Evaluation of New York's Phase III Watershed Implementation Plan (WIP)
Executive Summary
The U.S Environmental Protection Agency (EPA) is providing this evaluation of New York's Phase III
Watershed Implementation Plan (WIP). EPA's review of New York's Phase III WIP found areas in
which the state addressed the goals of the Chesapeake Bay Total Maximum Daily Load (Bay TMDL)
and the expectations set by the Chesapeake Bay Program (CBP) partnership.
New York's Phase III WIP proposes reductions in agriculture based on extensive coordination between
farmers, the Upper Susquehanna Coalition (USC, representing all County Soil and Water Conservation
Districts in the watershed), New York State Department of Environmental Conservation, and the New
York Department of Agriculture and Markets. New York also provides a thorough gap analysis of the
stormwater sector and has provided a detailed list of strategies to achieve reduction targets which New
York believes will be necessary to achieve the nitrogen and phosphorus 2025 stormwater planning
targets. New York has also committed to upgrading wastewater treatment plants (WWTPs), which will
significantly improve nitrogen load reductions in the wastewater sector.
New York's Phase III WIP meets its numeric planning target for phosphorus at the state and state-basin
(Susquehanna) levels through the proposed implementation of Best Management Practices (BMPs) and
wastewater reductions. However, despite New York's extensive work in the agriculture communities of
the Chemung and Susquehanna watersheds, the nitrogen reduction resulting from full implementation of
the programs and practices detailed in the Phase III WIP falls short of the planning target by a total of
almost one million pounds per year. Therefore, EPA recommends that to continue to honor its
commitment to meet the CBP partnership's Bay TMDL planning goals for nitrogen by the 2025 date,
New York should develop annual numeric targets beginning in 2020-2021 that are based on
implementing programs and practices that result in meeting 100% of the planning target for nitrogen by
2025. EPA stands ready to assist in that development in any way possible.
In its Phase III WIP, New York identified implementation of five specific BMPs that account for 80% of
the WIP nitrogen load reduction moving forward. For confidence the planned load reductions will occur,
New York's WIP could have included detailed explanations about how New York will strengthen these
practices and programs, including the inspection and maintenance of the BMPs already implemented.
These concerns could be addressed through development of specific and detailed numeric targets for
BMP implementation in selected source sectors. New York should include 2-year numeric BMP
implementation targets for these five practices as part of its programmatic milestones.

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Evaluation of New York's Phase III Watershed Implementation Plan (WIP)
Background
The seven jurisdictions (Delaware, the District of Columbia, Maryland, New York, Pennsylvania,
Virginia, and West Virginia) in the Chesapeake Bay Program (CBP) partnership agreed to develop
Watershed Implementation Plans (WIPs) in three phases to provide a framework for reducing nitrogen,
phosphorus, and sediment loads to meet water quality standards in the Chesapeake Bay and its tidal
tributaries. The CBP partnership established the goal to have all practices in place by 2025 that were
necessary to achieve applicable water quality standards in the tidal Bay. The Chesapeake Bay TMDL
(Bay TMDL), which is an informational planning tool, established goals to be met using the CBP
partnership's timeline of 2025. In 2010, EPA worked with the CBP partnership to establish the Bay
TMDL based primarily on the Phase I Watershed Implementation Plan (WIP) commitments made by
each of the Bay jurisdictions. The CBP partnership agreed to develop Phase II and Phase III WIPs to set
out an adaptable approach for achieving the pollutant reductions and programmatic commitments that
New York intended to implement in each Phase so that it would meet its commitment to the CBP
partnership's 2025 goals.
The CBP partnership agreed that EPA should help provide accountability and assess whether (1) each
jurisdiction's WIP sets out sufficient commitments to meet the 2025 goals and (2) whether there is an
adequate level of confidence that the jurisdiction will achieve those specific commitments. While EPA
does not approve or disapprove a WIP, EPA provides the assessment for the benefit of the CBP
jurisdictions, and, as appropriate, may provide additional recommendations for strengthening the WIP or
its components. EPA evaluated New York's Phase III WIP to assess whether New York commitments
will meet the 2025 statewide and state-basin Phase III WIP planning targets and whether New York
included sufficient information in the WIP to provide confidence that New York will achieve these
targets by 2025.
Overview
In reviewing New York's Phase III WIP, EPA found areas in which the state addressed the expectations
set by the CBP partnership. Using the CBP partnership's suite of modeling tools, simulations indicate
that full implementation of New York's plan is expected to achieve 100% of the statewide and state-
basin (Susquehanna) Phase III WIP planning targets for phosphorus and 66% of the statewide planning
target for nitrogen.
Additionally, Phase III WIP planning targets for sediment were approved by the CBP partnership's
Management Board on October 17, 2019 and recommended to the Principal Staff Committee (PSC) for
final approval. In its Phase III WIP, New York committed to provide an addendum to its Phase III WIP
once the PSC approves these sediment targets. The Phase III WIP sediment targets will not affect the
BMPs called for in the WIP and are not intended to be the driver for implementation moving forward.
Some of the notable strengths identified in the Phase III WIP include:
• New York is pursuing dedicating a portion of the Environmental Protection Fund to the
Chesapeake Bay to increase funding.
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•	New York is considering tax credit programs for farmers to incentivize implementing agriculture
conservation practices. New York State Department of Environmental Conservation (NYSDEC)
expects to submit a legislative proposal to that effect.
•	New York has provided a detailed list of potential strategies and funding mechanisms in section
7.10 to increase stormwater BMP implementation.
•	Planned reductions in agriculture are based on extensive coordination between farmers, the
Upper Susquehanna Coalition (USC, representing all County Soil and Water Conservation
Districts in the watershed), NYSDEC, and the New York Department of Agriculture and
Markets. This outreach included numerous meetings and open houses held across the watershed
and several farmer surveys and follow-up analysis.
•	The long-established partnership of the State of New York with the local county soil and water
conservation districts through the USC provides a framework for and the ability to encourage
communications and outreach between the partnership and local agricultural producers and
service providers.
EPA's review, however, also noted remaining areas in New York's Phase III WIP that New York should
address moving forward to satisfy its commitments to the CBP partnership in meeting the 2025 goals.
Generally, New York's Phase III WIP lacks detail on how it will acquire additional funding and better
harness its existing funding to meet the nitrogen targets in the agriculture sector. In addition, New York
lacks an enhanced outline of how it will increase stormwater BMP implementation through additional
funding efforts and on the ground efforts, as all the funding sources proposed are already in use.
EPA Oversight and Assistance-
As it has done since the release of the Bay TMDL, EPA plans to continue to commit staff, contractual,
and funding resources to support the implementation of New York's Phase III WIPs and future two-year
milestones. This support includes evaluation of the most-effective practices and locations, annual WIP
assistance funding to address priority implementation needs, evaluation of New York's implementation
capacity under various staffing, funding, regulatory and programmatic scenarios, local planning
outreach, legislative and regulatory gap analysis, and monitoring trend analyses. In addition, EPA will
continue to work with federal partners to provide leadership and coordinate with New York on WIP and
two-year milestone implementation to reduce pollution from federal lands. EPA will continue its
commitment to track annual progress of New York and all the other Bay jurisdictions and make those
results available to the partnership and the public. [See: https://www.epa.gov/chesapeake-bav-
tmdl/epa-oversight-watershed-implementation-plans-wips-and-milestones-chesapeake-bav ]
Although New York made a commitment to the CBP partnership that it will achieve its numeric
planning targets for phosphorus and nitrogen at the state and state-basin (Susquehanna) levels through
the submission of best management practices (BMPs) and wastewater reductions, New York's Phase III
WIP acknowledges that the programs and practices to be implemented would result in achieving 66% of
its numeric planning targets for nitrogen. The Phase III WIP suggests additional measures that may be
pursued to close the nitrogen reduction gap through adaptive management - such as increasing voluntary
1 This Evaluation is not a final agency action and does not create any right, responsibility, or benefit, substantive or
procedural, enforceable by law or equity. Pursuant to the Anti-Deficiency Act, 31 U.S.C. §§ 1341 and 1342, all commitments
made by EPA in this Evaluation are subject to the availability of appropriated funds and budget priorities. Nothing in this
Evaluation obligates EPA to obligate or transfer any funds.
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participation, increased local partner capacity, and research into innovative techniques - without a clear
commitment for the implementation of those suggestions.
In our role to help New York improve its accountability to the CBP partnership in meeting its
commitment to the 2025 goals, EPA recommends that the following be included in New York's 2020-
2021 milestones to enhance the Phase III WIP as submitted and at the same time address New York's
recognized nitrogen gap.
Recommended Enhancements to the
Phase III WIP (See Detailed Review)
Recommended Actions
Information on several agriculture and
stormwater BMPs that were identified
as being widely under reported or
never reported in the WIP.
Develop specific numeric BMP implementation goals
within the 2020-2021 milestone period that directly address
the following underreported practices:
o Manure incorporation/manure injection
o Off-stream watering without fencing
o Tree planting
o Dairy precision feed management
o Land retirement/alternative crops
o Stream restoration
o Urban forestry
o Street sweeping
o Catch basin cleaning
o Retrofitting
Close the nitrogen gap that remains
after full implementation of New
York's Phase III WIP that
demonstrates only a 66 percent
achievement of its 2025 nitrogen
planning target.
Consider increasing the following BMPs (and strengthening
associated planned programs) to help close its 1 million-
pound nitrogen gap:
o Cover and Commodity Cover Crops
o Forest and Grass Buffers
o Livestock Waste Management Systems
o Soil and Water Conservation Plans
o Pasture Management BMPs
o Retirement of Highly Erodible Land
o Non-Urban Stream Restoration
o Manure Incorporation
Additional information to increase
confidence that practices that account
for most nitrogen load reductions will
be implemented.
•	Develop a specific milestone in the 2020-2021 period
that addresses progress on acquiring additional funding
for agriculture reductions.
•	Develop a specific milestone that addresses which
BMPs it will implement that will yield the highest
reductions using the most cost-effective approach.
Information to support significant
increases in BMP implementation
Develop specific numeric and programmatic milestones that
link specific programs or strategies with the BMP
implementation increase for the 2020-2021 period for the
BMPs expected to provide the most significant reductions
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levels and wastewater reductions, in
order from greatest to least.
(listed from greatest to least). These BMP account for 80%
of the WIP nitrogen load reduction:
o Bioretention/raingardens - A/B soils, no underdrain
o Infiltration Practices w/o Sand, Veg. - A/B soils, no
underdrain
o Forest Harvesting Practices
o Animal Waste Management Systems
o Soil Conservation and Water Quality Plans
o New York should include specific milestones on
wastewater reductions expected to be achieved.
Strategies to increase financial
incentives for producers in the
agriculture sector where New York is
relying on voluntary implementation.
Include a specific programmatic milestone for the 2020-
2021 period on its progress towards implementing BMP tax
credit programs.
Strategies to expand the technical
assistance capacity through Agriculture
Environmental Management (AEM)
Base Program.
Include a specific programmatic milestone for the 2020-
2021 period on progress toward increasing farm
participation in the AEM Program.
Explore Construction Stormwater and
MS4 general permit modifications as
well as strategies to increase
participation in the MS4 program.
Include a specific programmatic milestone for the 2020-
2021 period on its progress towards enhancing permits and
permit coverage to further reduce loading from regulated
areas.
Over the 2020-2021 milestone period, EPA plans to provide the following specific assistance to New
York to increase the level of confidence:
General
•	Provide annual grant (e.g., Chesapeake Bay Implementation Grant, Chesapeake Bay Regulatory and
Accountability Program, Local Government, etc.) and WIP assistance funding to New York to
support implementation of their Phase III WIP.
•	Track New York's progress with its initiatives and report to the CBP partnership.
•	Assist New York in such actions as targeting practices in higher loading counties, EPA plans to
continue to provide technical assistance, data and tools to aid New York in conducting assessments
at local levels, including water quality monitoring data, model analyses, high-resolution land cover,
improved stream networks, BMP opportunity layers and application of management-relevant
research findings, upon request.
Agriculture
•	Continue to work with New York to provide targeted financial assistance, if available, to support its
agricultural initiatives.
•	Advance opportunities to provide EPA grant funding directly to the New York's Department of
Agriculture and Markets, particularly in those instances where it can improve the timely expenditure
of Federal funds to support environmental protection goals (e.g., Chesapeake Bay Program grants).
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Stormwater
•	Provide New York with the opportunity to discuss current and future needs (financial,
programmatic, staffing) towards making progress on updating the Municipal Separate Storm Sewer
(MS4) permit to include Chesapeake Bay reporting requirements specific to part 9 section d of the
New York MS4 General Permit.
Wastewater
•	Track the progress on New York's WWTP upgrades, specifically its progress toward reducing its
average nitrogen treatment level for significant WWTP's.
Trading and Offsets
•	Continue to provide oversight and input into New York's trading and offset program by reviewing
draft regulations, and policies as well as participating on regulatory advisory committees.
Growth
•	Provide to New York a sector growth breakout for each sector based on state submitted progress data
each milestone period.
Detailed Evaluation of Overall Load Reduction and Source Sectors
The following sections provide specific highlights of key strengths of New York's Phase III WIP. These
sections also highlight areas for enhancement to assist New York in implementing its Phase III WIP and
subsequent two-year milestones to provide confidence that New York will have programs and practices
in place by 2025 to achieve its Phase III WIP planning targets.
Load Reduction Review
When evaluating New York's Phase III WIP numeric commitments, EPA modeled implementation
scenarios through the CBP partnership's Phase 6 suite of modeling tools and compared those simulated
nutrient2 loads to the New York's 2025 statewide and state-basin Phase III WIP planning targets. New
York provided two implementation scenarios (Current Program Scenario and 2025 Program Scenario) in
support of its draft Phase III WIP. The "Current program" scenario describes the numeric goals that
New York is committed to achieving by 2025. This scenario extends the Phase II level of
implementation into Phase III and assumes current levels of effort and funding. The 2025 Program
Scenario is a theoretical scenario that New York could use to close the gap between its Current Program
Scenario for agriculture and New York's Phase III WIP planning targets assuming significant additional
funding and resources. The following discussion of final numeric Phase III WIP loads is based on the
Current Program Scenario.
Simulations indicate that full implementation of New York's plan is expected to achieve 100% of the
statewide and state-basin Phase III WIP planning target for phosphorus (with an excess of 73,000
pounds). New York's plan does not achieve its statewide Phase III WIP planning target for nitrogen.
New York's plan will achieve 66% of needed statewide nitrogen reductions by 2025.
2 Phase III WIP planning targets for sediment were developed by the CBP partnership after the Phase III WIP submittal and New York
committed to address the sediment targets approved by the CBP partnership and to amend its Phase III WIP once the CBP partnership
approves these sediment targets.
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New York has divided its respective Phase III WIP planning targets into source sector goals to
demonstrate how pollutant load reductions will be achieved by 2025. In New York's Phase III WIP,
nitrogen load reductions are planned from implementation of best management practices (BMPs) in the
following sectors: stormwater (37%), wastewater (25%) and agriculture (24%). Phosphorus load
reductions are planned from implementation of BMPs in the following sectors: wastewater (25%),
stormwater (21%), and agriculture (9%).
Source Sectors
Agriculture
Key Strengths
Key strengths in New York's Phase III WIP include:
•	New York has committed to increase its implementation of nutrient management plans from 10%
(77,000 acres) to 19% (151,000 acres).
•	Planned reductions have been a result of extensive coordination between farmers, the Upper
Susquehanna Coalition (USC), New York State Department of Environmental Conservation, and the
New York Department of Agriculture and Markets. This outreach included numerous meetings and
open houses held across the watershed and several farmer surveys and follow-up analysis.
•	The long-established partnership of the State of New York with the local county soil and water
conservation districts through the USC provides a framework for and the ability to encourage
communications and outreach between the partnership and local agricultural producers and service
providers.
•	New York released an updated version of the Clean Water Act State Pollutant Discharge Elimination
System (SPDES) Concentrated Animal Feeding Operation (CAFO) General Permit in February
2019. This permit includes mandatory training of farm staff, enhanced practices in sensitive
groundwater areas, in-person oversight of manure transfer systems, and should help ensure that
previously implemented agricultural practices and management systems are properly utilized and
maintained through improved education and oversight.
•	New York created the CAFO Waste Storage and Transfer Program to assist CAFO farms with
meeting the minimum storage capacity required by the CAFO permit.
•	New York provided a detailed list of potential funding strategies and funding initiatives to fill the
gap in the agriculture sector. Potential strategies include increase voluntary implementation,
increase local partner capacity, expand BMP reporting and verification, account for state-specific
data in the Chesapeake Bay Watershed Model, support development of innovative tools and
research, explore new funding strategies including access to additional state funds.
•	New York has committed to adopting core nutrient management on 22% of available acres with a
goal to increase this number to 50% of available acres. In addition, New York has proposed a goal of
implementing supplemental rate, placement and timing on 40% of available acres.
•	New York has committed to pursuing additional funding to increase staff in the USC and its member
districts.
•	New York has provided more strategies and opportunities to effectively use its existing resources
and access additional state funding. More information is available in section 5.10.
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Enhancements
EPA recommends New York address the following in its 2020-2021 milestones to satisfy its CBP
partnership commitments:
•	In its 2020-2021 milestones, New York could report out on the progress made on acquiring
additional funding. Despite New York's efforts to implement the 2025 Program Scenario, the 2025
nitrogen target was missed by 900,000 lbs./year. It is estimated that an additional $92,000,000
would be required to meet the 2025 nitrogen targets. New York provided a list of potential funding
strategies to fill the agriculture gap, however EPA does not have confidence that the proposed
funding sources will be sufficient.
•	Include a more detailed explanation of how these BMP practices will be strengthened, including the
inspection and maintenance of the BMPs already on the ground in its 2020-2021 milestones. There is
a significant portion of planned nitrogen reductions, 80%, coming from BMP implementation.
Storm water
Key Strengths
Key strengths in New York's Phase III WIP include:
•	This is the first time that New York plans to achieve significant reductions in this sector.
•	New York proposed a detailed list of potential strategies to improve its stormwater sector program
delivery. Funding sources have been identified for each strategy and lead partners have been
identified. Additional information is available in section 7.10.
•	New York is currently revising the MS4 general permit. Any changes will be included as an
addendum to the Phase III WIP.
•	New York has provided additional information on strategies and funding mechanisms for achieving
implementation levels for each BMP or group of BMPs listed in Table 20 for MS4 and non-MS4
areas.
Enhancements
EPA recommends New York address the following in its 2020-2021 milestones to satisfy its CBP
partnership commitments:
•	Continue to track and report on the progress they are making towards achieving stormwater BMP
implementation levels listed in table 20 and focus specifically on those BMPs which are the most
cost effective.
•	Consider whether certain communities, facilities, or sources in the Chesapeake Bay Watershed might
qualify for designation as MS4s and, if such designations are made, consider including those sources
under the NYSDEC MS4 General Permit.
Wastewater
Key Strengths
Key strengths in New York's Phase III WIP include:
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•	New York is extending its Phase IIWIP level of effort for nutrient and sediment reductions into the
Phase III WIP, providing a high level of confidence that New York's wastewater strategy is feasible.
•	New York plans to remove the nitrogen bubble permit and nitrogen and phosphorus trading as
described in its Phase II WIP from existing permits to improve New York's ability to achieve
reductions at individual facilities.
•	The most updated model delivery factors to calculate the current delivery load and projected 2025
delivery load to the wastewater sector were used.
•	New York's commitment to planned WWTP facility upgrades should yield positive results and an
overall reduction in nitrogen concentrations.
Enhancements
EPA recommends New York address the following in its 2020-2021 milestones to satisfy its CBP
partnership commitments:
•	Consider reducing its average nitrogen treatment level (8.0 milligrams per liter) for those plants
receiving upgrades to compensate for smaller reductions in the agriculture and stormwater sectors.
Trading & Offsets
Key Strengths
Key strengths in New York's Phase III WIP include:
•	New York does not have any reserve nitrogen or phosphorus allocations for new or expanded
dischargers from WWTPs of any size. All such discharges are expected to offset 100% of new
loadings and SPDES permits are expected to include enforceable provisions to implement offsets.
Facilities may secure offsets by assimilation of existing septic systems, consolidation with other
WWTPs having wasteload allocations (WLAs), expanded facilities improve treatment, and/or use of
future trading programs.
•	New York plans to consider individual trading among SPDES with a WLA as a means of providing
flexibility for the implementation of the TMDL.
Federal Facilities
Federal facilities contribute less than 1% of New York's total load to the Bay.
Changing and Local Conditions
Growth
Key Strengths
Key strengths New York's Phase III WIP include:
•	New York developed its implementation scenarios based on 2025 forecasted growth conditions, per
the CBP partnership decision, and indicated that these growth conditions will be updated every two
years.
•	The nutrient and sediment loads in the agricultural and stormwater sectors are projected to change
over time. New York plans to address these increased loads with improved BMP reporting.
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Climate
Key strengths
Key strengths in New York's Phase III WIP include:
•	New York documented its jurisdiction-specific 2025 numeric climate change loads in the Phase III
WIP.
•	New York commits to several actions to address climate, including reducing greenhouse gas
emissions through its participation and development in ClimAid (the Integrated Assessment for
Effective Climate Change Adaptation strategies in New York), Smart Climate Communities, Cleaner
Greener Southern Tier Plan, and the Climate Resilient Farming Program. New York also fully
participates in the Regional Greenhouse Gas Initiative.
•	New York committed to adopting the new numeric climate change loads starting with the 2022-2023
milestones.
Local Engagement Strategies
Key Strengths
Key strengths in New York's Phase III WIP include:
•	New York's local engagement during the draft Phase III WIP development was strong in the
agriculture, wastewater, and stormwater sectors.
In its Phase III WIP, New York addressed the following potential enhancements that were suggested by
EPA in its draft Phase III WIP evaluation:
•	New York included detailed descriptions of local engagement strategies during Phase III WIP
implementation in its Phase III WIP.
Local Planning Goals
Key Strengths
Key strengths in New York's Phase III WIP include:
•	New York developed local planning goals that are measurable and below the major state-basin scale
in the Chesapeake Bay watershed, following the CBP partnership decision.
•	New York developed local planning goals at the sub-watershed scale and numeric BMP
implementation goals for the agricultural sector. New York also developed local planning goals at
the county scale and a percent reduction of existing loads will be tracked as the measurable outcome
for the stormwater sector.
•	New York explained that its local planning goals will be tracked using the Chesapeake Bay
Assessment Scenario Tool (CAST) and reported as part of New York's two-year milestones and/or
annual progress reporting.
•	New York provided further clarification of its key local partners responsible for implementing the
BMPs and load reductions in the agricultural and stormwater sectors. More information on these
partners is available in Section 3.
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BMP Verification
Jurisdictions agreed to follow CBP partnership-approved BMP verification protocols when developing
and implementing the Phase III WIPs. Because New York is proposing to increase BMP implementation
rates of some BMPs by 10-fold or more in the next seven years, New York should ensure that
implementation at this higher rate can be tracked, verified, and reported within that period in accordance
with the agreed upon verification protocols, or by another method established by the CBP partnership.
Regarding plans to conduct an inventory of data for BMPs that have already been implemented, it is
important that future reporting of this data include accurate implementation and inspection dates,
following the CBP partnership's verification protocols, or by another method established by the CBP
partnership..
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