 

small relative to the nonpoint source contribution and Vermont felt that investments in nonpoint source 

reductions should be a higher priority. 

As described in more detail in Section 6.1.2, eleven facilities (Burlington Main, East and North, 

Enosburg, Fair Haven, Middlebury, Montpelier, Richford, Rutland, St. Albans and Vergennes) have 

combined sewers in at least part of their sewer system and are subject to DEC’s Combined Sewer 

Overflow (CSO) policy for reducing CSO discharges. EPA has not made separate allocations for 

phosphorus loads from CSOs except for the partially treated CSO at Burlington Main. For the 

remaining ten combined systems, as well as the two untreated CSOs in the Burlington Main combined 

system, EPA has included the load from CSOs in the developed land wasteload allocation for the 

applicable lake segment watershed, as described in Section 6.1.2. 

Consistent with the 2002 TMDLs, individual wasteload allocations are specified for each WWTF 

discharge to Lake Champlain or to a lake tributary. Since EPA has evaluated the WWTF allocations at 

the segment level and then made assignments to individual facilities, EPA is providing in these TMDLs 

an option for Vermont to make changes to the individual WWTF allocations within a lake segment as 

long as the adjusted combined allocations do not exceed the total WWTF allocation for that segment.

The Main Lake and the relatively small and closely connected Burlington Bay and Shelburne Bay 

segments may be treated as a single lake segment for the purpose of wastewater load reallocations, since 

loads from each of these segment’s watersheds have an approximately equal impact on phosphorus 

concentrations in the critical Main Lake segment. If reallocations are to be made, DEC will follow its 

established Wasteload Allocation Process (VT Agency of Natural Resources, 1987 or any subsequent 

revision), which requires public notice and at least one public meeting. DEC must provide written 

notification to EPA if and when it commences proceedings under the Wasteload Allocation Process to 

reallocate WWTF loads within any Lake Champlain segment. 

When implementing the TMDLs through NPDES permits, EPA acknowledges and supports DEC’s

commitment to employ flexible approaches including: 
Page | 30 

 Expressing effluent phosphorus limits in permits as total annual mass loads. 

 Providing a period of time for optimization to be pursued and the corresponding load reduction 

results to be realized, and then commencement of the process to upgrade phosphorus treatment 

facilities will be required when actual phosphorus loads reach 80% of the TMDL limits.

(LaFlamme, 2016). 

 Establishing phosphorus compliance schedules in discharge permits that allow adequate time for 

planning, engineering and municipal budgeting. 

 Providing other forms of flexibility that support achieving the wasteload allocations in an 

optimally cost effective manner, including phosphorus trading and integrated planning and 

permitting. 

The specific application of this approach within each segment is described in the next section. The net 

effect of the WWTF WLAs is to reduce the allowable annual WWTF load from 55.8 metric tons to 32.3

metric tons, a 42% reduction compared to the WLAs established in the 2002 TMDL. 

6.1.1.1 SEGMENT-SPECIFIC WWTF ALLOCATIONS

This section describes how the facility specific WWTF allocations were developed for each lake 

segment. Segments with similar characteristics are grouped together. Consistent with the 2002 TMDLs, 

individual wasteload allocations are specified for each WWTF discharge to Lake Champlain or to a lake 

tributary. The facility-specific WWTF allocations are listed in Table 9 in the summary section at the end 

of this chapter. 

South Lake A & B 

The South Lake is shallow and narrow. It is divided into segments A (northern of the two) and B for 

water quality purposes. The phosphorus load is dominated by nonpoint sources; stormwater runoff from 

agricultural and forested lands contribute approximately 75% of the load. There are six WWTFs in the 

South Lake, three with flow greater than 0.20 MGD and three with flow less than 0.10 MGD. 

Consistent with the allocation approach described in Section 6.1.1, the three small facilities (Benson, 

Orwell and West Pawlet) were given the same allocations as in the 2002 TMDLs. The three larger 

facilities are all in South Lake B. At current permit limits, which are based on the 2002 WLAs, they 

account for only six percent of the total loading capacity for the segment. Although the nonpoint source 

reductions required in South Lake segments are high, EPA carefully evaluated the planned non-WWTF 

measures with the BMP Scenario Tool (described in Section 5.1.3) and determined that the expected 

reductions can and will be met. As described further in Section 7.1, EPA has determined that there is 

reasonable assurance that the modeled reductions will be achieved. EPA therefore has not required 

additional reductions at the three larger WWTFs (Castleton, Fair Haven and Poultney) and instead has 

established the same allocations as in the 2002 TMDL. 

Port Henry, Otter Creek, Malletts Bay, Northeast Arm, Isle LaMotte 

These five segments are generally the closest to meeting the applicable phosphorus criteria. There are 

no WWTFs discharging to the Port Henry and the Northeast Arm segments. In the Otter Creek, Malletts 

Bay and Isle LaMotte segments, the combined WWTF loads at current permit limits (which reflect the 

2002 WLAs) comprise less than 10% of the total phosphorus loading capacity and the developed land 
Page | 31 

and nonpoint reduction needed is 30% or less. Section 7.1 describes EPA’s determination that there is 

reasonable assurance that these reductions will be achieved. EPA therefore has not required additional 

reductions at the WWTFs in these segments and EPA has assigned the WWTFs the same wasteload 

allocation as in the 2002 TMDLs. The facilities are: Alburgh, Brandon, Fairfax, Hardwick, 

Jeffersonville, Johnson, Middlebury, Milton, Morrisville, Otter Valley Union High School, Pittsford, 

Pittsford Fish Hatchery, Proctor, Rutland City, Salisbury Fish Hatchery, Shoreham, Vergennes, 

Wallingford, West Rutland, and Perrigo Nutritionals. 

Main Lake, Shelburne Bay and Burlington Bay 

The Main Lake, Burlington Bay and Shelburne Bay segments generally receive inputs from the most 

developed parts of the Vermont portion of the Lake Champlain basin. EPA views the Burlington Bay 

and Shelburne Bay segments to be part of the larger Main Lake watershed, since loads from each Bay 

segment have an approximately equal impact on phosphorus concentrations in the critical Main Lake 

segment. The currently permitted WWTF contributions in these segments ranges from 16 to 97% of the 

total segment base load and should be reduced. EPA has made WWTF waste load allocations 

equivalent to setting the phosphorus limit at 0.2 mg/l at design flow for the 17 facilities with flows 

greater than 0.20 MGD. Those facilities are: Barre City, Burlington East, Burlington Main, Burlington 

North, Essex Junction, Hinesburg, Global Foundries, Shelburne #1 and #2, Montpelier, Northfield, 

Richmond, South Burlington Airport Parkway, South Burlington Bartletts Bay, Stowe, Waterbury and 

Winooski. Seven of these facilities have recently made upgrades or have the ability to make process 

improvements that would enable them to meet permit limits consistent with the new allocations without 

major construction upgrades. These include, Essex Junction, South Burlington Airport Parkway, 

Shelburne #1 and #2, South Burlington Bartlett Bay, Stowe, and Waterbury. EPA assigned WLAs for 

the two WWTFs in the middle-sized group (Plainfield and Williamstown) equivalent to setting the 

phosphorus limit at 0.8 mg/l at design flow. EPA assigned the two facilities with flows less than 0.10 

MGD (Cabot and Marshfield) the same WLAs as in the 2002 TMDLs. There are two exceptions to this

general approach. The 2002 WLAs for Weed Fish Culture Station and Burlington Electric were lower 

than a limit equivalent to 0.2 mg/l at design flow. The more stringent 2002 allocations have been 

retained and are already reflected in the permit limits for these facilities.

St. Albans Bay 

The St. Albans Bay watershed drains approximately 50 square miles of agricultural, forested, and urban 

land into the relatively shallow St. Albans Bay. The terrain is fairly flat and contains some of the richest 

farmland in the State. Agriculture, forested lands, and streambank instability account for 73% of the 

annual phosphorus loading. There are two WWTFs that discharge to this segment. Their currently 

permitted load accounts for 27% of the total loading capacity, and should be reduced. Consistent with 

the general approach, the St. Albans WWTF was assigned a load equivalent to setting the phosphorus 

limit at 0.2 mg/l at design flow. The Northwest State Correctional Institution has flow less than 0.10 

MGD was assigned the same allocation as in the 2002 TMDL. 

Missisquoi Bay 

Missisquoi Bay, although much larger in surface area and shared with the province of Quebec, shares 

some important features with St Albans Bay. It is shallow, and dairy farming dominates the phosphorus 

loading from the watershed. Agricultural and forested lands account for 91% of the land use in the 

Vermont portion of the basin. Agricultural and forested lands, and streambank instability, contribute 
Page | 32 

88% of the base load of phosphorus to the bay. Eight WWTFs discharge to Missisquoi Bay, five with 

flow greater than 0.20 MGD, two with flow less than 0.10 MGD and one in the middle group. 

Although the currently permitted WWTF loads account for 8.5% of the total loading capacity for the 

segment, EPA found that there were not sufficient non-WWTF measures that could meet water quality 

standards without reductions at the treatment plants. Consistent with the overall allocation approach, 

EPA assigned the five larger WWTFs (Enosburg Falls, Richford, Rock Tenn, Swanton and Troy/Jay) 

WLAs equivalent to setting the phosphorus limits at 0.2 mg/l at design flows. The Troy/Jay facility has 

already been upgraded and its current permit is already consistent with this new WLA. EPA assigned the 

one facility in the mid-size group (N. Troy) a WLA equivalent to setting the limit at 0.8 mg/l at design 

flow. Consistent with the overall approach, EPA assigned one of the small facilities (Sheldon Springs) 

the same allocations as in the 2002 TMDL. For the other (Newport Center), the 2002 allocation was 

based on assumptions that have proved to be operationally incorrect. EPA set the new allocation for 

Newport Center using assumptions similar to the other small facilities that are generally retaining the 

2002 allocation (equivalent to a phosphorus limit of 2.0 mg/l at design flow). 

6.1.1.2 FUTURE GROWTH IN WASTEWATER LOADS

EPA’s definitions of wasteload and load allocations refer to both future, as well as existing, point and 

nonpoint sources (40 C.F.R. 130.2(g) and (h)). The Vermont Wasteload Allocation Process requires that 

future population growth be considered in establishing wasteload allocations. Capacity for future 

growth in wastewater flows is built into the design and permitting of wastewater treatment facilities, and 

future growth capacity is therefore included in the individual facility wasteload allocations listed in 

Table 9. 

The allowance made within the TMDLs’ wasteload allocations for future increases in wastewater flows 

and phosphorus loads can be assessed by comparing the permitted flows and the phosphorus wasteload 

allocations with current discharge rates. The 2001-2010 average base load of phosphorus discharged 

from all Vermont WWTFs was 24.6 metric tons per year (mt/yr). This comprises 76% of the TMDLs’

combined WWTF wasteload allocation of 32.3 mt/yr. 

6.1.2 DEVELOPED LAND WASTELOAD ALLOCATIONS

EPA interprets 40 C.F.R. § 130.2(h) to mean that allocations for point source discharges subject to the 

NPDES permit program must be included in the wasteload allocation portion of the TMDL.2

(Wayland 

and Hanlon, 2002). In addition to wastewater treatment facility discharge permits, the NPDES program 

includes the following other permit types in Vermont. 

- Phase 2 municipal separate storm sewer system (MS4) permits 

- Permits issued for stormwater discharges from certain parcels based on Residual Designation 

Authority (RDA) 

 

2 Point source discharges that are not regulated by the NPDES program may be included in either the 

WLA or the LA portion of the TMDL. (Id.) 
Page | 33 

- Certain individual stormwater permits 

- Discharge permits which authorize combined sewer overflows (CSOs) 

- General construction site stormwater permits (CGP) 

- General multi-sector industrial stormwater permits (MSGP) 

- Concentrated Animal Feeding Operation (CAFO) permits 

Unlike continuous discharges from WWTFs, stormwater runoff is driven by brief and intermittent 

rainstorms or snowmelt events, and is highly variable in quantity and phosphorus content from one event 

to the next. Monitoring phosphorus loads in stormwater runoff is technically difficult and expensive 

because of the variable nature of these events, making it difficult to assign and enforce facility-specific 

effluent limits. Data are not available from CSOs (other than the partially treated CSO discharging to 

Burlington Bay) and stormwater outfalls to characterize their individual phosphorus loads for the 

purpose of the TMDLs. Phosphorus loads from construction sites are especially challenging to monitor 

or estimate. Because of these monitoring difficulties and the geographic scale of the Lake Champlain 

Phosphorus TMDLs, it was not technically feasible to separate the allocations for stormwater sources 

requiring NPDES permits from the allocations for other stormwater nonpoint and non-NPDES regulated 

point source categories based on land use. EPA guidance states that NPDES-regulated stormwater 

discharges may either be expressed as individual wasteload allocations (for each source, for example) or 

as a single categorical allocation for all NPDES-regulated stormwater discharges when data are 

insufficient to assign each source an individual wasteload allocation.(Wayland and Hanlon, 2002; 

Sawyers and Best-Wong, 2014). The 2002 guidance also explains that stormwater discharges from 

stormwater point sources not currently subject to NPDES regulations may also be included in the 

wasteload allocation portion of a TMDL. 

The NPDES stormwater-related phosphorus sources listed above (except for CAFOs and a discharge 

from a partially treated CSO facility, which are addressed by separate WLAs as discussed below) are 

included in the general aggregate WLA category of developed land sources. This category also includes 

runoff from non-NPDES regulated point source and nonpoint sources such as residential areas, small 

construction sites, and back roads, since it is not technically feasible to distinguish loads among the 

various sources and accurately separate the allocations into WLAs and LAs. In addition, some 

stormwater discharges from developed land may in the future become subject to NPDES permits 

(through the exercise of residual designation, for example), and including the loads within the WLA 

now is reasonable and consistent with EPA’s guidance discussed above. Phosphorus loading from 

developed land was estimated using the SWAT model, as described in Chapter 5. The WLA portion of 

these TMDLs includes a category for developed land sources, while recognizing that this category 

incorporates both point sources that require NPDES permits, and point and nonpoint sources that do not 

require such permits. An explanation of why EPA chose to establish an aggregate WLA for developed 

land sources is included below. 

Available Information on Phosphorus Loads in Vermont Stormwater and CSO Permitted Discharges in 

the Lake Champlain Basin 

EPA guidance encourages the establishment of separate WLAs for stormwater permit categories and 

even individual dischargers if sufficient information exists on phosphorus loads associated with each 
Page | 34 

NPDES permit category and/or discharger. (Sawyers and Best-Wong, 2014). EPA carefully reviewed 

available data pertaining to the permitting categories listed above. As shown in Table 5, EPA found that 

sufficiently detailed spatial and pollutant loading information is not available for any of the permit 

categories. Note that a category for future stormwater permits is also included in Table 5 because EPA 

is aware that Vermont intends to establish several new permit categories in the near future, one or more 

of which may require NPDES permits, as indicated in the revised Phase I Implementation Plan and in 

Act 64. 

The primary spatial data set that is available and relates to stormwater permitting is the “urbanized area” 

coverage. Municipal systems within the “urbanized area” are required to obtain MS4 permit coverage. 

In cases of highly urbanized municipalities, it may seem reasonable to assume that the “urbanized area” 

could be used to provide a reasonable approximation of the MS4 area. However, not all areas within the 

“urbanized area” are served by the MS4 drainage systems, as some areas are served by private storm 

sewer systems and other areas are served by natural drainage networks (i.e., stormwater flows directly 

into stream systems that are not part of the MS4 network). 

No pollutant loading-related information is available from MSGP facilities, and given the varied nature 

of the facility types, area covered, and exposure practices, there is no way to estimate the loading at the 

present time. Also, since the MSGP doesn’t cover stormwater from parking lots and roofs outside of 

areas of industrial activity, any MSGP load estimates would not reflect total loads from the entire 

operation. 

Another factor for consideration in setting appropriate stormwater related WLAs is that the sites covered 

by the RDA, MSGP, and CGP permits are located both within and outside of the “urbanized area.” This 

factor is important for two primary reasons: 

1. It further limits the use of the “urbanized area” as a surrogate for the MS4s since the area 

includes other permit categories; and 

2. The “urbanized area” does not encompass all stormwater permitted discharges so that the 

“urbanized area” cannot be used as a “catch all” for all stormwater permit categories.

A review of available information related to Vermont CSO discharges to Lake Champlain indicates that 

there is insufficient information to estimate annual phosphorus loads from untreated CSOs. However, 

average annual phosphorus loads have been calculated for the only CSO treatment facility in the Lake 

Champlain basin – the facility located in Burlington. Continuous simulation hydrologic/hydraulic 

models have not been developed for the other, untreated combined sewer systems in Vermont. 

Consequently, there is not a reliable means for calculating annual discharge volumes for the untreated 

CSOs, which are needed to calculate loads. 

Without estimates of loads, mass based WLAs are not possible for the untreated CSOs. The current plan 

is to have all untreated CSOs be in compliance with the level of control specified in the CSO policy, 

which is now being updated and converted to a rule. Quantifying the actual phosphorus load reduction 

associated with bringing the untreated CSOs into compliance is not possible at this time. However, 

these sources are accounted for in the TMDLs. The effects of CSO discharges were captured in the 

baseline tributary monitoring data used in both the BATHTUB and SWAT modeling steps and the 

phosphorus loads from these discharges are included in the developed land allocations. The TMDLs call 

for reductions in the amount of phosphorus entering these CSOs - and therefore discharged through CSO 

outfalls - through the developed land allocations described below. Since there are not separate 
Page | 35 

allocations for stormwater discharging from CSOs in compliance with the CSO policy, the State must 

account for these stormwater phosphorus loads within the allocations for developed land. While CSO 

discharges include a wastewater component of phosphorus as well as a stormwater component of 

phosphorus, both components are driven by (and can be controlled by) the magnitude of stormwater 

runoff entering the systems. 

Table 5: Summary of Assessment for Characterizing Loads for Stormwater, CSO, and Agricultural 

Production Area Permitting Universe for the Lake Champlain TMDL

NPDES Permit Category

Can Load 

be 

Calculated 

for 

TMDL?

Basis for Determining whether Loads can be Calculated

MS4 No

Actual drainage areas for the 15 MS4 systems are not 

sufficiently mapped. The mapping of urbanized areas includes 

non-MS4 area as well as area covered by some of the RDA, CGP,

and MSGP permits. 

Residual Designation Tier 1 & 

2

(> 1 impervious acre)

No

Spatial data exists for the sites but the scale and resolution of 

the spatial data used in the SWAT model are not sufficient to 

provide estimates for individual parcels. More detailed site 

level data are needed.

Residual Designation Tier 3

( < 1 impervious acre) No

Spatial data exists for the sites but the scale and resolution of 

the spatial data used in the SWAT model are not sufficient to 

provide estimates for individual parcels. More detailed site 

level data are needed.

Future Stormwater Permits No Scope of potential future permits is not yet determined. 

Construction General Permit No Spatial data of areas subject to CGP are not available. 

Multi-Sector General Permit No Spatial data of areas subject to MSGP are not available. 

Communities with Untreated 

CSO Discharges No Estimates of discharge flows from active untreated CSO are nonexistent. 

Treated CSO discharge Yes DMR flow and water quality data were used to quantify annual 

phosphorus loads to LC.

Agricultural Production Area 

Discharges Yes

SWAT-generated load data were used to quantify the existing 

loads from production areas

Estimates of annual phosphorus loads are available for Burlington’s CSO treatment facility. Therefore, 

a mass based WLA has been established for this discharge, as shown in Table 7. The WLA requires an

11.8% reduction below existing loading levels. This WLA was established by assuming the same level 

of source reduction to the impervious area draining to the CSO treatment facility as was assumed for the 

portion of Burlington draining directly to the Bay (i.e., the developed land WLA for Burlington Bay) –

see discussion in the following paragraphs for how the developed land WLAs were established. 

For the reasons discussed above, EPA has established WLAs for developed land within each lake 

segment (see Table 7). The developed land WLAs set overall allocations and reduction targets for all 
Page | 36 

developed land within each lake segment. To comply with the WLAs, the permitting authority (VT 

DEC) will need to demonstrate that the combined effect of the mix of permits issued will achieve 

enough phosphorus reduction to meet the allocation. Some permit categories are better suited than 

others at achieving phosphorus reductions through retrofit requirements. One benefit of establishing 

overall WLAs for developed land is that it provides a certain amount of flexibility to the permitting 

authority – DEC has the opportunity to consider the totality of the stormwater permitting programs as it 

designs the most effective program to achieve the overall load reduction. However, it will be important 

for DEC to establish a phosphorus load tracking and accounting system to guide permit requirements 

and eventually assess permit and WLA compliance. 

For municipalities with municipal stormwater, CSOs and wastewater facilities, EPA supports DEC’s 

commitment to employ flexible approaches to permitting that support achieving the wasteload 

allocations in an optimally cost effective manner, including phosphorus trading and integrated planning 

and permitting. 

Discharges of manure, litter, and process wastewater from CAFOs are subject to NPDES permits and, 

therefore, require wasteload allocations. Vermont issued a general permit for medium CAFOs in 2013 

but to date, there are no CAFOs currently covered by the permit. Large and small CAFOs would receive 

individual permits and the State has not permitted any at this time. Any NPDES permits issued by DEC 

for CAFOs would prohibit discharges of manure, litter, and process wastewater except when 

precipitation causes an overflow during greater than 25 year/24 hour storm events. In anticipation of the 

possibility that a number of CAFOs may be permitted in the future, the TMDL includes allocations for 

all agricultural production areas in the Champlain Basin (based on data available in 2013, as described 

in Tetra Tech, 2015b) on the wasteload allocation side of the TMDL equation. This is similar to the 

approach described above for developed land stormwater WLAs, in that the agricultural production 

areas WLAs cover discharges from both NPDES-regulated and non-NPDES regulated agricultural 

production areas. The allocations were determined by applying an 80% reduction to the SWATgenerated base loads for production areas (referred to as “farmsteads” in the SWAT modeling and 

scenario tool reports). The 80% reduction level was used to approximate the reduction estimated to be 

feasible with state-of-the-art barnyard management BMPs that will be required as part of the State’s 

commitment to inspections and required BMP implementation in addition to CAFO inspections. This 

reduction level is also consistent with what would be achieved by CAFOs subject to NPDES permit 

requirements, as described above. The remaining 20% of the base load was used as the wasteload 

allocation. This allocation was totaled for each lake segment watershed to establish an overall wasteload 

allocation for agricultural production areas for each lake segment watershed, as shown in Table 7. Note 

that any phosphorus runoff from fields, including runoff from land application of manure, litter, and 

process wastewater by CAFOs consistent with nutrient management plans developed in accordance with 

CAFO requirements, will remain part of the load allocation as an agricultural stormwater discharge see 

40 CFR § 122.23(e)), which is excluded from the definition of “point source” (see 40 CFR § 122.2). 

6.1.2.1 SETTING THE WLA LEVELS FOR DEVELOPED LAND

The approach to setting the developed land WLAs varied by lake segment. For Missisquoi Bay and 

South Lake B segments, where the achievement of the total loading capacity will be extremely 

challenging, EPA used the scenario tool to simulate a level of stormwater treatment considered 

aggressive but still feasible to accomplish given EPA’s experience with other watersheds in New 
Page | 37 

England.3 For South Lake B, the WLA was based on reductions that could be achieved with stormwater 

retrofits equivalent to the combination of 85% of unpaved road segments connected via direct surface 

flow to Lake Champlain or its tributaries, and 25% of other impervious area (commercial, industrial, and 

residential land uses, excluding area above class D soils), and 25% of paved roads on A and B soils. For 

Missisquoi Bay, the WLA was based on retrofits to 100% of unpaved road segments connected via 

direct surface flow, and retrofits to 60% of other impervious area (excluding impervious area above 

class D soils) and 50% of paved roads above A and B soils. 

For the Otter Creek, Main Lake, Shelburne Bay, Burlington Bay, Malletts Bay and St. Albans Bay 

segments, where less overall reduction is needed (and where the Scenario Tool indicates more 

opportunities for reduction exist than are needed across all sector sources), the developed land WLAs 

were based on a more moderate level of stormwater retrofits. These WLAs were set based on reductions 

achievable through retrofitting the equivalent of the combination of 13% of non-road impervious area 

above A and B soils, 25% of paved roads on A and B soils, and 65% of unpaved road segments 

connected via direct surface flow. 

Four small lake segment watersheds (South Lake A, Port Henry, Isle LaMotte and Northeast Arm) 

include so little developed land that phosphorus reductions from the developed land sector can generally 

only be influenced by treatment of roads rather than other impervious cover. Therefore, the WLAs for 

these segments were set based on the same level of road retrofits as described immediately above (i.e., 

65%), but without any retrofits to non-road impervious cover beyond that needed to meet the future 

growth allocations (see next section for a description of how the future growth allocations were derived 

and factored into the wasteload allocations). Refer to Appendix B for a more detailed description and 

matrix of the extent and type of stormwater retrofits simulated for each lake segment watershed. The 

simulations also took into account phosphorus reductions associated with the Vermont restrictions on 

phosphorus lawn fertilizer use, as described in Tetra Tech (2015c). 

6.1.2.2 FUTURE GROWTH FROM DEVELOPED LAND

DEC developed estimates for future growth of impervious area over the next 20 years based on past 

development trends, a few local assessments, and the number of past construction permits. The analysis 

considered new phosphorus loads from both jurisdictional development (future development subject to 

stormwater permits) and sub-jurisdictional development (future growth associated with smaller 

developments not currently subject to stormwater permits). The analysis assumed a high level of 

phosphorus treatment for future jurisdictional development (based on provisions in the new Vermont 

stormwater manual currently in preparation) and very little phosphorus control for sub-jurisdictional 

development. EPA used the results of this analysis to establish future growth allocations for each lake 

segment watershed as shown in Table 7. These allocations were subtracted from the initial developed 

land wasteload allocation (as established using the procedures described above) for each lake segment. 

The DEC future growth analysis (October 8, 2015) is included in Appendix A. 

 

3

 EPA updated the scenario tool simulations for all lake segments during the period between the release of the August 2015 

proposed TMDLs and final TMDL issuance. The level of retrofits presented in this section reflects adjustments stemming 

from the updated simulations. 
Page | 38 

6.2 LOAD ALLOCATION

The TMDL load allocations apply to nonpoint sources in the categories of agriculture, forest land, and 

streambank erosion, as well as to any non-NPDES regulated point sources to the extent they exist (EPA 

is not specifically aware of such sources). The approach to setting the load allocations varied by lake 

segment. For Missisquoi Bay and South Lake B segments, where the achievement of the total loading 

capacity will be extremely challenging, EPA’s Scenario Tool indicated that the maximum amount of 

BMP implementation possible within the watersheds will be necessary to meet the total loading capacity 

(in combination with applicable WLAs). Therefore, EPA set the allocations based on phosphorus 

reductions simulated to result when a very extensive suite of management practices are implemented 

within each sector.4 For Missisquoi Bay, the allocations reflect a 68% reduction from streambanks, a 

50% reduction from forest lands, and an 83% reduction from agricultural sources. For South Lake B, 

where a little less overall reduction is needed, the allocations reflect a47% reduction from streambanks, 

a 40% reduction from forest lands, and a 63% reduction from agricultural sources. The streambank 

reduction is greater in the Missisquoi Bay watershed because of the greater amount (and higher erosion 

status) of unstable stream reaches in that watershed. 

For most of the remaining lake segments, where less overall reduction is needed (and where the 

Scenario Tool indicates that more opportunities for reduction exist than are needed across all sector 

sources), the allocations were set as follows: EPA first analyzed how much reduction could be achieved 

from all sources of phosphorus, and then established the wastewater treatment plant and developed land 

WLAs as described in Section 6.1 for each segment. EPA then established LAs for agriculture, 

streambanks and forests to achieve the remaining needed reductions. The South Lake A, Port Henry, 

Burlington Bay, Northeast Arm and Isle LaMotte segments each have relatively small amounts of 

unstable stream corridors and were not broken out separately due to modeling constraints. Any 

streambank erosion discharges in these segments are captured in the developed land, agriculture and 

forest allocations and will be addressed by measures that will reduce erosion within the stream corridors.

Note that virtually all of the land in the Burlington Bay watershed is in the developed land category, so 

there are no load allocations for Burlington Bay. 

As a general procedure, EPA set the forest and streambank loads in all segments first, and then set the 

agriculture loads based on the remaining capacity, taking into account the amount of reduction found to 

be achievable from agricultural sources using the Scenario Tool. Given that there is less detailed 

information on the forest load sources and magnitudes available from the SWAT modeling work, EPA 

chose to rely on only a modest reduction (5%) from the forest sector for the lake segment watersheds 

where less overall reduction is needed. However, as noted above, in Missisquoi Bay and South Lake B, 

the forest reduction goals were set at 5060% and 40% respectively, due to the large reductions needed in 

these segments and the relatively large phosphorus loads from forest lands in these segment watersheds. 

Streambank allocations were set at a moderate reduction level for most of for the large lake segment 

watersheds other than Missisquoi Bay and South Lake B. Reductions from streambanks are important, 

but are expected to take many decades to occur, as the restoration strategy depends in part on actions 

that will facilitate natural stream evolution processes. Note that the scale of the SWAT modeling effort 

did not permit the generation of streambank loading estimates for many of the smaller lake segment 

 

4

 EPA updated the simulations for all lake segments between release of the August 2015 proposed TMDLs and final TMDL 

issuance. The allocations presented in this section reflect the adjustments stemming from these scenario updates. 
Page | 39 

watersheds dominated by direct drainage to the lake. This precluded EPA from establishing separate 

streambank load allocations for these segments. As noted above, for South Lake B, a higher level of 

reduction from streambanks was established, based on stabilization of reaches with phosphorus loads 

above the 25th percentile. For Missisquoi Bay, given that nearly all reaches are unstable (not at 

equilibrium conditions), the streambank allocation was set at a level that assumed phosphorus reduction 

from all reaches. 

The agricultural load allocations were then set based on the remaining loading capacity available, with 

consideration of the total amount of reduction found to be achievable in each sector. As noted in Section 

5.2, consistent with Vermont’s desire to apply basic measures uniformly across the basin, a minimum 

reduction in agricultural source loads was applied to all lake segment watersheds except for Burlington 

Bay, where no reduction was applied since agricultural sources are minimal. Beyond the 20% minimum, 

agricultural source load reduction percentages were applied equally to the South Lake B and South Lake 

A watersheds since both watersheds have common characteristics and influence the loads that would 

achieve the phosphorus criterion in the South Lake A segment. Additional agricultural source load 

reduction percentages were applied equally to the Otter Creek and Main Lake watersheds to ensure 

consistent treatment of agricultural lands in the central part of the lake when determining the loads that 

would achieve the phosphorus criterion in the Main Lake. For more information on the bases for the 

estimates of phosphorus reductions achievable in each sector, refer to Appendix B. 

6.2.1 INTERNAL SEDIMENT CONSIDERATIONS – ST. ALBANS BAY AND MISSISQUOI 

BAY

One challenge inherent in lake phosphorus modeling efforts is to characterize the transfer of phosphorus 

between the water column and the bottom sediment. A certain portion of the phosphorus in particulate 

form typically settles out of the water column and becomes part of the bottom sediment. In addition, 

depending on the amount of phosphorus stored in the bottom sediment and the chemical characteristics 

of the water/sediment interface, some phosphorus can be released back into the water column. The 

modeling took this exchange of phosphorus with the bottom sediment into account for all segments as 

part of the model calibration step, as described in Tetra Tech (2105a). Whether the bottom sediment acts 

as either a source or a sink for phosphorus, the transfer is factored into the model’s indication of the 

reductions needed from watershed sources to meet the water quality targets in each segment. 

In 10 out of 12 lake segments, much more phosphorus is settling out into the bottom sediments than is 

being returned. In the other two segments, St. Albans Bay and Missisquoi Bay, site specific studies 

(referenced below) have found that a large internal load from the sediment will persist for many years. 

Additional information on the sediment/phosphorus dynamics in both St Albans Bay and Missisquoi 

Bay is included below.

Studies have found that St. Albans Bay and Missisquoi Bay have accumulated substantial amounts of 

phosphorus in the bottom sediment. This stored phosphorus represents an additional source of 

phosphorus for these segments, expected to be released to the water column over time. 

The 2002 Lake Champlain Phosphorus TMDL included a discussion of the internal phosphorus loading 

problem in St. Albans Bay. The Bay has been subject to excessive phosphorus loading over a period of 

many decades, resulting in severe algae blooms during the summer. A major phosphorus removal 

upgrade of the St. Albans City Wastewater Treatment Facility in 1987 significantly reduced phosphorus 
Page | 40 

loading to the Bay. However, phosphorus concentrations in the Bay did not decline as expected after the 

treatment plant upgrade. Internal phosphorus loading from phosphorus stored in the Bay’s sediments, 

along with ongoing, excessive phosphorus loading from the Bay’s watershed, were found to be 

responsible for the continued high phosphorus concentrations in St. Albans Bay. 

The phosphorus modeling analysis used to derive the total loading capacity for St. Albans Bay in the 

2002 Lake Champlain TMDL assumed that net internal loading to the Bay would decline to zero over 

time once external watershed loads were reduced. This assumption was considered to be conservative 

since in most other Lake Champlain segments, much more phosphorus is being transferred to the bottom 

sediment than is being returned to the water column. 

To test the assumption that internal loading would decline within a reasonable time period without inlake intervention, DEC sponsored research on the phosphorus content of St. Albans Bay sediments and 

the chemical mechanisms that lead to its release into the water column. The study (Druschel et al., 2005) 

concluded that there remains a substantial reservoir of phosphorus in the sediments of St. Albans Bay 

which has the potential to contribute phosphorus to the water in the Bay for a long period of time into 

the future. 

In light of these findings, DEC initiated a “Phase 1 Feasibility Study for the Control of Internal 

Phosphorus Loading in St. Albans Bay” which was completed by ENSR Corp. (ENSR, 2007). The study 

evaluated several alternative methods for controlling internal loading in the Bay as to technical 

feasibility, cost, and environmental impacts. Methods evaluated included circulation, dredging, chemical 

phosphorus inactivation in the sediments, and tributary dosing. 

Phosphorus concentrations in the tributary streams draining to St. Albans Bay are among the highest in 

the Lake Champlain basin because of uncontrolled nonpoint sources in the Bay’s watershed. If these 

external phosphorus sources are not adequately reduced before an in-lake treatment takes place, the 

longevity and effectiveness of an internal treatment would be seriously compromised. The 2002 Lake 

Champlain TMDL stated that progress in reducing nonpoint source phosphorus loading to St. Albans 

Bay should be a prerequisite before any in-lake treatment is attempted to control internal phosphorus 

loading. The Phase 1 Feasibility Study reiterated this strong recommendation. EPA concurs with this 

recommended approach, and expects that the load and wasteload allocations applying to the watershed 

sources (shown in Table 7) will be achieved prior to controlling internal loading sources. 

Based on the extensive research and modeling done on internal phosphorus dynamics in St. Albans Bay, 

it is unlikely that control of external watershed phosphorus loading sources alone will result in the full 

attainment of water quality standards in the Bay. An in-lake treatment to control internal phosphorus 

loading will likely be necessary as a final step in the restoration of the Bay. Given that such an in-lake 

treatment approach is expected to be feasible and implemented if necessary, EPA did not establish a 

separate sediment load allocation for St. Albans Bay and assumed a net sedimentation balance, similar 

to that of other Lake Champlain segments without excessive internal loading. 

The internal sediment situation in Missisquoi Bay is somewhat different. Similarly to St. Albans Bay, 

recent detailed studies of phosphorus dynamics in Missisquoi Bay (LimnoTech, 2012 and 2015) found 

that a large amount of phosphorus is currently stored in the bottom sediments and is expected to be 

released gradually for many decades to come. However, unlike the St. Albans Bay case, there does not 

appear to be an option to control (as with an alum treatment, for example) the bottom sediment source, 

should that be deemed desirable in the future. This is because the phosphorus sediment build-up covers 

a very large area (22,000 acres) and much of this area is within a national wildlife refuge or outside the 
Page | 41 

U.S. border (making such approaches much more challenging), and the potential environmental impacts 

of such treatment to such a large area would be much greater. The allocations in Table 7 for the 

watershed sources take into account a continual source from the sediment that would decline sharply 

once adequate watershed load reductions are achieved. The allocations were based on the level of 

reduction the LimnoTech report (2015) indicated would be needed to achieve the phosphorus criterion in 

the bay, factoring in the long-term loading from the bottom sediment. 

6.3 MARGIN OF SAFETY

The statute and regulations require that a TMDL include a margin of safety (“MOS”) to account for any 

lack of knowledge concerning the relationship between load and wasteload allocations and water quality 

(CWA §303(d)(1)(C); 40 C.F.R. §130.7(c)(1) ). EPA’s 1991 TMDL Guidance (USEPA, 1991) explains 

that the MOS may be implicit, i.e., incorporated into the TMDL through conservative assumptions in the 

analysis, or explicit, i.e., expressed in the TMDL as loadings set aside for the MOS. If the MOS is 

implicit, the conservative assumptions in the analysis that account for the MOS must be described. If the 

MOS is explicit, the loading set aside for the MOS must be identified. 

Although there are conservative assumptions built into the modeling approach, one of the lessons 

learned from the review of the 2002 TMDL approval, where an implicit margin of safety was used, was 

that in a system as complex as Lake Champlain, it is difficult to assure conservatism in every lake 

segment. In light of this complexity, EPA has allocated an explicit margin of safety equal to five 

percent of the total loading capacity for each segment. The uncertainty analysis completed as part of the 

lake modeling indicated that the average area-weighted prediction error of the model for 1991-2010 

(which includes both the calibration and validation periods) was +4.15 percent. A positive prediction 

error value means that the model predicted higher phosphorus concentrations than monitored values, 

indicating that there is conservatism built into the model. Negative prediction error values indicate that 

the model predicted somewhat lower phosphorus concentrations than the actual monitored 

concentrations for this period, indicating that the model is somewhat under estimating (on average) the 

extent to which phosphorus loads elevate in-lake concentrations. On a segment by segment basis, the 

average prediction error for the 1991-2010 period ranged from -7.97% to +17.77% across the 12 TMDL 

segments (see Table 6). The prediction error for 10 of 12 segments was above zero, with only two 

segments below zero – Northeast Arm and Isle LaMotte (at -2.8 and -7.97 respectively). Both of these 

segments receive an extremely small percentage of the total phosphorus load to the lake (2.8% and 0.6% 

respectively), and are assigned allocations that translate to only modest overall reductions (12% and 

13%). These two segments are also dominated by agricultural land, and the specified reductions from 

agricultural sources are just a small fraction of the anticipated phosphorus reduction expected as a result 

of the State’s new required agricultural practices, based on EPA’s Scenario Tool analysis. Specifically, 

the TMDLs include agricultural source reductions of approximately 20% for these two segments, and 

EPA’s analysis indicates that agricultural load reductions of more than 60% are expected in each case 

(see Appendix B). Given these mitigating circumstances for the two segments with the negative 

prediction errors, and the conservatism demonstrated by the modeling results for all other segments and 

the lake as a whole, EPA is confident that the 5% explicit MOS is adequate for these TMDLs. 
Page | 42 

Table 6. BATHTUB Model Prediction Error, 1991-2010. Source: (Tetra Tech, 2015a).

Lake Segment Model Prediction Error

South Lake B +0.05

South Lake A +13.16

Port Henry +9.57

Otter Creek +13.57

Main Lake +5.25

Shelburne Bay +17.77

Burlington Bay +5.16

Malletts Bay +5.72

Northeast Arm -2.80

St. Albans Bay +5.65

Missisquoi Bay +13.32

Isle LaMotte -7.97

Lake-wide areaweighted average +4.15
Page | 43 

6.4 TMDL ALLOCATION SUMMARY

The resulting allocations by sector for each lake segment are shown in Table 7. The percent reductions 

needed to achieve these various allocations by lake segment are shown in Table 8. The final WWTF 

allocations are listed in Table 9. Facilities with allocations different from the 2002 TMDLs are shown in 

italics. Figure 7 presents a graphical depiction of the change from the base loading to the TMDL 

allocation. 
Page | 44 

Table 7. Allocations by Lake Segment.

Lake Segment

2001-

2010 

Base 

Load

Total 

Loading 

Capacity

WWTF 

WLA

CSO

WLA

Developed 

Land WLA

Future 

Growth 

WLA

Ag. Prod. 

Area 

WLA

Total 

WLA

Forest 

LA

Streams 

LA

Agriculture 

LA

Total 

LA

5% 

MOS

01. South Lake B 51.09 29.95 1.62 * 7.12 0.04 0.22 9.01 8.17 4.41 6.86 19.44 1.50

02. South Lake A 26.45 11.77 0.23 - 1.86 0.00 0.16 2.24 0.47 † 8.47 8.94 0.59

03. Port Henry 7.02 3.13 0.00 - 0.61 0.00 0.02 0.64 0.04 † 2.30 2.34 0.16

04. Otter Creek 140.52 107.35 11.98 * 17.13 0.43 0.41 29.96 22.78 13.76 35.48 72.02 5.37

05. Main Lake 162.18 128.96 9.85 * 28.02 1.44 0.43 39.74 30.90 35.66 16.22 82.77 6.45

06. Shelburne Bay 10.18 9.00 0.72 - 2.68 0.34 0.04 3.77 0.30 0.09 4.39 4.78 0.45

07. Burlington Bay 4.54 3.13 1.46 0.77 0.62 0.10 0.00 2.94 0.02 † 0.00 0.03 0.16

09. Malletts Bay 56.39 46.45 3.24 - 13.66 0.68 0.31 17.88 7.19 3.58 15.48 26.24 2.32

10. Northeast Arm 17.82 15.60 0.00 - 3.65 0.03 0.08 3.76 1.71 † 9.34 11.05 0.78

11. St. Albans Bay 13.94 10.53 1.13 * 2.03 0.36 0.04 3.56 0.23 0.69 5.52 6.44 0.53

12. Missisquoi Bay 136.33 48.64 2.00 * 11.19 0.34 0.64 14.17 10.03 12.66 9.35 32.04 2.43

13. Isle La Motte 4.10 3.62 0.11 - 0.79 0.02 0.02 0.94 0.08 † 2.42 2.50 0.18

TOTAL 630.56 418.12 32.34 0.77 89.37 3.78 2.38 128.63 81.91 70.85 115.83 268.59 20.91

*CSO allocation included as part of Developed Land †Stream allocation included in Developed Land WLA and Agriculture and Forest LA 

- No CSOs in segment 
Page | 45 

Table 8. Percent reductions needed to meet TMDL allocations.

Lake Segment

Total 

Overall Wastewater1 CSO

Developed 

Land2

Agricultural 

Production 

Areas Forest Streams

Agricultural 

Nonpoint

01. South Lake B 41.4% 0.0% 21.1% 80.0% 40.0% 46.7% 62.9%

02. South Lake A 55.5% 0.0% 18.1% 80.0% 5.0% 62.9%

03. Port Henry 55.4% 7.6% 80.0% 5.0% 62.9%

04. Otter Creek 23.6% 0.0% 15.0% 80.0% 5.0% 40.1% 46.9%

05. Main Lake 20.5% 61.1% 20.2% 80.0% 5.0% 28.9% 46.9%

06. Shelburne Bay 11.6% 64.1% 20.2% 80.0% 5.0% 55.0% 20.0%

07. Burlington Bay 31.2% 66.7% 11.8% 24.2% 0.0% 0.0% 0.0%

09. Malletts Bay 17.6% 0.2% 20.5% 80.0% 5.0% 44.9% 28.6%

10. Northeast Arm 12.5% 7.2% 80.0% 5.0% 20.0%

11. St. Albans Bay 24.5% 59.4% 21.7% 80.0% 5.0% 55.0% 34.5%

12. Missisquoi Bay 64.3% 51.9% 34.2% 80.0% 50.0% 68.5% 82.8%

13. Isle La Motte 11.7% 0.0% 8.9% 80.0% 5.0% 20.0%

TOTAL 33.7% 42.1% 11.8% 20.9% 80.0% 18.7% 45.4% 53.6%

1Percent change from current permitted loads

2

Includes reductions needed to offset future growth
Page | 46 

Table 9. Vermont Individual WWTF Phosphorus Wasteload Allocations 

(Facilities with allocations different from the 2002 TMDLs are shown in italics.) 

Facility Lake Segment

Design 

Flow 

(mgd)

Current

Permit 

Load 

(mt/yr)

TMDL

Wasteload

Allocation

(mt/yr)

Change in 

Permitted 

Load (mt/yr)

Benson 01 South Lake B 0.018 0.122 0.122 0.000

Castleton 01 South Lake B 0.480 0.397 0.397 0.000

Fair Haven 01 South Lake B 0.500 0.414 0.414 0.000

Poultney 01 South Lake B 0.500 0.414 0.414 0.000

West Pawlet 01 South Lake B 0.040 0.276 0.276 0.000

Orwell 02 South Lake A 0.033 0.228 0.228 0.000

Brandon 04 Otter Creek 0.700 0.580 0.580 0.000

Middlebury 04 Otter Creek 2.200 1.823 1.823 0.000

Otter Valley Union High School 04 Otter Creek 0.025 0.173 0.173 0.000

Pittsford 04 Otter Creek 0.085 0.483 0.483 0.000

Pittsford Fish Hatchery 04 Otter Creek 2.600 0.691 0.691 0.000

Proctor 04 Otter Creek 0.325 0.359 0.359 0.000

Rutland City 04 Otter Creek 8.100 5.634 5.634 0.000

Salisbury Fish Hatchery 04 Otter Creek 1.310 0.181 0.181 0.000

Shoreham 04 Otter Creek 0.035 0.242 0.242 0.000

Vergennes 04 Otter Creek 0.750 0.621 0.621 0.000

Wallingford 04 Otter Creek 0.120 0.829 0.829 0.000

West Rutland 04 Otter Creek 0.450 0.364 0.364 0.000

Barre City 05 Main Lake 4.000 3.314 1.105 -2.209

Burlington East 05 Main Lake 1.200 0.994 0.331 -0.663

Burlington Electric 05 Main Lake 0.365 0.017 0.017 0.000

Burlington North 05 Main Lake 2.000 1.657 0.552 -1.105

Cabot 05 Main Lake 0.050 0.041 0.041 0.000

Essex Junction 05 Main Lake 3.300 2.569 0.911 -1.658

Global Foundries 05 Main Lake 8.000 5.531 2.210 -3.321

Marshfield 05 Main Lake 0.045 0.311 0.311 0.000

Montpelier 05 Main Lake 3.970 3.290 1.097 -2.193

Northfield 05 Main Lake 1.000 0.829 0.276 -0.553

Plainfield 05 Main Lake 0.125 0.691 0.138 -0.553

Richmond 05 Main Lake 0.222 0.184 0.061 -0.123

South Burlington Airport Park. 05 Main Lake 3.300 1.906 0.911 -0.995

Stowe 05 Main Lake 1.000 0.282 0.276 -0.006

Waterbury 05 Main Lake 0.510 0.563 0.141 -0.422

Weed Fish Culture Station 05 Main Lake 11.500 0.914 0.914 0.000

Williamstown 05 Main Lake 0.150 1.036 0.166 -0.870

Winooski 05 Main Lake 1.400 1.160 0.387 -0.773
Page | 47 

Hinesburg 06 Shelburne Bay 0.250 0.276 0.069 -0.207

Shelburne #1 06 Shelburne Bay 0.440 0.348 0.122 -0.226

Shelburne #2 06 Shelburne Bay 0.660 0.497 0.182 -0.315

South Burlington Bart. Bay 06 Shelburne Bay 1.250 0.878 0.345 -0.533

Burlington Main 07 Burlington Bay 5.300 4.392 1.464 -2.928

Fairfax 09 Malletts Bay 0.078 0.539 0.539 0.000

Hardwick 09 Malletts Bay 0.371 0.410 0.410 0.000

Jeffersonville 09 Malletts Bay 0.077 0.532 0.532 0.000

Johnson 09 Malletts Bay 0.270 0.224 0.224 0.000

Milton 09 Malletts Bay 1.000 0.829 0.829 0.000

Morrisville 09 Malletts Bay 0.550 0.352 0.352 0.000

Perrigo Nutritionals 09 Malletts Bay 0.425 0.352 0.352 0.000

Northwest State Correctional 11 St. Albans Bay 0.040 0.028 0.028 0.000

St. Albans City 11 St. Albans Bay 4.000 2.762 1.105 -1.657

Enosburg Falls 12 Missisquoi Bay 0.450 0.373 0.124 -0.249

Newport Center 12 Missisquoi Bay 0.042 0.006 0.116 0.110

North Troy 12 Missisquoi Bay 0.110 0.760 0.122 -0.638

Richford 12 Missisquoi Bay 0.380 0.420 0.105 -0.315

Rock Tenn 12 Missisquoi Bay 2.500 1.260 0.691 -0.569

Sheldon Springs 12 Missisquoi Bay 0.054 0.373 0.373 0.000

Swanton 12 Missisquoi Bay 0.900 0.746 0.249 -0.497

Troy/Jay 12 Missisquoi Bay 0.800 0.221 0.221 0.000

Alburgh 13 Isle LaMotte 0.130 0.108 0.108 0.000

 Total 55.802 32.336 -23.465
Page | 48 
Page | 49 

CHAPTER 7: REASONABLE ASSURANCE & ACCOUNTABILITY FRAMEWORK

7.1 REASONABLE ASSURANCE – BACKGROUND

Section 303(d) of the CWA requires that a TMDL be “established at a level necessary to implement the 

applicable water quality standard.” EPA regulations define a TMDL to include WLAs and LAs, and 

provide that “[i]f best management practices or other nonpoint source pollution controls make more 

stringent load allocations practicable, then wasteload allocations can be made less stringent.” 40 C.F.R. 

§130.2(i). EPA’s TMDL guidance further explains that when a TMDL is developed for waters impaired 

by both point and nonpoint sources, and the WLA is based on an assumption that nonpoint source load 

reductions will occur, the TMDL must provide “reasonable assurances” that nonpoint source control 

measures will achieve expected load reductions in order for the TMDL to be approvable (USEPA, 1991; 

see also Perciasepe, 1997). This information is necessary for EPA to determine that the TMDL, 

including the load and wasteload allocations, has been established at a level necessary to implement 

water quality standards. 

Where a TMDL is developed for waters impaired by both point and nonpoint sources (and non-NPDESregulated point sources), EPA’s determination of reasonable assurance that the TMDL’s LAs will be 

achieved considers whether practices capable of achieving the specified pollutant load: (1) are 

technically feasible at a level required to meet allocations; and (2) have a high likelihood of 

implementation. Where there is a demonstration that nonpoint source (and non-NPDES regulated point 

source) load reductions can and will be achieved, a TMDL writer can determine that reasonable 

assurance exists and may also, if sufficient load reductions are reasonably assured, allocate greater 

loadings to NPDES-regulated point sources as WLAs than would otherwise be required. 

One basis for EPA’s disapproval of the 2002 TMDLs was a finding that the establishment of wasteload 

allocations based on assumptions that nonpoint source reductions would be achieved was inadequate and 

inconsistent with EPA regulations and guidance (USEPA 2011a, b). EPA examined two questions: 1) 

Was there reasonable assurance that nonpoint source control actions will occur, and 2) If these actions 

occur, was there reasonable assurance that they would achieve enough phosphorus reduction to meet the 

load allocations specified in the TMDL. 

EPA found that the 2002 TMDL document identified only one program which provided reasonable 

assurance that specified nonpoint source control measures would occur and would result in specific 

phosphorus reductions compared to baseline loads. The magnitude of reductions expected from this 

program was less than one percent of the reductions needed to meet the load allocations. EPA was 

unable to identify any programs or activities in existence at the time of the TMDL submittal that 

provided assurance that nonpoint source reductions would occur, and that anticipated reductions would 

be sufficient to meet the TMDL load allocations. EPA thus concluded that the TMDL’s level of 

assurance that necessary load reductions would occur was insufficient to support establishment of less 

stringent wasteload allocations for the wastewater treatment plants than would otherwise be required. 

As described below, for the new Lake Champlain TMDLs, numerous elements combine to provide 

robust assurance that the necessary load reductions will occur and will achieve sufficient phosphorus 

reductions to meet the specified load allocations. 
Page | 50 

7.2 REASONABLE ASSURANCE – GENERAL APPROACH 

Each of the Vermont segments of Lake Champlain is dominated by nonpoint sources, with the exception 

of Burlington Bay. Without a demonstration of reasonable assurance that relied-upon nonpoint source 

reductions will occur, the Lake Champlain TMDLs would have to assign commensurate reductions to 

the point sources. EPA communicated this point in an October 22, 2013 letter to DEC Commissioner 

Mears (USEPA, 2013). Vermont subsequently indicated a clear policy preference to focus on obtaining 

most if not all of the necessary reductions from nonpoint sources and the point sources (both NPDES 

and non-NPDES regulated) associated with developed lands, through application of measures uniformly 

across the Lake Champlain basin. In addition to the policy benefit of consistent requirements across the 

basin, Vermont was also hoping to minimize reductions at wastewater treatment facilities (WWTFs). 

After analyzing all available information, EPA determined that there is reasonable assurance that the 

nonpoint source (and non-NPDES regulated point source) reductions can and will be achieved and that 

such reductions are sufficient to enable EPA to allocate greater loadings to the WWTFs than would 

otherwise be required. EPA’s conclusion that there is reasonable assurance that such reductions can and 

will be achieved rests on the following major factors: 

1. Vermont’s Phase 1 Implementation Plan, as revised in August, 2015, contains a detailed listing 

of specific, technically feasible commitments made by the State. Many of the most important 

milestones in the Plan are included in Act 64, signed into law by Governor Shumlin on June 16, 

2015. 

2. EPA’s modeling and scenario tools enabled the quantification of reductions achievable from the 

measures contained in the Phase 1 Implementation Plan, and allowed for verification that these 

reductions are sufficient to meet load allocations for each segment. This is described in detail in 

Appendix B. 

3. EPA has developed an Accountability Framework to provide a sufficient backstop to ensure a 

high likelihood that implementation of the nonpoint source measures will occur. 

Each factor is further described below. 

The step-wise manner in which the Lake Champlain TMDLs were developed has yielded a very detailed 

description of the nonpoint source reductions needed to achieve the load allocations and the stormwater 

sources in the wasteload allocations. EPA’s initial modeling of the revised phosphorus capacity of each 

lake segment provided an early target for the State and EPA to use in determining the suite of measures 

necessary to achieve water quality standards. Vermont developed a draft implementation plan and EPA 

provided extensive comments. The final set of nonpoint source measures and measures applicable to 

runoff from developed lands were submitted in advance of the final TMDL development as part of the 

Phase 1 Implementation Plan and reflected the State’s commitments as transmitted by Governor 

Shumlin on May 29, 2014 to the EPA Administrator and Regional Administrator. Authorization for key 

actions included in the plan and milestone dates were included in Act 64. Vermont provided a revised 

Phase 1 Implementation Plan in August, 2015, incorporating the deadlines contained in Act 64. Vermont 

provided additional commitments in a letter from DEC Commissioner Schuren on February 23, 2016 

(Vermont DEC, 2016). 

Key among these new measures are the following, which will be applied across the entire watershed: 

 Issuance of general permits to control runoff from State Highways, and municipal paved and 

unpaved roads; 
Page | 51 

 Issuance of a general permit to address stormwater from existing developed lands equal or 

greater than 3 acres; 

 Revision of the Municipal Separate Storm Sewer System (MS4) general permit; 

 Revision of the Vermont Stormwater Management Manual; 

 Adoption of a “stormwater practices handbook” for managing runoff from non-jurisdictional 

projects; 

 Revision of the “Required Agricultural Practices” (formerly the “Accepted Agricultural 

Practices”) including such programs as Nutrient Management Planning, Livestock Exclusion and 

certification of manure applicators; 

 Creation of a Small Farm Operation certification program; and 

 Revision of the Acceptable Management Practices for forestry; 

 Implementation of recently adopted rules controlling stream alterations and development in 

floodplains; 

 Issuance of a new CSO Rule, replacing the 1990 CSO Control Policy; 

 Development of a comprehensive TMDL implementation tracking and reporting system; 

 Revision of the Agency of Natural Resources (ANR)/Agency of Agriculture, Food and Markets 

(AAFM) Memorandum of Understanding for the agricultural nonpoint source program ;

 Establishing a long-term revenue source to support water quality improvement via the Clean 

Water Fund, and 

 Revision of the MS4 general permit to require existing regulated municipalities to control 

discharges consistent with the TMDLs’ wasteload allocations.

As such, EPA had a very specific and well defined list of measures to use to evaluate expected 

phosphorus reduction amounts in each lake segment watershed. 

Of equal importance are the financial resources needed to implement the new and revised programs 

identified in the revised Phase 1 Implementation Plan. In January 2015, Governor Shumlin’s Inaugural 

Address and his recommended budget for state fiscal year 2016 provided the details of the financial 

foundation. At the end of the legislative process, Act 64 established a Clean Water Fund, structured so 

that it can serve as a repository for federal and private funding sources in addition to state 

appropriations. Vermont will contribute approximately $5.3 million annually, to be raised from a 

surcharge on the value of property subject to property transfer tax for three years. The criteria for 

prioritizing allocation of funds are aligned well with the new programs required in Act 64. In the 

interim, alternative approaches to generating revenue for the Clean Water Fund beyond 2018 will be 

considered. The Vermont Capital Bill also increased the amount of funding dedicated to 

implementation of polluted stormwater runoff by $1.25 million over the next two years. Act 64 also 

appropriates funds for 13 new positions at DEC and 7 new positions at the Agency of Agriculture in the 

fiscal year beginning July 1, 2015. The new staff positions will give these agencies the additional 

resources needed to implement the Phase 1 Implementation plan, and track progress over time. 

Significant new federal funding has also been secured to support TMDL-related actions in Vermont. In 

August, 2014, U.S. Department of Agriculture Secretary Vilsack announced that that up to $45 million 

will be provided to protect and improve soil and water quality in the Lake Champlain Basin in Vermont 

over the next five years. This represents nearly a doubling of the pace of investments made through the 

Natural Resource Conservation Service. In January, 2015 the USDA announced another $16 million in 

federal funds to improve Lake Champlain’s water quality as part of USDA’s Regional Conservation 

Partnership Program. 
Page | 52 

As described in Chapter 5, EPA expended significant time and effort to build Lake Champlain-specific 

models and scenario tools to support the development of the TMDLs. These tools were built with the 

kinds of pollution reduction measures in mind that EPA expected would be required during the 

implementation phase. Once Vermont had identified the measures and the scope and scale of their 

application, EPA was able to quantify the reductions achievable in each of the lake segments. These 

reductions were then fed back into the lake model to ensure that the net effect of the Wasteload and 

Load allocations would achieve the water quality standards. The specific BMPs chosen for simulation 

were based on the available data and their suitability for modeling. These BMPs can be implemented 

and will achieve the allocated loads. Other combinations of BMPs can achieve the same result. In 

implementing the allocations Vermont may choose other combinations of measures based on factors 

such as site-specific conditions, cost-effectiveness, or newly developed measures, as long as they 

achieve the same (or better) outcome. EPA conducted additional analyses upon consideration of public 

comment and the decision of the Secretary of Agriculture, Food and Markets to require Best 

Management Practices in Franklin County (see next section for additional information). 

A summary of how the measures in the State’s plan were translated to BMPs in the Scenario Tool and 

the associated phosphorus reductions is included in Appendix B. A description of the additional 

assurance provided for Missisquoi Bay is described in the next section (7.2.1). 

Finally, EPA has developed an Accountability Framework, detailed in section 7.3, to provide a 

transparent and understandable way for all interested parties to gauge Vermont’s progress in 

implementing the TMDLs. The milestones are all drawn from Vermont’s Phase 1 Implementation Plan 

and the February 23, 2016 letter from the DEC Commissioner and thus reflect the State’s commitments. 

EPA will provide interim and final assessments of Vermont’s progress against these milestones to the 

state and the public. EPA has also laid out the range of actions EPA would consider taking if Vermont 

does not make satisfactory progress. 

7.2.1 REASONABLE ASSURANCE – MISSISQUOI BAY

 

Missisquoi Bay presents the greatest challenge in attaining water quality standards. It is dominated by 

nonpoint sources and will require implementation measures above and beyond what will be required in 

other segments. EPA’s analysis assumed especially large reductions from agricultural, streambank, and 

forest sources in the Missisquoi Bay lake segment watershed. The additional measures described below 

provide assurance that the additional reductions from these sources will be achieved. 

On February 3, 2016, the Secretary of Agriculture, Food and Markets, in a revised decision, determined 

that BMPs are generally necessary on farms in the Missisquoi Bay Basin watershed to achieve 

compliance with state water quality goals (Vermont AAFM, 2016). The revised decision provides a 

framework for outreach, education and assessment of farms in the watershed and a process for farmspecific development and implementation of a Farm Plan to address identified water quality resource 

concerns, where needed. Farm assessments may conclude that practices required by the RAPs are 

sufficient to protect water quality and that BMPs may not be required due to a farm’s specific 

characteristics or management, but in general, the presumption is that BMPs are required. 

The BMPs required in the Secretary’s decision support EPA’s determination that the allocation for 

agriculture in Missisquoi Bay will be met. 
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The Secretary’s decision provides additional assurance that the widespread application of measures 

assumed in EPA’s modeling analyses will be carried out on the ground. The focus on critical source 

areas also provides assurance that the especially large reduction amounts required in the Missisquoi 

watershed will be achieved. This is because EPA’s analysis of the maximum achievable reduction 

amount for Missisquoi Bay assumed average phosphorus loading rates based on soil type, slope, and 

land use. However, it has been well documented (Stone Environmental, 2011) that much greater than 

average phosphorus loads can be generated from small pockets of land that EPA’s modeling was unable 

to detect due to the relatively coarse modeling scale. By focusing on these critical source areas, in 

addition to other areas, the State will be able to achieve greater reductions than those estimated by EPA. 

The streambank source is unique in that loads are expected to decrease over time even without 

significant additional interventions, due to natural stream evolution processes. Therefore, the reasonable 

assurance measures are generally focused on actions designed to speed up these natural processes (and 

to allow streams sufficient corridor space to evolve) rather than BMP-type interventions. In this case, the 

strong body of scientific data assembled by the State’s geomorphic assessment program provides the 

assurance that most eroding stream reaches will eventually become stable if humans do not continue to 

further stress these systems with additional floodplain encroachments and destabilizing channel 

alterations. This is why the State’s regulations that are designed to protect floodplains from further 

development and guard against stream channel alterations are key parts of the reasonable assurance 

provisions. There are also new regulatory measures in Act 64 and the Phase 1 Implementation Plan that 

will speed up the transition of stream reaches to a more stable (equilibrium) condition. Examples include 

the riparian buffer and livestock exclusion requirements required by Act 64 to be included in the new 

RAPs. Both the 25 foot buffer requirement for agricultural lands and the livestock exclusion requirement 

will lead to more stable (well vegetated) streambanks and eliminate erosion caused by livestock 

trampling. In addition, the State’s recently revised stream alteration regulations require that failed 

culverts be replaced typically with larger structures, meeting design requirements and performance 

standards that will minimize channel erosion – this is another requirement that will speed the transition 

to more stable channel conditions. 

In addition to the floodplain and stream alteration rules and related actions described in the river 

management section of the Phase 1 Plan (which provide reasonable assurance that reductions from 

stream corridors will occur for all lake segment watersheds), DEC has committed in the revised Phase 1 

Implementation Plan to the following supplemental measures for Missisquoi Bay: 

1) The State will put extra resources/effort into identification of opportunities for re-establishing 

connections to floodplains, and working with landowners to make these reconnections happen; 

and 

2) The State will invest extra resources/effort into identification of opportunities where active 

intervention in bank erosion processes could be most effective, and then implementing practices 

as further described in Chapter 5, Section J of the revised Phase 1 Implementation Plan. 

These measures have been shown to be effective at reducing phosphorus loading from streambanks, and 

the extra effort DEC is committing to these actions provides additional assurance that the substantial 

phosphorus reductions assumed (in EPA’s modeling analysis) from streambank erosion in the 

Missisquoi Bay watershed will eventually be achieved. 

For forests, beyond the updates to the Acceptable Management Practices described in the forest 

management section of the Phase 1 Implementation Plan, the State has committed to the following 
Page | 54 

additional actions in the Missisquoi and South Lake watersheds: Two foresters with the Department of 

Forests, Parks and Recreation will lead a focused effort in these two lake segment watersheds to 

accelerate implementation of NRCS cost-share practices funded through the Regional Conservation 

Partnership Program (RCPP) to improve water quality and reduce phosphorus. These practices include 

erosion control on active forest trails and landings; installation of bridges, fords, and culverts at stream 

crossings; restoring forest riparian areas; and mulching. This efforts, combined with the major 

enhancements to the Acceptable Management Practices (including in particular practices that address 

erosion and sedimentation at water crossings, forest roads, log landings, and forest harvest sites) 

provides assurance that the additional phosphorus reductions assumed from forest lands (in EPA’s 

analysis for these watersheds) will be achieved. In addition, the Healthy Forest Cover Strategy in the 

Phase 1 Implementation Plan includes a detailed sequence of action steps to achieve no net forest loss 

and improve the health and extent of forests throughout the state. Among other implementation steps, 

the Strategy includes aggressive, incentive-based measures to restore forest buffers to riparian areas 

currently lacking adequate buffers. The Healthy Forest Cover Strategy is an important program (already 

underway) that adds assurance that the phosphorus reductions from forest land will be achieved. 

7.2.2 REASONABLE ASSURANCE – SOUTH LAKE B

Although the South Lake B segment is physically very different from Missisquoi Bay, significant 

reductions from forested lands are also necessary in this segment’s watershed. Forested land contributes 

close to 25% of the phosphorus load in the South Lake B segment – the highest percent contribution 

from forests of any segment. Similarly to Missisquoi Bay, EPA’s analysis assumed a much greater 

reduction of phosphorus from forest land for the South Lake B watershed than from other lake segment 

watersheds. See the discussion of forest management measures included immediately above for 

Missisquoi Bay for a description of the reasonable assurance that the additional phosphorus reductions 

from forest land in the South Lake B watershed will occur. 

7.3 ACCOUNTABILITY FRAMEWORK 

EPA’s prior experience with implementation of the 2002 Lake Champlain TMDLs and with the 

development of the Chesapeake Bay TMDL, suggests that it is important to establish an accountability 

framework that guides water quality restoration of Lake Champlain. The accountability framework, 

including Vermont’s Phase 1 and Phase 2 Implementation Plans, will help ensure implementation of the 

Lake Champlain TMDL but is not itself part of the TMDLs. The Lake Champlain TMDL accountability 

framework has the following elements: 

1. The “Vermont Lake Champlain Phosphorus TMDL Phase 1 Implementation Plan,” May 29, 

2014, as revised in August 2015, and augmented by DEC Commissioner Schuren’s February 23, 

2016 letter and the decision by the Secretary of AAFM on February 2, 2016 regarding Best 

Management Practices in the Missisquoi Bay basin; 

2. The Tactical Basin Plans (also referred to as “Phase 2 Implementation Plans”) that DEC will 

develop for each of the major basins in Vermont; 

3. EPA’s commitment to track and assess Vermont’s progress through a clear and transparent 

“report card” process; and 
Page | 55 

4. EPA’s commitment to take appropriate federal action if Vermont fails to meet the key milestones 

in the Phase 1 report card or the implementation schedules in the Phase 2 (Tactical Basin) Plans. 

A major basis of EPA’s determination that there is reasonable assurance of load reductions for the Lake 

Champlain TMDLs is the revised Phase 1 Implementation Plan. The plan is the roadmap for how 

Vermont, in partnership with federal and local governments, will achieve and maintain the reductions 

necessary to meet the TMDLs’ phosphorus allocations. The accountability framework covers two 

distinct timeframes. Through the end of 2017, the major focus is on putting in place the regulatory 

changes or new programs identified in the Phase 1 Implementation Plan that provide the platform for 

longer term success, along with the resources needed to accomplish them. Also important during this 

period is the development of four Phase 2 Implementation Plans and the enhanced implementation of 

key programs already in place. Beginning in 2018, the accountability framework is built around the 

priority milestones contained in the each of the Phase 2 Implementation (Tactical Basin) Plans. 

In addition, as described in the Phase 1 Implementation Plan, the Vermont agencies are developing the 

capability to track BMP implementation for both agricultural and non-agricultural BMPs. DEC is 

developing a primary system that will document the location and phosphorus reduction capabilities of all 

BMPs for projects supported by DEC and Clean Water Fund dollars or implemented as part of 

compliance with regulatory programs. The Agency of Agriculture is developing a database in 

partnership with USDA and seven other organizations to track the implementation of agricultural 

BMPs. Using data exchange capabilities, projects and BMP implementation tracked by the agricultural 

BMP database will be brought into DEC’s system at the appropriate summary level. In addition, for road 

networks, DEC will incorporate BMP tracking either directly, or through data exchange approaches, in 

partnership with VT Agency of Transportation. EPA is helping to support the development of parts of 

this tracking system, but the system will be managed and populated by DEC in cooperation with other 

Vermont agencies. The tracking system will be used to assess progress, particularly at the lake segment 

watershed scale as the Phase 2 plans are implemented. Credit may be given for structural projects 

completed after 2010 (i.e., after the modeling period) that are documented as working as designed. In 

addition, DEC, in its role as lead entity for tracking and accounting, may determine that certain projects 

completed prior to 2010 may also be eligible for credit. This is because the TMDL modeling was not 

sensitive enough to specifically account for the presence of the small number of stormwater retrofit 

projects in place just prior to 2010. Therefore, EPA’s recommendation is that, in determining whether 

credit should be provided in these cases, VT DEC should consider the level of phosphorus reduction 

achieved by the practice, how close the installation was to 2010, and whether the practice has been 

documented to still be performing as designed.

7.3.1 ACCOUNTABILITY FRAMEWORK THROUGH 2017

EPA has identified early key milestones in the Phase 1 Implementation Plan that are crucial to the longterm success of implementing the TMDLs and will constitute the main component of the accountability 

report card. A few other milestones are focused on implementation of key existing programs. These 

items were initially taken directly from the August 2015 Phase 1 Implementation Plan. Several items 

were revised or added based on suggestions provided by VT DEC (Vermont DEC, 2016). EPA considers 

the revised set of milestones to be more comprehensive and a better reflection of the critical tasks that 
Page | 56 

must be accomplished in 2016 and 2017.5 Many of the items are either authorized by or have deadlines 

for completion in Act 64, as noted below. 

By December 30, 2016 

 Required Agricultural Practices (RAP) revisions adopted [with expected elements] (Act 64, Sec. 

4) 

 Small Farm Operation certification program rule adopted (Act 64, Sec. 3) 

 Livestock exclusion incentive program in place (Act 64, Sec. 4) 

 Develop matrix and small farm template for nutrient management planning 

 Develop Environmental Stewardship Incentive program in priority watersheds 

 Mandate certification of custom manure applicators (Act 64, Sec. 16) 

 Develop requirements for farmer training programs (Act 64, Sec. 15) 

 Issue Final TS4 permit 

 Adopt final Vermont Stormwater Management Manual 

 Forestry AMP revisions completed (Act 64, Sec. 49) 

 Legislature establishes Clean Water Improvement Fund (completed by passage of Act 64) 

 Tactical Basin Plans (Phase 2) complete for Lamoille and Missisquoi basins 

 Updated Report to EPA with spending plan capacity 

 Issue new CSO Rule, replacing 1990 CSO Control Policy 

 Develop comprehensive TMDL implementation tracking and reporting system 

 Revise the Agency of Natural Resources/Agency of Agriculture, Food and Markets 

Memorandum of Understanding for the agricultural nonpoint source program 

EPA will issue an interim report card in early 2017 assessing Vermont’s success in meeting these 

milestones. EPA will evaluate the substance of the various outputs as well as the completion date in 

assessing whether the milestone has been satisfactorily completed. Where applicable, EPA will evaluate 

the requirements in the various rules and programs to ensure that they include comparable measures to 

those EPA simulated in determining that measures would be sufficient to achieve the load and wasteload 

allocations. 

By December 30, 2017 

 NMP milestones completed 

 Targeted funding for agricultural BMP and Nutrient Management Plan implementation provided

in Missisquoi Bay, St. Albans Bay and South Lake 

 Report to legislature on recommendations for tile drains (Act 64, Sec. 5) 

 Issue Final Municipal Roads General Permit (Act 64, Sec. 31) 

 Issue Final Developed Lands General Permit (Act 64, Sec. 31) 

 Tactical Basin Plans (Phase 2) completed for Poultney, Mettawee and Lower Lake Champlain

 Establish long-term revenue source to support water quality improvement via the Clean Water 

Fund (Act 64, Sec. 40) 

 Revise MS4 general permit to require existing regulated municipalities to control discharges 

consistent with the TMDLs’ wasteload allocations

 

5 The milestones scheduled for completion in 2015 in EPA”s August 2015 proposed TMDLs, have been completed. 
Page | 57 

 Propose amendments to Required Agricultural Practices to include requirements for reducing 

nutrient contributions form subsurface tile drainage (Act 64, Sec. 4) 

 Update the Vermont Water Quality Standards, including anti-degradation, by adding a new tier 

that will allow for an upward reclassification of designated uses to a new, more protective class 

 Complete education, outreach and compliance activities with farms in the Missisquoi Bay 

watershed as detailed in Section III, 6 in the Secretary of Agriculture, Food and Markets 

February 3, 2016 decision. 

 Commence notification of affected farms about the Assessment and Plan process as detailed in

section III, 7 in the February 3, 2016 decision. 

EPA will issue a final report card in early 2018 assessing Vermont’s success in meeting these 

milestones. If EPA finds Vermont has failed to make satisfactory progress, EPA may take one or more 

of the following actions: 

 Revise the TMDLs to reallocate additional load reductions from nonpoint to point sources, such 

as wastewater treatment plants (e.g., reduce the wasteload allocations for facilities in the South 

Lake B, Main Lake, Shelburne Bay, Burlington Bay, St. Albans Bay and Missisquoi Bay 

segments to loads equivalent to the limit of phosphorus removal technology). 

 Expand NPDES permit coverage to unregulated sources. For example, exercise Residual 

Designation Authority (RDA) to increase the number of sources or communities regulated under 

the NPDES permit program. 

 Increase and target federal enforcement and compliance assurance in the watershed. 

7.3.2 ACCOUNTABILITY FRAMEWORK BEYOND 2017

Beyond 2017, the accountability framework will shift to gauging progress on a watershed- specific 

basis, keyed to whether VT implements the measures in each of the Phase 2/Tactical Basin Plans. Each 

Tactical Basin Plan will cover a 5 year period and be subsequently revised and reissued for the next 5 

year phase. Interim updates will be made as needed during the cycle. Each Tactical Basin Plan will 

include an “Implementation Table” that lays out the priority actions to be taken by specific dates. Those 

actions and dates will constitute the report card elements for the specific basin. EPA envisions issuing 

an interim report card halfway through each cycle and a formal assessment at the end of the cycle. 

The tactical basin plan implementation tables translate the results of the integrated assessments into 

specific geographically explicit areas for project-level intervention, and to support programmatic and 

partner installation of BMP’s in order to reduce phosphorus loads by a projected amount for each 

tactical plan cycle. These science-based assessments also serve to identify where additional regulatory 

program requirements may be brought to bear by the relevant programs. Tactical plan implementation 

tables will be frequently updated to reflect the implementation of practices that are required as a result of 

regulatory program requirements. 

The issuance of the initial Phase 2 Implementation Plans for four of the six basins are included as key 

milestones in the first phase of the accountability framework. The Phase 2 Implementation Plans for the 

other two basins will be part of the 2018 and 2019 revision of those Tactical Basin Plans. The cycles for 

the Tactical Basin Plans are staggered to better distribute the workload. The expected schedule for the 

plans and report cards over three cycles (15 years) is outlined below. 
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Lamoille and Missisquoi Basins 

2016 – Tactical Basin Plan (Phase 2) issued [included in 1st phase accountability framework] 

2019 – Interim report card 

2021 – Final report card; revised Tactical Basin Plan (Phase 3) 

2024 – Interim report card 

2026 – Final report card; revised Tactical Basin Plan (Phase 4) 

2029 – Interim report card 

2031 – Final report card; revised Tactical Basin Plan (Phase 5) 

Poultney, Mettawee and Lower Lake Champlain Basins 

2017 – Tactical Basin Plan (Phase 2) issued [included in 1st phase accountability framework] 

2020 – Interim report card 

2022 – Final report card; revised Tactical Basin Plan (Phase 3) 

2025 – Interim report card 

2027 – Final report card; revised Tactical Basin Plan (Phase 4) 

2030 – Interim report card 

2032 – Final report card; revised Tactical Basin Plan (Phase 5) 

Winooski Basin 

2018 – Tactical Basin Plan (Phase 2) issued [included in 1st phase accountability framework] 

2021 – Interim report card 

2023 – Final report card; revised Tactical Basin Plan (Phase 3) 

2026 – Interim report card 

2028 – Final report card; revised Tactical Basin Plan (Phase 4) 

2031 – Interim report card 

2033 – Final report card; revised Tactical Basin Plan (Phase 5) 

Otter Creek, Little Otter Creek, Lewis Creek Basin 

2019 – Tactical Basin Plan (Phase 2) issued [included in 1st phase accountability framework] 

2022 – Interim report card 

2024 – Final report card; revised Tactical Basin Plan (Phase 3) 

2027 – Interim report card 

2029 – Final report card; revised Tactical Basin Plan (Phase 4) 

2031 – Interim report card 

2034 – Final report card; revised Tactical Basin Plan (Phase 5) 

Upper Lake Champlain Basin 

2015 – Tactical Basin Plan issued [precedes TMDL, not yet Phase 2 in scope] 

2020 – Feedback on 2015 plan implementation; revised Tactical Basin Plan (Phase 2) 

2023 – Interim report card 

2025 – Final report card; revised Tactical Basin Plan (Phase 3) 

2028 – Interim report card 

2030 – Final report card; revised Tactical Basin Plan (Phase 4) 

If EPA finds Vermont has failed to make satisfactory progress in any of the report cards described 

above, EPA may take one or more of the following actions for the lake segment in question: 
Page | 59 

 Revise the TMDL for the segment to allocate load reductions from nonpoint to point sources, 

such as wastewater treatment plants. 

 Expand NPDES permit coverage to unregulated sources. For example, exercise Residual 

Designation Authority (RDA) to increase the number of sources, operations or communities 

regulated under the NPDES permit program. 

 Increase and target federal enforcement and compliance assurance in the watershed. 

EPA expects that such actions would be tailored to address any shortcoming in the specific basin or 

segment. However, if EPA determines that systemic shortcomings are occurring in multiple basins, 

EPA reserves the option to consider broader scale actions. 
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CHAPTER 8: IMPLEMENTATION

EPA guidance (USEPA, 1999) recommends that each TMDL have associated implementation plan, 

although such plan is not part of the TMDL. As discussed below, Vermont has developed a detailed 

implementation framework for the Lake Champlain TMDLs, which involves several phases of actions 

designed to achieve the phosphorus reductions established in the TMDLs. The first phase focuses on 

policy decisions and programs that would apply across the Vermont portion of the Lake Champlain 

watershed. The second phase focuses on the six major basins through tactical plans that determine what 

specific programs will be applied to specific parts of a basin and in what priority order. Future phases 

are envisioned as five year updates to the second phase plans. 

Phase 1 

At EPA’s request, Vermont developed and submitted the “Vermont Lake Champlain Phosphorus TMDL 

Phase 1 Implementation Plan” in May, 2014. The Phase 1 Implementation Plan provided Vermont’s 

detailed strategy for addressing nonpoint sources and stormwater point sources across Vermont portion 

of the Lake Champlain basin. Vermont updated the Phase 1 Implementation Plan in August 2015 to 

include measures and programs developed subsequent to the original plan and to include relevant 

references to Act 64, which provides authorization for some programs and deadlines for implementing 

certain actions. Table 1 and Figure 1 in the Executive Summary of the revised Phase 1 Implementation 

Plan provide the major steps the State will take, by major source category, to put in place all the 

programs that will be deployed across the Lake Champlain basin. Some steps have already been 

completed, and many more steps will be completed between 2016 and the end of 2017. 

As described in Chapter 7, the Phase 1 Implementation Plan submitted in 2014 and revised in 2015 and 

as augmented by the Secretary of AAFM’s decision affecting the Missisquoi Bay basin and DEC 

Commissioner Schuren’s letter of February 23, 2016, were sufficiently detailed to allow EPA to quantify 

the associated reductions and determine that the load allocations and the stormwater portions of the 

wasteload allocations can and will be achieved. Elements of the revised Phase 1 Implementation Plan, 

the Secretary’s decision, and the Commissioner’s letter also provide the key milestones in the 

Accountability Framework.

The 2014 Phase 1 Implementation Plan did not provide detail on how the wasteload allocations for the 

Wastewater Treatment Facilities would be implemented since EPA had not yet identified the WLAs for 

those facilities. The revised plan provides a schedule by which Vermont will reissue WWTF permits, 

generally following the basin planning approach described further below in Phase 2. 

When implementing the wasteload allocations for WWTFs through NPDES permits, EPA acknowledges 

and supports DEC’s commitment to employ flexible approaches including: 

 Expressing effluent phosphorus limits in permits as total annual mass loads. 

 Providing a period of time for optimization to be pursued and the corresponding load reduction 

results to be realized, and then commencement of the process to upgrade phosphorus treatment 

facilities will be required when actual phosphorus loads reach 80% of the TMDL limits. 

 Establishing phosphorus compliance schedules in discharge permits that allow adequate time for 

planning, engineering and municipal budgeting. 
Page | 61 

 Providing other forms of flexibility that support achieving the wasteload allocations in an 

optimally cost effective manner, including phosphorus trading and integrated planning and 

permitting. 

As described in Section 6.1.1, some reallocation between WWTFs within the same lake segment may be 

considered, following DEC’s Wasteload Allocation Process (Administrative Rule 87-46). The Main 

Lake, Burlington Bay and Shelburne Bay segments may be treated as a single segment for the purpose 

of wastewater reallocation since loads from each of these segment’s watersheds have an approximately 

equal impact on phosphorus concentrations in the critical Main Lake segment. 

EPA encourages states to consider trading programs where opportunities exist to achieve water quality 

improvements at reduced costs. The choice to design, adopt and implement a trading program is one for 

Vermont to make since DEC is the permitting authority. Any trading program must be consistent with 

EPA's 2003 Water Quality Trading Policy (USEPA, 2003) and the 2009 Water Quality Trading Toolkit 

for Permit Writers (USEPA, 2009). If a trading program allows for trading between nonpoint and point 

sources, it must be consistent with EPA guidance regarding accounting for uncertainty when crediting 

nonpoint source reductions. Should DEC chose to consider such a program, EPA encourages broad 

stakeholder involvement in the developing the program. It is unlikely that a workable trading system is 

possible in the South Lake A and Missisquoi Bay segments because the necessary levels of pollutant 

reduction are so large that all sources in the watershed must reduce nearly as much as possible to 

achieve the total reduction needed. Thus there will likely not be surplus reductions to sell or purchase.

Phase 2 

For many years Vermont has employed a river basin planning process. In recent years the process was 

revised to develop tactical plans that highlight the projects or actions needed to protect or restore 

specific waters and identify appropriate funding sources to complete the work. These Tactical Basin 

Plans are designed to guide all watershed work; the issues identified in these plans are the ones that will 

be prioritized for management attention, including funding. The Tactical Basin Plans have a five year 

cycle, with updates on a biannual basis. 

The second phase of implementing the Lake Champlain TMDLs will connect the tools developed in the 

first phase to Vermont’s existing tactical basin planning process. This allows Vermont to take advantage 

of existing planning processes, watershed coordinators, and all the connections to watershed groups and 

other partners who do implementation on the ground. It ensures that the strategic thinking in the 

TMDLs development and Phase 1 implementation is translated into prioritized tactics. As described in 

Section 7.3.2, the Accountability Framework for implementation beyond 2017 will be based on the 

actions contained in the prioritized implementation tables contained in these Phase 2 plans. In addition 

to the implementation of actions geared to reduce discharges of phosphorus from nonpoint sources and 

developed lands in each basin, the DEC will also revise affected WWTF NPDES permits, generally 

during the first year of implementation in each basin. The expected issuance of specific permits is 

included in the Wastewater Treatment Facility section of the revised Phase 1 Implementation Plan 

(Chapter 3, Section B, Vermont, 2015). 

The first of the Phase 2 Tactical Basin Plans will be developed in 2016 for the Lamoille and Missisquoi 

basins. Phase 2 plans for the Poultney, Mettawee and Lower Lake Champlain basins will be developed 

in 2017. The Phase 2 plan for the Winooski basin will be completed in 2018. The Phase 2 plan for the 
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Otter, Little Otter and Lewis Creek basin will be completed in 2019. The Phase 2 plan for the Upper 

Lake Champlain Basin will be completed in 2020. 

Phase 3 and Beyond 

EPA and Vermont anticipate that the revisions to the Phase 2 Tactical Basin Plans will benefit not only 

from what has been learned in the specific basin, but from lessons learned across the whole Lake 

Champlain basin. Those revised Tactical Basin Plans will constitute the third phase of implementation. 

Subsequent iterations of the Tactical Basin Planning process would constitute further phases of 

implementation. 

Staged Implementation in St. Albans Bay 

Compared to most of Lake Champlain, there are additional challenges to achieving water quality 

standards in St. Albans Bay. There is a significant sediment phosphorus load in this relatively shallow 

bay. It will take a significant amount of time before there will be a net reduction in the amount of 

phosphorus sequestered in the sediments. The implementation strategy for St. Albans Bay is designed to 

minimize the input of new phosphorus from the tributaries first. Thus the first stage will focus primarily 

on nonpoint source reductions and upgrading the St. Albans WWTF. Once the tributary input of 

phosphorus has been substantially reduced, if water quality standards are not yet attained in the bay, 

Vermont will continue with the evaluation, design, and permitting of an in-lake treatment to control 

internal phosphorus loading in the bay. 

The most heavily phosphorus laden sediments in St. Albans Bay are confined to a relatively welldefined area. Prior studies have evaluated the possibility of treatment with alum at the hot spot area. 

Once the tributary input of phosphorus to St. Albans Bay has been significantly reduced, Vermont will 

evaluate whether an intervention is feasible, affordable and would accelerate achieving water quality 

standards. 

Implementation in Missisquoi Bay 

Missisquoi Bay faces the most significant challenges in attaining water quality standards. This basin has 

the largest percent of land in agricultural use, and many of its streams are in unstable condition. There is 

also already a significant sediment phosphorus load. Achieving the load allocation in Missisquoi Bay is 

a long-term proposition. 

In light of the many challenges in the basin, Vermont has included a specific Missisquoi Bay section in 

the revised Phase1 Implementation Plan intended to accelerate the reduction of phosphorus inputs from 

the tributaries to the bay. The AAFM Secretary’s decision that BMPs are generally required in the 

watershed, further strengthens Vermont’s commitments to action. As detailed in the Reasonable 

Assurance discussion for Missisquoi Bay (Section 7.2.1), the State will make enhanced phosphorus 

reduction efforts to address agricultural, forestry, and unstable stream corridor sources, 

Unlike St. Albans Bay, there are no real prospects for interventions to address the existing sediment 

phosphorus sediment load in Missisquoi Bay. It is significantly larger than St. Albans Bay and the 

phosphorus-rich sediments are more widely distributed. Parts of the bay are in Canada and other 

sections are part of a wildlife refuge. Given these constraints, it is unlikely that dredging or treatment of 
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the sediments will be feasible. Natural processes will deplete the phosphorus in the sediment over a long 

period of time as watershed load reductions are achieved. 

Monitoring Plan 

While not a required part of a TMDL, EPA guidance recommends that TMDL submittals include a 

monitoring plan to determine whether implementation of the TMDL has resulted in attainment of water 

quality standards and to support any revisions to the TMDL that might be required. 

The ultimate measure of the success of the Lake Champlain Phosphorus TMDLs is the extent to which 

the in-lake phosphorus criteria are achieved. Lake phosphorus concentrations can be monitored 

relatively easily and unambiguously. However, in-lake phosphorus concentrations may or may not 

respond as expected to phosphorus management programs in the watershed. A more extensive 

monitoring effort – beyond simply measuring in-lake concentrations -- is necessary in order to 

understand the reasons for any changes, or lack of changes, observed in lake phosphorus levels so that 

management efforts can be redirected if necessary. 

There are six main monitoring and tracking activities ongoing or planned in the Lake Champlain Basin 

that, collectively, will support assessments of TMDL implementation progress and attainment of water 

quality standards. These monitoring activities will also provide data that can support future TMDL 

revisions. First, the lake long-term monitoring program collects a variety of water quality data, 

including phosphorus concentrations on each lake segment, including phosphorus concentrations. This 

monitoring will allow for the most direct evaluation of progress towards attainment of the TMDL goals 

(phosphorus criteria) for each lake segment. Second, water quality and flow data are collected at each 

major tributary to the lake. These two programs have been on-going since 1992, and are planned to 

continue into the future, with the support of the Lake Champlain Basin Program, the States of Vermont 

and New York, and the USGS. Third, wastewater treatment plant phosphorus loads are monitored by 

effluent sampling and flow measurements at all wastewater treatment facilities in the basin in order to 

verify compliance with the phosphorus wasteload allocation for each facility. Fourth, tributary 

monitoring in certain small watersheds (such as the Rock River and Mackenzie Brook) is on-going or 

planned in order to detect the effects of BMP implementation at a smaller scale. Fifth, edge-of-field 

monitoring to improve our understanding of the effectiveness of selected BMPs (especially agricultural 

and back road BMPs) is underway in several parts of the basin. The sixth element is the basin-wide 

BMP tracking program described in Section 7.3. This program, being established by VT DEC, will 

account for all BMPs implemented, and track associated phosphorus reductions. This program will also 

track land use changes that may affect phosphorus loads. Beyond these six activities, certain in-lake 

monitoring and modeling studies designed to improve our understanding of internal phosphorus 

dynamics (including exchanges with bottom sediments) have been supported in recent years through the 

Lake Champlain Basin Program and the University of Vermont. Some of this work is planned to 

continue. These monitoring and tracking efforts together constitute a comprehensive monitoring plan 

well suited for evaluating TMDL implementation progress, assessing attainment of water quality 

standards, and supporting future TMDL revisions. 
Page | 64 

CHAPTER 9: PUBLIC PARTICIPATION

The Lake Champlain TMDLs were developed with extensive public participation over the course of 

three and one half years. Much of the participation was conducted jointly by EPA and the Vermont 

agencies, the remainder was conducted by the Vermont agencies. 

Public participation was initiated in the fall of 2011 through a series of outreach sessions hosted by EPA, 

the Vermont DEC and Agency of Agriculture at various locations across the basin. Stakeholders were 

invited to provide input on sources of the phosphorus problem and suggested solutions. Participants of 

an In-Lake Modeling Workgroup and a Watershed Analysis Workgroup provided input on models for 

use in developing the TMDL. EPA invited scientists and others with technical expertise to contribute 

data and their opinions on the models. These workgroup meetings continued over the course of nearly 

two years. 

In early 2013, the Agency of Agriculture launched a facilitated dialogue with interested farmers which 

evolved into a working group that continued to provide input to the Agency on measures under 

consideration for the farming sector. At the same time, the DEC was engaged in dialogue with 

stormwater and wastewater sector groups. In the summer of 2013, EPA held a modeling workshop, 

providing interested parties with a view of the fruits of the in-lake and watershed models. 

In November 2013, DEC and the Agency of Agriculture released a draft “State of Vermont Proposal for a 

Clean Lake Champlain” for public review (Vermont, 2013). In December, EPA, the DEC and the Agency 

of Agriculture hosted public outreach sessions in Rutland, Middlebury, Montpelier, Burlington, St. 

Albans and Swanton. The meetings were advertised on the EPA and DEC websites and through press 

announcements. The meetings provided interested parties an update on the TMDL development process 

and the opportunity to provide feedback on a draft set of measures the Vermont agencies were 

considering to address nonpoint sources and point sources of stormwater, posted on their websites. 

Summaries of the feedback provided by meeting attendees were later posted on the DEC website. 

On March 31, 2014, Vermont released a draft Phase 1 Implementation Plan for EPA review and posted 

the document and transmittal letter on DEC’s website. On May 29, 2014, Governor Shumlin sent 

Vermont’s Phase 1 Implementation Plan to EPA and DEC posted the letter and document on its website. 

In December 2014, EPA, the DEC and the Agency of Agriculture again hosted public outreach sessions 

in Rutland, Middlebury, Burlington and St. Albans. The meetings were advertised on the EPA and DEC 

websites and through press announcements. EPA presented proposed wasteload and load allocations for 

each lake segment and the Vermont agencies reviewed the control strategies that would be used to 

achieve the stormwater portion of the wasteload allocations and the load allocations. The public 

presentation was posted on EPA’s website. A summary of the feedback received at the sessions and 

comments received after the meetings was posted on the DEC website. 

Pursuant to 40 C.F.R. § 130.7(d)(2), on August 15, 2015 EPA issued a public notice and provided a 30 

day period, later extended by 30 days for a total of 60 days, for the public to comment on the August 14, 

2015version of the TMDLs. EPA considered public comment, conducted additional analyses and made 

revisions deemed appropriate. EPA prepared a Response to Comments document and a document 

highlighting the changes between the August 15, 2015 proposed TMDLs and the final TMDLs, to 

accompany the TMDLs. EPA has transmitted the final Lake Champlain TMDLs to Vermont for 

incorporation into its current Water Quality Management plan. 
Page | 65 
Page | 66 

CHAPTER 10: REFERENCES

Web links provided where available. 

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phosphorus concentrations in St. Albans Bay, Lake Champlain: Assessment of internal loading and 

seasonal variations of phosphorus sediment-water column cycling. University of Vermont, 

Burlington, VT. Prepared for Agency of Natural Resources, Waterbury, VT. 

http://www.anr.state.vt.us/Dec/Waterq/erp/docs/StAlbansBaySedimentPstudy.pdf

ENSR Corporation, 2007. Feasibility Study for the Control of Internal Phosphorus Loading in St. 

Albans Bay, Lake Champlain, Phase 1: Evaluation of Alternatives. Prepared for the Agency of 

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http://www.watershedmanagement.vt.gov/erp/docs/StAlbansBay-FinalReport-Phase1.pdf

LaFlamme, P., 2016. Email communication from Pete LaFlamme, Vermont Department of 

Environmental Conservation, to Stephen Perkins, June 15, 2016. 

Lake Champlain Basin Program. 2013. Long-Term Water Quality and Biological Monitoring Program 

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Lewis, W.M., Jr., W.A. Wurtsbaugh, and H.W. Paerl. 2011. Rationale for control of anthropogenic 

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45:10300–10305. dx.doi.org/10.1021/es202401p. 

http://cires1.colorado.edu/limnology/pubs/pdfs/Website/Pub205.pdf

LimnoTech, Inc., 2012. Development of a Phosphorus Mass Balance Model for Missisquoi Bay. Tech. 

Rep. No. 65. Lake Champlain Basin Program. Grand Isle, VT. http://www.lcbp.org/wpcontent/uploads/2013/03/65_PhosphorusMassBalanceModel_MissisquoiBay_2012.pdf

LimnoTech, Inc., 2015. Missisquoi Bay Phosphorus Model – Extended Load Reduction Simulation 

Period Results. Memorandum to the Lake Champlain Basin Program. [See link on EPA’s Lake 

Champlain TMDL page: http://www.epa.gov/region1/eco/tmdl/lakechamplain.html ] 

Mearns, L. 2009. The North American Regional Climate Change Assessment Program (NARCCAP): 

overview of Phase II results. IOP Conf. Series: Earth and Environmental Science, 6: 022007. 

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Perciasepe, R. 1997. New policies for establishing and implementing Total Maximum Daily Loads 

(TMDLs). U.S. Environmental Protection Agency. Washington, DC. 

http://water.epa.gov/lawsregs/lawsguidance/cwa/tmdl/ratepace.cfm

Quebec, Gouvernment du and Government of the State of Vermont. 2002. Agreement Concerning 

Phosphorus Reduction in Missisquoi Bay. http://www.lcbp.org/wpcontent/uploads/2012/08/missbay_agreeEN.pdf
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Sawyer, A and B. Best-Wong. 2014. Revisions to the November 22, 2002 Memorandum “Establishing 

Total Maximum Daily Load (TMDL) Wasteload Allocations (WLAs) for Storm Water Sources and 

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Washington, DC. 

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1-12. doi:10.1098/rspb.2012.1032. 

http://rspb.royalsocietypublishing.org/content/early/2012/08/14/rspb.2012.1032

Smeltzer, E. 1999. Phosphorus management in Lake Champlain. pp. 435-451 In Manley, T.O. and P.L. 

Manley. eds. Lake Champlain in Transition: From Research Toward Restoration. American 

Geophysical Union. Water Science and Application 1. Washington D.C. 

Smeltzer & Quinn. 1996. A phosphorus budget, model, and load reduction strategy for Lake Champlain. 

Lake and Reservoir Management. 12:381-393.

http://www.watershedmanagement.vt.gov/lakes/docs/lp_lcmphosphorusbudget1996.pdf

Smeltzer, E, F Dunlap and M Simoneau. 2009. Lake Champlain Phosphorus Concentration and Loading 

Rates, 1990 - 2008. Tech. no. 57. Grand Isle: Lake Champlain Basin Program. 

http://www.lcbp.org/techreportPDF/57_Phosphorus_Loading_1990-2008.pdf

Sterner, R.W. 2008. On the phosphorus limitation paradigm for lakes. Internat. Rev. Hydrobiol. 93:433-

445. 

Stone Environmental. 2011. Identification of Critical Source Areas of Phosphorus within the Vermont 

Sector of the Missisquoi Bay Basin. Prepared for the Lake Champlain Basin Program, Grand Isle, 

VT, by Stone Environmental, Inc., Montpelier, VT. 

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Tetra Tech, Inc. and William Walker. 2011. Lake Champlain TMDL Support, Lake Modeling Approach 

Recommendation. Prepared for U.S. EPA Region 1. Fairfax, VA. 

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Tetra Tech, Inc. 2012a. Lake Champlain Phosphorus TMDL Watershed Modeling Approach 

Recommendation. Prepared for U.S. EPA Region 1. Fairfax, VA. 

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Tetra Tech, Inc. 2012b. Quality assurance project plan for Lake Champlain TMDL support. Prepared for 

EPA Region 1, Boston, MA, by Tetra Tech, Inc., Fairfax, VA. [See link on EPA’s Lake Champlain 

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Tetra Tech, Inc. 2014a. Technical Memorandum: Lake Champlain BATHTUB Model Quality 

Assurance. Fairfax, VA. [See link on EPA’s Lake Champlain TMDL page: 

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Page | 68 

Tetra Tech, Inc. 2014b. Technical Memorandum: Lake Champlain SWAT Model Quality Assurance. 

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Tetra Tech, Inc. 2015a. Lake Champlain BATHTUB Calibration Report; April 30, 2015. Prepared for 

U.S. EPA Region 1. Fairfax, VA. [See link on EPA’s Lake Champlain TMDL page: 

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Tetra Tech, Inc. 2015b. Lake Champlain Basin SWAT Model Configuration, Calibration, and 

Validation; April 30, 2015. Prepared for U.S. EPA Region 1. Fairfax, VA. [See link on EPA’s 

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Tetra Tech, Inc. 2015c. Lake Champlain BMP Scenario Tool: Requirements and Design; April 30, 2015. 

Prepared for U.S. EPA Region 1. Fairfax, VA. [See link on EPA’s Lake Champlain TMDL page: 

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Tetra Tech, Inc. 2015d. Lake Champlain Basin SWAT Climate Response Modeling; January, 2015. 

Prepared for U.S. EPA Region 1. Fairfax, VA. [See link on EPA’s Lake Champlain TMDL page: 

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Process. EPA 440/4-91-001. Washington, DC. 

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U.S. Environmental Protection Agency. 1999. Regional guidance on submittal requirements for lake and 

reservoir nutrient TMDLs. U.S. EPA New England Region. Boston, MA. 16 pp. 

http://www.epa.gov/region1/eco/tmdl/guidance.html

U.S. Environmental Protection Agency. 2003. Water Quality Trading Policy Statement. Washington, 

DC. http://www3.epa.gov/npdes/pubs/wqtradingtoolkit_appendices.pdf (see Appendix B) 

U.S. Environmental Protection Agency. 2009. Water Quality Trading Toolkit for Permit Writers. EPA 

833-R-07-004. Washington, DC. http://www3.epa.gov/npdes/pubs/wqtradingtoolkit.pdf

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ANR Secretary Markowitz. U.S. EPA New England Region, Boston, MA. 

http://www.epa.gov/region1/eco/tmdl/pdfs/vt/LakeChamplainTMDLDisapprovalDecision.pdf

U.S. Environmental Protection Agency. 2011b. Reconsideration of EPA’s Approval of Vermont’s 2002 

Lake Champlain Phosphorus Total Maximum Daily Load (“TMDL”) and Determination to 

Disapprove. U.S. EPA New England Region, Boston, MA. 

http://www.epa.gov/region1/eco/tmdl/pdfs/vt/LakeChamplainTMDLDisapprovalDecision.pdf

U.S. Environmental Protection Agency. 2013. Letter to DEC Commissioner David Mears. U.S. EPA 

New England Region, Boston, MA. 
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Vermont, State of. 2013. State of Vermont Proposal for a Clean Lake Champlain. Montpelier, Vermont. 

http://www.watershedmanagement.vt.gov/erp/champlain/docs/2013-11-

20_DRAFT_Proposal_for_a_Clean_Lake_Champlain.pdf

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Montpelier, Vermont. 

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Vermont, State of. 2015. Vermont Lake Champlain Phosphorus TMDL Phase 1 Implementation Plan, 

(Draft, August 2015). Montpelier, Vermont. [See link on VT DEC’s web page at: 

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Vermont Agency of Agriculture, Food and Markets. 2016. In re: CLF Petition to Require Mandatory 

Pollution Control Best Management Practices for Agricultural Non-Point Sources Identified in the 

Missisquoi Basin Plan. Revised Secretary’s Decision. AAFM Docket # 2014-6-14 ARM. 

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Revised-Secretary-Decision-CLF-Petition.pdf

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46). Waterbury, Vermont. http://www.anr.state.vt.us/dec/rules/pdf/chap17.pdf

Vermont Agency of Natural Resources, 2014. Vermont Water Quality Standards (effective October 30, 

2014). Montpelier, Vermont. 

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Vermont Department of Environmental Conservation and New York State Department of 

Environmental Conservation. 1997. A phosphorus budget, model, and load reduction strategy for 

Lake Champlain. Lake Champlain Diagnostic-Feasibility Study final report. Waterbury, VT and 

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Environmental Conservation. 2015. Lake Champlain Long-Term Water Quality and Biological 

Monitoring Program: Program Description. Montpelier, VT and Ray Brook NY. 

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Vermont DEC. 2016. Letter from Alyssa Schuren to Stephen Perkins. Re: Accountability Framework. 

Montpelier, VT. 

Walker, W.W. 1987. Empirical methods for predicting eutrophication in impoundments. Report 4: 

Applications manual. Tech. Rep. E-81-9. Prepared for U.S. Army Corps Eng. Waterways Exp. Sta. 

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Wayland, R and J. Hanlon, 2002. Establishing Total Maximum Daily Load (TMDL) Wasteload 

Allocations (WLAs) for Storm Water Sources and NPDES Permit Requirements Based on Those 

WLAs. U.S. Environmental Protection Agency. Washington, DC. 

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WaterVision, 2015. Technical Review of Lake Champlain TMDL Modeling Tools. Prepared for U.S. 

EPA Region 1, Acton, MA. [See link on EPA’s Lake Champlain TMDL page: 

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Wetzel, R.G. 2001. Limnology: Lake and River Ecosystems, Third Edition. Academic Press. San Diego, 

CA. 
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CHAPTER 11: ABBREVIATIONS AND ACRONYMS

AAFM Vermont Agency of Agriculture, Food and Markets 

ANR Vermont Agency of Natural Resources 

BMP Best Management Practice 

CAFO Consolidated Animal Feeding Operation 

CFR U.S. Code of Federal Regulations 

CGP Construction General Permit 

CLF Conservation Law Foundation 

CSO Combined Sewer Overflow 

CWA Clean Water Act 

DEC Vermont Department of Environmental Conservation 

EPA U.S. Environmental Protection Agency 

HRU Hydrologic Response Unit 

HUC Hydrologic Unit Code 

LA Load Allocation 

LCBP Lake Champlain Basin Program 

MDDEP Quebec Ministry of Sustainable Development, Environment, and Parks 

MGD Million Gallons per Day

mg/l milligrams per liter 

μg/L micrograms per liter 

MOS Margin of Safety 

MSGP Multi-sector General Permit 

MS4 Municipal Small Separate Sewer System 

mt/yr Metric tons per year 

NPDES National Pollutant Discharge Elimination System 

NRCS Natural Resource Conservation Service, U.S. Department of Agriculture 

NYSDEC New York State Department of Environmental Conservations 

RDA Residual Designation Authority 

SWAT Soil and Water Assessment Tool 

TMDL Total Maximum Daily Load 

USGS U.S. Geological Survey 

WLA Wasteload Allocation 

WQS Water Quality Standards 

WWTF Wastewater Treatment Facility
Page | 72 

APPENDICES

APPENDIX A

Future Growth from Developed Lands in the Lake Champlain Basin, Stormwater Management 

Program, VTDEC. October 8, 2015 

Available at: https://www.epa.gov/tmdl/lake-champlain-phosphorous-tmdl-commitment-cleanwater

APPENDIX B

Cross-walk between the Phase 1 Plan and EPA’s scenario runs to be inserted here 

Available at: https://www.epa.gov/tmdl/lake-champlain-phosphorous-tmdl-commitment-cleanwater