(Photo) The Lower Stewart Ditch Salinity Project. Paonia, Colorado 

National Environmental Policy Act 

(NEPA) – Guidance for Preparing 

Salinity Control Program Projects

August 2018
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Table of Contents

Abbreviations and Acronyms ......................................................................................................... 1

Introduction to NEPA ..................................................................................................................... 2

NEPA Compliance .......................................................................................................................... 2

General Schedule for NEPA Compliance of Salinity Control Projects .......................................... 3

BLM Rights-of-Way and Other Requirements ............................................................................... 5

Habitat Replacement and Salinity Control Projects........................................................................ 5

Determining Habitat Losses ............................................................................................................ 5

Developing a Habitat Replacement Project and Plan ..................................................................... 6

Habitat Replacement Maintenance and Monitoring ....................................................................... 6

National Historic Preservation Act Compliance ............................................................................. 7

Endangered Species Act Compliance ............................................................................................. 8

Clean Water Act Compliance ......................................................................................................... 9

Draft Environmental Assessment ................................................................................................. 10

Final Environmental Assessment and FONSI .............................................................................. 11

Summary of Grant Recipient Responsibilities .............................................................................. 11

APPENDIX A – April 2018 Habitat Evaluation Procedures........................................................ 13
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Abbreviations and Acronyms

ACHP Advisory Council on Historic Preservation

APE Area of Potential Effect

BA Biological Assessment

BLM Bureau of Land Management

BO Biological Opinion

CE Categorical Exclusion

CEC Categorical Exclusion Checklist

CWA Clean Water Act

EA Environmental Assessment

EIS Environmental Impact Statement

ESA Endangered Species Act

FONSI Finding of No Significant Impact

FWS U.S. Fish and Wildlife Service

MOA Memorandum of Agreement

NEPA National Environmental Policy Act

NHPA National Historic Preservation Act

NRHP National Register of Historic Places

PBO Programmatic Biological Opinion

Reclamation Bureau of Reclamation

ROD Record of Decision

Salinity Control 

Projects

Basinwide or Basin States Salinity Control 

Program projects

SHPO State Historic Preservation Officer

USACE U.S. Army Corps of Engineers
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Introduction to NEPA

The National Environmental Policy Act (NEPA) of 1969, as amended, was created to assure that 

federal agencies, including the Bureau of Reclamation (Reclamation), consider environmental 

values and alternative uses of resources prior to undertaking any federal action. Using the 

NEPA process, agencies evaluate the environmental and related social and economic effects of 

their proposed actions. Through the NEPA process, agencies also provide opportunities for 

public involvement. The agency carrying out the federal action is responsible for complying 

with the requirements of NEPA. In some cases, there may be more than one federal agency 

involved in the proposed action. In this situation, a lead agency is designated to supervise the 

preparation of the environmental analysis. 

For salinity control projects awarded through the Basinwide or Basin States Salinity Control 

Programs (herein referred to as “salinity control projects”), the federal action is authorizing the 

use of federal funds to implement the salinity control project. Therefore, before Reclamation can 

decide to fund a salinity control project, Reclamation must comply with NEPA and other 

environmental laws. This guidance document focuses on the NEPA process associated with 

salinity control projects. 

NEPA Compliance

Compliance with NEPA can be accomplished in three ways, depending upon the degree and 

significance of environmental impacts associated with the application: 

• Some types of projects have been determined to have no significant effect on the 

environment and are “categorically excluded” (CE) from NEPA review. Reclamation 

policy is that CE reviews are documented by a Categorical Exclusion Checklist (CEC), 

prepared by agency staff and approved by the Area Manager or Regional Director. 

• If a project cannot be excluded from NEPA (does not fit within a CE), it requires 

preparation of an Environmental Assessment (EA). Salinity control program grant 

recipients should plan to hire an environmental consultant to prepare an EA and related 

compliance documents. If no potentially significant impacts are identified, the NEPA 

process ends with the preparation of a Finding of No Significant Impact (FONSI). 

• Certain projects have been determined by Reclamation to be major actions significantly 

affecting the environment. They require an Environmental Impact Statement (EIS). Major 

actions are listed in 516 Department Manual 14.4 and include construction of a new 

water project or major unit of an existing Reclamation project. It is not anticipated that 

salinity control projects will require completion of an EIS.

For salinity control projects, the grant recipient should plan to hire an environmental consultant 

to prepare an EA and related environmental compliance activities, with coordination, guidance, 

and document review by Reclamation. This is called third-party contracting. 
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General Schedule for NEPA Compliance of Salinity Control Projects 

While the timeframe for completing NEPA depends on the time of year in which NEPA 

preparation is initiated and the complexity of a proposed project, the grant recipient should plan 

for the EA and related compliance to take about one year to prepare. Certain resources which 

must be analyzed under NEPA have timing restrictions which may extend the time required to 

prepare the NEPA document. For example, surveys for endangered plant species may be 

required to be conducted during the plant’s flowering season, which may be a specific and short 

annual period, and may require more than one survey season. Following this example, if the 

environmental consultant is hired in July and plant surveys must be completed in June, finalizing 

the NEPA document would likely take longer than one year. This period is needed to collect and 

analyze the data for inclusion in the NEPA document, and to potentially conduct any required 

consultation with other agencies. 

A general schedule outlining common NEPA considerations and common permitting processes 

is included in Figure 1. Asterisks draw attention to those activities which have important timing 

considerations. More detailed information regarding the items mentioned in Figure 1 are 

discussed later in this guidance document. 

To help expedite the NEPA process as much as practicable, the following items should be 

identified as soon as possible: 

• Identification of all areas which have the potential to be impacted by the proposed 

project.

o This should include, but is not limited to, all potential pipeline alignments, 

existing canal alignments, entire construction corridor(s) width and length, 

staging areas, borrow areas, access routes, and habitat replacement areas. 

• Identification of potential habitat replacement projects.

It is important to include all areas required for implementing the project as part of the NEPA 

analysis. If specific plans are unclear, it is better to include an area in all surveys and in the 

NEPA document upfront, rather than identifying them later and potentially requiring additional 

surveys or overhauls of the drafted NEPA document. 
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Action Month 1 Month 2 Month 3 Month 4 Month 5 Month 6 Month 7 Month 8 Month 9 Month 10 Month 11 Month 12

Initiate NEPA XXX

Proposed Alignment XXX

Scoping XXX

Cultural Resources

 Cultural Resource Inventory* XXX XXX

 Cultural Resource Draft Report Review XXX

 Finalize Report and Consult with CO SHPO XXX XXX

 Invite ACHP if impacts to Historical 

Properties XXX XXX

 Prepare, Distribute, and Execute MOA XXX XXX XXX

Conduct Surveys and Inventories* 

 (T&E species, Sensitive Species, etc.) XXX XXX XXX

Discuss Potential Habitat Replacement Plan 

w/Reclamation XXX XXX XXX

Evaluate Habitat Losses->Reclamation 

review/concurrence* XXX XXX XXX

Prepare Draft EA XXX XXX XXX XXX

BOR Review Draft EA XXX XXX

Distribute Draft EA for Public Comment XXX

Estimate Project Depletions XXX

Consult with FWS on impacts to T&E species

and Historic Depletions XXX XXX

Sign Recovery Agreement XXX

Develop Habitat Replacement Plan XXX XXX XXX XXX

Prepare Final EA XXX

BOR Review Final EA XXX

Issue Finding of No Significant Impact XXX

Construct Habitat Improvements* XXX XXX XXX XXX

Figure 1. General NEPA Process and Documentation Schedule1

1 All schedules and general timeframes contained in this guidance document are for planning purposes only. Actual timelines may vary, as each salinity control project carries its own unique complexities, and review times are 

dependent on the individual schedules of multiple individuals across various agencies.
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BLM Right-of-Way Acquisition and Other Requirements

Some salinity control projects include construction on lands managed by the Bureau of Land 

Management (BLM). In these cases, it may be necessary for the grant recipient to obtain 

temporary or permanent right-of-way permits for construction activities or new canal alignments 

on BLM managed lands. The issuance of right-of-way permits is a federal action by the BLM, 

and therefore requires compliance with NEPA. In cases where two federal agencies have an 

action on the same project, the agencies streamline the NEPA process by ensuring a NEPA 

document is prepared which addresses both federal actions. For salinity control projects in 

which the BLM has a federal action, the BLM typically reviews cultural resource (i.e., NHPA 

Section 106) and threatened and endangered species consultation documentation (i.e., ESA 

Section 7), provides comments on the Draft EA prior to the public notification, and prepares a 

separate FONSI. As a result, review times for these items may be extended beyond what is 

shown in Figure 1. 

If a salinity control project is located within any BLM lands, BLM may require a survey for 

BLM sensitive species. The grant recipient is responsible for coordinating with BLM to 

determine if it is necessary to survey for BLM sensitive species, and for conducting the survey. 

This survey could be performed during the threatened and endangered species survey. 

Habitat Replacement and Salinity Control Projects

The Colorado River Basin Salinity Control Act, as amended, requires that salinity control 

projects implement measures to replace incidental fish and wildlife values foregone as a result of 

implementing a salinity control project. Riparian and/or wetland habitat which was 

anthropogenically established due to the water available from canal seepage is typically the type 

of habitat permanently foregone as a result of lining or piping canals. Once canal seepage is no 

longer available, the riparian/wetland habitat will be permanently lost. Therefore, habitat 

replacement projects are included as required mitigation for most salinity control projects. 

Reclamation has developed procedures for determining habitat value in this context. The April

2018 Salinity Control Program: Fish and Wildlife Habitat Evaluation Procedures (evaluation 

procedures) provide a consistent format for quantifying habitat losses and evaluating habitat 

replacement sites. These procedures are provided in Appendix A. 

Determining Habitat Losses

The grant recipient is responsible for conducting habitat loss surveys utilizing the evaluation 

procedures and preparing a habitat losses report. The habitat losses report will identify the 

amount and value of riparian/wetland habitat that will be permanently lost due to implementing 

the salinity control project. This value is represented as a “habitat unit,” and is the numerical 

representation of the habitat which will need to be replaced through the development of a habitat 

replacement project. Reclamation will review and approve this report prior to its finalization. 
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Developing a Habitat Replacement Project and Plan

The grant recipient is responsible for replacing all lost riparian and/or wetland habitat. This is 

done by identifying a suitable habitat replacement site, then developing and implementing a 

habitat replacement plan. Early coordination between the grant recipient, Reclamation, and the 

U.S. Fish and Wildlife Service (FWS) is important to identify a potential habitat replacement 

site, determine objectives for a habitat replacement project, and to develop a habitat replacement 

plan that will meet the project objectives. This process is arguably the most time-consuming 

NEPA-related activity, so it should be started as early as possible. s 

The following list outlines the typical approach and requirements for developing a habitat 

replacement project:

• Identify a suitable habitat replacement site.

o The land must contain riparian or wetland areas that can be restored or enhanced. 

o Existing and proposed private land uses must be compatible with habitat 

objectives.

o Private property must be adequately protected, such as through a conservation 

agreement or deed restriction. 

o Public lands must have compatible land management to safeguard habitat 

objectives. If public lands are considered, the managing entity must be involved 

in the development of the habitat project objectives and must ultimately approve 

the habitat replacement project plan.

• In the event any new open water features are proposed as a component of the habitat 

replacement project, water samples for selenium testing will be required. In cases where 

sampling is required, the selenium levels must be below current selenium standards for 

the project to be considered further. 

• A site visit must be conducted with the grant recipient, Reclamation, and FWS to 

determine if the area appears to be compatible with anticipated objectives of the habitat 

replacement project. If it is determined the area is acceptable for a habitat replacement 

project, the grant recipient may move forward with developing the habitat replacement 

plan. 

• A habitat replacement plan must be developed by the grant recipient and reviewed by 

Reclamation. Each Reclamation Area Office can offer guidance on what is required in a 

habitat replacement plan, so it is important to ask for any templates or other resources 

which may be available. The habitat replacement plan must be finalized prior to signing 

a FONSI for the salinity control project. Habitat replacement projects are required to be 

implemented concurrently with the salinity control project.

Habitat Replacement Maintenance and Monitoring

The habitat replacement project is required to function for the life of the salinity control project, 

which is typically 50 years. The grant recipient is responsible for maintaining the habitat 

replacement project. Salinity funds cannot be used for maintenance. While all habitat 

replacement projects will require maintenance, some projects will require more than others, so it
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is important to develop a plan which minimizes the amount of ongoing maintenance. Future 

weed control, replanting or reseeding, water control structure maintenance, fencing, sediment 

removal, etc. are considered maintenance, and will be the responsibility of the grant recipient for 

the life of the project.

Monitoring is required for the life of the project. How monitoring is conducted may vary 

between Reclamation Area Offices. Monitoring may include site visits with Reclamation for the 

first five years, with yearly reporting to Reclamation. After five years, monitoring and reporting 

frequency may be adjusted to every three to five years for the remaining life of the project.

National Historic Preservation Act Compliance

Cultural resources are defined as physical or other expressions of human activity or occupation. 

Section 106 of the National Historic Preservation Act (NHPA) requires the lead federal agency 

to consider potential effects to cultural resources that are listed on, or eligible for listing on, the 

National Register of Historic Places (NRHP). 

Surveys are conducted to determine if there are any cultural resources within a proposed 

project’s Area of Potential Effect (APE); if cultural resources are identified, recommendations 

are made for NRHP listing eligibility. Reclamation coordinates with each state’s State Historic 

Preservation Officer (SHPO) for an official determination on resource eligibility and effect

proposed by a federal action. Adverse effects often require mitigation. 

The grant recipient is responsible for hiring a contractor qualified by the State Historic 

Preservation Officer or BLM to conduct “Class III” cultural resource surveys under the National 

Historic Preservation Act. The contractor will provide Reclamation with a report and site forms. 

Class III surveys include literature reviews of the project area, as well as on-the-ground 

pedestrian surveys. Surveys must be conducted while the ground is visible, so there cannot be 

snow cover. The surveys must cover the APE, which includes all potential pipeline alignments, 

existing canal alignments, construction corridors, staging areas, borrow areas, access routes, and 

habitat replacement areas. Reclamation archaeologists will review the APE prior to the survey 

being conducted and will review the draft survey report and site forms prior to finalization. 

Once finalized, Reclamation will consult with the appropriate SHPO, and will invite the 

Advisory Council on Historic Preservation (ACHP), the local government, and the appropriate 

Indian tribes to participate in the Section 106 process. A general timeframe after receipt of the 

draft report and forms is:

• Reclamation reviews the draft survey report and site forms and provides any comments – 

2 weeks

o If an APE extends onto lands under a different agency’s jurisdiction (e.g., BLM), 

that agency will be given the chance to review the report as well, and will be 

invited to participate in the Section 106 process. 

• Reclamation receives the final survey report and site forms and submits them to the 

SHPO along with findings of eligibility and effect to historic properties – 2 weeks

• The SHPO reviews the findings of eligibility and effect. If the finding is no adverse 

effect, the SHPO has 30 days to concur or disagree. 
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• If it is determined that there will be an adverse effect to an eligible historic property, a 

Memorandum of Agreement (MOA) will be required to agree upon mitigation measures. 

• Once Reclamation receives the SHPO’s determination, Reclamation invites the ACHP to 

participate in the Section 106 process – 15-30 days 

• Reclamation invites the local government and the appropriate Tribes to participate in the 

Section 106 process – 30 days 

• Reclamation drafts an MOA and distributes it to the SHPO and the grant recipient for 

comment – 1 week

• Reclamation routes the MOA to the SHPO, applicant, and all participating parties for 

signature – 30-60 days 

o A signed MOA is required prior to Reclamation signing a CE or FONSI.

o The grant recipient typically has a one-year period from the execution of the 

MOA to fulfill the stipulations outlined in the MOA. For historic structures or 

buildings, mitigation generally consists of archival-quality photographic 

documentation. 

Endangered Species Act Compliance

The process of complying with the Endangered Species Act (ESA) includes identifying any 

federally listed endangered, threatened, and proposed plant and animal species and their 

proposed and designated critical habitats, assessing effects of the project on them, and 

consultation about ways to avoid, reduce or mitigate adverse effects or “take." The grant 

recipient is responsible for hiring a qualified biologist, who will survey and/or perform a data 

review to determine presence of threatened and endangered species in the action area. The 

biologist is also responsible for preparing a biological assessment that analyses effects to listed 

species that may result from the proposed action. Reclamation will utilize this information to 

consult with the FWS. 

A general timeframe for ESA compliance, after completion of all surveys, is:

• Reclamation reviews the draft biological assessment (BA) and provides any comments – 

2 weeks

• If the finding is no effect, no further action under the ESA is required; Reclamation 

documents this finding in the CE or EA. 

• If the finding is “may affect, not likely to adversely affect”, Reclamation requests 

informal section 7 consultation by forwarding the BA to the FWS. The FWS will issue a 

concurrence letter if they are in agreement with the effects determination. FWS has 30 

days to respond with their concurrence. 

• If the finding is “may affect, likely to adversely affect”, Reclamation forwards the BA to 

the FWS to initiate formal consultation. The FWS is required to prepare a biological 

opinion. Formal consultation completion may take up to 135 days once the FWS 

receives the BA.

There are four endangered fish species within the upper Colorado River basin; the Colorado 

pikeminnow, razorback sucker, humpback chub, and bonytail, and all havedesignated critical 
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habitat. Historic and current water depletions in the Colorado River system due to irrigation 

practices and other consumptive uses have been determined to be an adverse effect to the four 

fish species. Reclamation and the FWS have worked together to develop Programmatic 

Biological Opinions (PBO) to address historic depletions within some river basins. When 

salinity control projects are located within basins covered by a PBO, the grant recipient is 

required to enter into a Recovery Agreement with the FWS to officially document that the grant 

recipient’s historic depletions have previously been consulted on and included under the 

umbrella of the PBO. Grant recipients who have previously entered into a Recovery Agreement 

may not need to repeat this process if their Recovery Agreement included all their historic 

depletions. 

A general timeframe for each component of Section 7 ESA consultation is: 

• Reclamation reviews the draft survey report and provides any comments – 2 weeks

o If the salinity control project extends onto lands under a different agency’s 

jurisdiction (e.g., BLM), that agency will be given the chance to review the report 

as well, and will be invited to participate in the consultation process.

• Reclamation receives the final survey report and submits it to the FWS, initiating 

consultation. The FWS receives the survey report and makes the decision of whether 

they concur with Reclamation’s effect determination – 90 days 

• If a BO is required, the FWS prepares the BO – 45 days 

o The Recovery Agreement, if needed, is executed during this time, and is included 

in the BO. 

Clean Water Act Compliance

Reclamation must ensure the salinity control project complies with the Clean Water Act (CWA)

and will coordinate with the U.S. Army Corps of Engineers (USACE) to ensure compliance. 

Typically, proposed work included in salinity control projects are the types of activities that are 

included in the Section 404(f) exemption for the construction or maintenance of farm or stock 

ponds or irrigation ditches, or the maintenance (but not construction) of drainage ditches. 

However, work associated with the habitat replacement project may require a Section 404 CWA 

permit. Each Reclamation Area Office will coordinate with the USACE to verify that the 

salinity project falls within this exemption. In the event the salinity control project does not fall 

within this exemption, the grant recipient is responsible for obtaining a Section 404 permit from 

the USACE.

There is a general assumption that wetlands associated with canal and lateral seepage do not 

meet the definition of jurisdictional wetlands in the 1989 Federal Manual for Identifying and 

Delineating Jurisdictional Wetlands and the 1987 Corps of Engineers Wetlands Delineation 

Manual. Therefore, the USACE typically does not require wetland mitigation for wetland loss 

associated with canal and lateral irrigation service removal. If it is determined that any wetland 

area is jurisdictional under the Clean Water Act, additional permitting and mitigation may be 

required. 
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Draft Environmental Assessment

The grant recipient is responsible for preparing a Draft EA for their salinity control project. 

Please contact your local Reclamation Area Office for an example or template for an EA. EAs 

must be no longer than 75 pages, not including appendices. The Draft EA must analyze the 

Proposed Action and No Action Alternatives. EAs identify the purpose and need for the 

proposed action, describe the alternatives, and analyze impacts to resources which may occur as 

a result of implementation of either the Proposed Action or No Action Alternatives. The 

Proposed Action Alternative description must include all components of the salinity control 

project, including the salinity control project itself (i.e. lining or piping a canal) and the habitat 

replacement project. Depending on the potential for public controversy or heightened public 

interest in the salinity control project, the grant recipient may choose to hold a public scoping 

meeting and/or formal public scoping period to identify potential resources of concern to address 

in the environmental analysis. Resources analyzed may include (as appropriate), but are not 

limited to:

• Water Rights & Use

• Water Quality

• Air Quality

• Access, Transportation, & Public 

Safety

• Recreational & Visual Resources

• Livestock Grazing 

• Vegetative Resources

• Wildlife Resources

• Special Status Species

o Migratory Birds & Raptors 

o Threatened & Endangered 

Species

o BLM Sensitive Species

• Cultural Resources

• Agricultural Resources & Soils

• Cumulative Impacts

Once the Draft EA is prepared, Reclamation will review and make comments on the draft. This 

review typically takes one month to complete. In some instances, more than one review of the 

document may be necessary. When all comments and edits have been incorporated, the Draft 

EA must be made “508 Compliant,” or compliant with Section 508 of the Rehabilitation Act of 

1973. A 508 Compliant document is an electronic document which has been made accessible to 

people with disabilities; these documents are structured to be readable by electronic accessibility 

software.

The grant recipient is responsible for developing a distribution list of appropriate contacts to 

inform of the availability of the Draft EA for public comment. The distribution list could include 

landowners near the canal (i.e. adjacent to the canal, within a specified distance of the project, 

etc.), shareholders, and agencies. Agencies may include, but are not limited to: 

• Department of Transportation 

• Historical Societies and State SHPOs

• Division of Wildlife/Parks and 

Wildlife

• Colorado River Water Conservation 

District

• State Water Conservation Boards

• County Planning and Development 

• County Road and Bridge 
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• Towns 

• US Army Corps of Engineers 

• BLM

• FWS

• Conservation Centers

The Draft EA is posted on Reclamation’s website for public review and comment typically for a 

period of 30 days. Notice of the availability of the Draft EA is sent to the contacts on the 

distribution list on the first day of the public comment period. 

Final Environmental Assessment and FONSI

The grant recipient is responsible for preparing a Final EA and FONSI (if appropriate) for their 

salinity control project. Any substantive comments received during the Draft EA comment 

period will be included in the Final EA, and responses will be provided for any substantive 

comments. Reclamation will review and make comments on the draft. Depending on the 

comments received and the need to make substantial changes within the document, this review 

may take one month to complete, and more than one review of the draft may be necessary. Once 

all comments and edits have been incorporated and the Final EA/FONSI is made 508 Compliant, 

Reclamation will present the Final EA/FONSI to the decision maker. After reviewing the 

document, if the decision maker determines that the project will not result in a significant 

environmental impact, he/she will sign the FONSI. Once the FONSI is signed, the NEPA 

process for the salinity control project is complete. No work may be initiated on any portion of 

the salinity control project until the FONSI is signed. 

Summary of Grant Recipient Responsibilities

The following actions must be completed by the grant recipient during the NEPA process: 

• The grant recipient performs NEPA compliance activities, with coordination, guidance, 

and document review by Reclamation. Grant recipients typically contract this work out 

to consultants with appropriate NEPA, biological and natural resource policy expertise. 

• The grant recipient is responsible for obtaining any temporary or permanent rights-ofway permits required for construction activities or new canal alignments on BLM 

managed lands. 

• The grant recipient is responsible for conducting habitat loss surveys utilizing the 

evaluation procedures and preparing a habitat losses report.

• The grant recipient is responsible for identifying a suitable habitat replacement site, and 

developing and implementing a habitat replacement project. 

• The habitat replacement project is required to function for the life of the salinity control 

project, which is typically 50 years. The grant recipient is responsible for maintaining the 

habitat replacement project. Salinity funds cannot be used for maintenance. 

• The grant recipient is responsible for obtaining an intensive “Class III” cultural resource 

surveys on their salinity control project’s APE. If an MOA is executed, the grant 

recipient is responsible for fulfilling the stipulations outlined in the MOA.

• The grant recipient is responsible for obtaining a threatened and endangered species 

survey and, if applicable, a BLM sensitive species survey on their project area. A 

biologist with ESA-BA expertise will prepare a BA for Reclamation. 
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• In the event the salinity control project does not qualify for a Section 404 permitting 

exemption, the grant recipient is responsible for obtaining a Section 404 permit from the 

USACE.

• The grant recipient is responsible for preparing an EA for their salinity control project.

• The grant recipient is responsible for developing a distribution list of appropriate contacts 

to inform of the availability of the EA for public comment. 

• The grant recipient is responsible for preparing a Final EA and FONSI (as appropriate) 

for their salinity control project.
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APPENDIX A – April 2018 Habitat Evaluation Procedures

Salinity Control Program:

Fish and Wildlife Habitat Evaluation Procedures

SUMMARY: These habitat evaluation procedures have been prepared by a joint Bureau of 

Reclamation (Reclamation) – U.S. Fish and Wildlife Service (FWS) team to satisfy the 

requirements of the Salinity Control Act. Salinity control projects must provide for the 

mitigation of fish and wildlife (habitat) values lost as a result of implementing a project. A 

standardized methodology for determining habitat functions and values is presented. 

Monitoring and recordkeeping are discussed.

I. AUTHORITY

The requirement and authority to implement habitat replacement features were first included in 

the 1984 amendments, Public Law 98-569, to the Salinity Control Act, Public Law 93-320 

(Act). The Act, as amended, states:

• Section 202(a)(l)-(5): “The Secretary shall construct, operate, and maintain the salinity 

control units ... consisting of measures to replace incidental fish and wildlife values 

foregone.” 

• Section 202(b)(6): "In implementing the units authorized to be constructed pursuant to 

subsection (a) of this section, the Secretary shall implement measures to replace incidental 

fish and wildlife values foregone concurrently with the implementation of a unit's, or a 

portion of a unit's, related features.”

The Salinity Control Act’s 1995 and 2008 amendments, Public Law 104-20 and Public Law 

110-246, created the Basinwide Salinity Control Program and the Basin States Program, 

respectively. These amendments authorized Reclamation to implement cost-effective 

opportunities to control salinity via a one-time grant that is limited to an applicant’s 

competitive bid. The cost of this mitigation has typically been included in the costs of the 

salinity control projects used in computing cost effectiveness. Habitat replacement 

requirements established in the 1984 amendments extend to salinity control projects 

implemented under the Basinwide and Basin States Programs.

II. IMPORTANT CONSIDERATIONS

A. Funding Opportunity Announcement (FOA)

The costs of implementing habitat replacement projects are calculated as part of the salinity 

project’s cost effectiveness value (cost per ton). If the habitat replacement project will involve 

the construction of water features, there may be a reduction in salt credit for the salinity project, 
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which may impact the project’s cost effectiveness value or result in a decrease of funding. If 

habitat replacement project costs are unknown, an assumption of 5% can be used as a minimum

for calculating the salinity project’s cost effectiveness; however, the habitat project could cost 

more. Successful project applicants become responsible for formulation, implementation, and 

long-term operation and maintenance of their habitat replacement projects. Any avoidance 

measures or land acquisition should be identified and authorized prior to project submittal 

through the FOA. Approval must be requested and obtained prior to FOA submittal if an 

applicant wishes to utilize “excess” habitat credits created by a previous habitat replacement 

project.

B. Regulatory Requirements

Habitat losses and the habitat replacement plan will be included in the salinity control project’s 

NEPA analysis. The habitat replacement portion of a salinity control project is subject to the 

same regulatory requirements as the salinity control project. Therefore, the Endangered 

Species Act, Clean Water Act, National Historic Preservation Act, and other considerations 

need to be evaluated and accounted for. Selenium sampling of water used for any proposed 

open water features is needed to ensure compliance with state water quality standards. 

Reclamation should be included during the development stages of any habitat replacement plan

to help ensure compliance with regulatory requirements. 

There is a general assumption that wetlands associated with canal and lateral seepage do not 

meet the definition of jurisdictional wetlands in the 1989 Federal Manual for Identifying and 

Delineating Jurisdictional Wetlands and the 1987 Corps of Engineers Wetlands Delineation 

Manual. If wetland sites are classified as jurisdictional under the Clean Water Act, additional 

permitting and mitigation may be required after consulting with the U.S. Army Corps of 

Engineers.

III. GOAL

The intent of these procedures is to provide a consistent methodology for quantifying habitat 

losses and evaluating habitat replacement sites. 

IV. DEFINITIONS

Acquisition is the purchase of land and/or recordation of an approved, protective mechanism 

for the benefit of restoration, preservation and/or protection from imminent threat of 

development.

Additionality is a project or practice that will improve upon an existing condition, which is 

demonstrably new and would not have occurred otherwise. When identifying potential habitat 

replacement projects on land currently managed for wildlife, or on public lands with 

management criteria for wildlife, documentation will be needed to address additionality.

Avoidance of impacts means incorporating measures in a salinity control project that will 
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avoid impacts to existing wetland and riparian habitat. This is the preferred approach to project 

planning and implementation if it neither results in deep percolation nor contributes to salinity 

loading into the Colorado River. Maintaining open segments of canals should be identified and 

included as part of the applicant’s FOA project submittal. When impacts to wetland or riparian 

habitat are unavoidable, then habitat losses need to be calculated and habitat replacement is 

required.

Habitat losses include habitat which will be permanently lost due to implementation of the salinity 

control project. Riparian and wetland habitat types are generally the habitats types which are 

permanently lost due to their reliance on canal seepage, and therefore are the only habitat types 

which should be considered when determining habitat losses. 

Habitat Quality Score (HQS) is the average value of habitat quality assigned to an area that is 

calculated using the habitat evaluation criteria set forth in this document. 

Preservation of existing pre-project habitat means the habitat will persist in some form after 

implementing the salinity project due to the presence of other water sources. For example, 

habitat along a canal which is also located near a natural seep or drainage.

Replacement means the creation or enhancement of riparian or wetland habitat to replace 

habitat values lost as a result of implementation of a salinity control project. Replacement must 

result in no net loss of habitat values. Following is an example:

• The implementation of a salinity control project is determined to cause the loss of 20 

habitat units.

• To replace that loss, a replacement property is located where the 20 units can be created 

by enhancing habitat through plantings, grazing management, wetland or riparian area 

development, weed control, etc.

• The replacement property is determined to have a baseline of 10 habitat units in its

current condition; therefore, once the habitat replacement plan is implemented, the 

habitat replacement project area would need to create 20 habitat units, for a total of 30 

habitat units overall.

Total Habitat Value (THV) is a calculation based on the HQS multiplied by the total acreage of a 

habitat area.

V. ASSUMPTIONS

Basic assumptions of the habitat evaluation procedures include:

• Riparian/wetland habitat should be the main focus when determining habitat value lost, since 

upland habitat would persist after project implementation. Typically, an evaluator can refer to a 

plant species’ wetland indicator status rating. However, evaluators should have an 

understanding of the ecological community they are evaluating. Their expertise should be 

relied upon when determining whether vegetation is present solely or primarily due to the 

increased soil moisture from canal seepage. 
16 | Page

• Unless stated otherwise, noxious weeds (regardless of wetland indicator status rating) should be 

considered in the habitat value scoring. 

• The determination of each habitat’s source(s) of water should be made by studying aerial 

photography, topographic maps, and simple on-site ocular analysis of the habitat site, its 

surrounding terrain, and the location of the site in relation to its nearest potential water 

source(s). 

• For the purposes of estimating habitat losses, piping or lining an open ditch is assumed to 

eliminate 100% of the seepage from that ditch. In this case, 100% of adjacent riparian or 

wetland vegetation providing habitat would be assumed to be lost unless there is some other 

water source nearby (e.g., an irrigated field, groundwater from another source, or natural 

seeps and drainages) to maintain a portion of the vegetation. This loss is assumed to be 

immediate, regardless of how long it might actually take for the vegetation to be lost. 

Therefore, habitat values calculated for these areas are assumed to be a 100% loss.

• When identifying the apparent source or sources of water supporting each habitat area, wetland 

and riparian vegetation immediately downslope from a canal can be attributed to canal or lateral 

seepage, particularly if upland vegetation is found in the area directly upslope from the canal. 

• Wetland and riparian vegetation along and immediately downslope of farm ditches within

irrigated fields can usually be attributed to deep percolation from on-farm irrigation 

management, and would therefore remain after construction of the project. 

• Streamside habitat and wetlands obviously entirely supported by natural hydrology should not 

be calculated as a habitat loss. In these situations, identify the area in the losses report and 

provide rationale for not including the area in the habitat losses calculation.

• In situations where both natural hydrology and canal seepage contribute to a riparian/wetland 

area, best professional judgment should be used to estimate preservation. To account for the 

estimated preservation, complete an existing and anticipated future score for the area. The 

difference between the two should be included in the total habitat units lost.

• The surface area of the open water of the canal should not be included in the acreage when 

calculating habitat loss. Any open water acreage within a habitat replacement area can be 

considered when scoring the habitat replacement project. 

• Habitat replacement projects must be located on lands where a recorded, legal protective 

mechanism is in place to ensure the habitat will persist for the required 50 years (i.e. 

conservation easement). 

VI. PROCEDURES

A. Introduction
17 | Page

This protocol has been designed to assess the habitat value of a specified area in a timely and 

cost-effective manner. Habitat quality will be ascertained using a standardized habitat 

assessment protocol. This protocol examines various components of both the habitat impacted 

in the project area and proposed replacement habitat(s) to calculate a value for wildlife and to 

assign a Habitat Quality Score (HQS). The HQS is calculated using criteria which have been 

developed to examine aspects of habitat that are essential for wildlife. For each of the habitat 

evaluation criterion provided in this document, the habitat area is scored from 0 – 10, with 10 

having the most value to wildlife and 0 having the least value. After all criteria have been 

evaluated, the total points are added together and divided by ten (or the total number of criteria 

evaluated) to determine the HQS. Once the HQS is calculated, the total wildlife habitat value 

of an area is determined with the following formulas:

For Habitat Losses: 

Area (acres) of impacted habitat X Habitat Quality Score (HQS) of the impacted habitat

= Total Habitat Value (THV) (aka Habitat Units lost)

A x HQS = THV lost

Mathematical rounding rules should be used to round THV figures to the nearest tenth.

For Habitat Replacement: 

Step 1. 

Area (acres) of proposed habitat project X Habitat Quality Score (HQS) of existing habitat

condition

= Total Habitat Value (THV) baseline

A x HQS = THV baseline

Step 2. 

Area (acres) of proposed habitat project X Habitat Quality Score (HQS) of projected habitat

condition

= Total Habitat Value (THV) replacement habitat

Step 3. 

THV replacement habitat – THV baseline = Habitat Credits generated

Mathematical rounding rules should be used to round THV figures to the nearest tenth.

Using these calculations, a quantitative value for habitat units lost from implementing a salinity 

control project and created from implementing a habitat replacement project can be generated. 

Example:

Five miles of lateral are to be placed in pipe. There are 5 acres of wetlands/riparian vegetation 

supported by seepage from the lateral. These 5 acres have an HQS of 3. Using the equation, 

habitat losses for the project equal 15 habitat units (5 acres x 3 HQS = 15).
18 | Page

Replacement lands are typically lands that currently have a low HQS due to current or past 

management practices, but have the potential for habitat enhancement and/or can be managed 

in a manner to restore the habitat. Using the example above, the lands will need to have the 

THV improved from existing conditions by 15 habitat units in order to have no net loss of 

habitat value. In this example, the replacement area is 5 acres and has an HQS of 4. Therefore,

the existing value of the replacement lands is 20 habitat units. A habitat replacement project 

must be designed to increase the habitat value of the replacement lands to a value of 35 in order 

to replace the 15 habitat units lost from the salinity project (20 existing habitat units + 15 

habitat units lost = 35 habitat units). 

B. Habitat Quality Scoring Evaluation Criteria

To proceed with the HQS, examine the habitat types. Riparian and wetland communities serve a 

broader and more diverse species base as compared to upland communities. Only riparian and 

wetland community types are evaluated for losses, and habitat replacement projects must

restore, enhance and/or protect riparian or wetland habitat to be eligible for further 

consideration. Evaluators should have an understanding of the ecological community they are 

evaluating. Best professional judgment is applied during the evaluation, with justification or 

rationale provided for each score. In some instances, the evaluation criteria may need to be 

adapted, adjusted, or eliminated to appropriately characterize a specific site. In these cases, 

written justification must be supplied, explaining those changes and rationale for the changes.

Habitat Losses: 

Prior to evaluating the area, determine if the project will result in the loss ofriparian or wetland

habitat: YES or NO

If YES, proceed to evaluating the habitat. If NO, the habitat does not need to be considered 

further. 

Habitat Replacement: 

Prior to evaluating the area, determine if the habitat replacement project will

restore/enhance/protect riparian or wetland habitat: YES or NO

If YES, proceed to evaluating the habitat. If NO, the area should not be considered further. 

On-site evaluations shall be conducted during the growing season to best determine habitat value. 

Evaluation Criteria: 

• Vegetative Diversity: Evaluate the composition of readily observable 

riparian/wetland plant species providing wildlife habitat. Determine the number of 

species of shrubs, grasses, forbs, and trees present.

0 3 5 7 10

Very Low Diversity

(Ex. Monoculture) Low Diversity Moderate 

Diversity High Diversity Very High Diversity

(Ex. Multiple species)
19 | Page

• Stratification: Examine the presence of riparian/wetland trees, shrubs, and herbaceous 

species on site. Evaluate the canopy coverage of the different height levels of vegetation. 

Layers are considered to be functioning when there are various age classes of trees and

shrubs, and/or the layer provides expected cover for that strata. For example, sapling 

cottonwood trees are not functioning as a tree layer, and therefore would be considered 

present, but not functioning. 

0 2 4 6 8 10

Two layers 

are absent, 

the other 

layer is not 

functioning. 

(Ex. 

Sparsely 

vegetated; 

mostly bare 

ground.)

Two layers 

are absent, 

the other 

layer is 

functioning. 

One layer is 

absent; one 

layer is 

functioning; 

one layer is 

present but 

not 

functioning.

One layer is 

absent, but 

the other 

two layers 

are present 

and

functioning.

All 

appropriate 

layers are 

present, but 

one layer is 

not 

functioning.

All 

appropriate 

layers are 

present and 

functioning.

• Noxious Weeds: Evaluate the presence of noxious weeds. Noxious weeds are considered 

to be those weeds included on state and/or county noxious weed lists or watch lists. Are 

noxious weeds present? What is their relative abundance?

0 2 4 6 8 10

Weeds cover 

25% or more

of evaluation 

area.

Weeds cover 

20% of 

evaluation 

area.

Weeds cover 

15% of 

evaluation 

area. 

Weeds cover 

10% of 

evaluation 

area.

Weeds cover 

5% of 

evaluation 

area.

Evaluation 

area is weedfree.

• Overall Vegetative Condition/ Health: Evaluate the overall health and condition of the 

riparian/wetland plant species. Noxious weeds should not be included in the evaluation of 

the overall vegetative condition and health. Are the plants healthy or stressed? Examine 

leaf color, leaf size, percent of dead material, and evidence or absence of new growth. Are 

any diseases or insect infestations present?

0 2 4 6 8 10

60% or more

plants are 

stressed, 

diseased, or 

infested.

At least 50% 

of plants are 

stressed, 

diseased or 

infested.

At least 40% 

of plants are 

stressed, 

diseased, or 

infested.

At least 30% 

of plants are 

stressed, 

diseased, or 

infested.

At least 20% 

of plants are 

stressed, 

diseased, or 

infested.

100% of 

plants are 

healthy. 
20 | Page

• Interspersion of Open Water with Vegetation: Examine the arrangement of the site’s 

open water features in relation to existing vegetation. For habitat loss evaluations, include 

the canal open water when scoring this criterion if the canal will be piped, as that open 

water feature will be lost. When examining an area, the surrounding landscape should be 

considered. For example, open water adjacent to a habitat replacement site should be 

considered in the baseline score, even if it is not within the project boundary. 

• Connectivity: Examine the proximity of other wildlife habitat areas, and examine 

the degree to which the landscape facilitates animal movement and other ecological 

processes. A project area near other valuable riparian/wetland habitats can add value to the 

overall complex and can help support larger wildlife populations. If a project area provides a 

corridor for wildlife movement, its value is disproportionately larger than would be expected 

when considering its acreage alone. If nearby riparian/wetland habitats are protected and 

expected to persist long-term, then their association with the project area provides greater 

habitat value. Protected areas include, but are not limited to, lands in conservation easements 

and federal or state lands managed for wildlife. 

0 3 5 7 10

Isolated, and 

not contiguous 

to lands with 

any wildlife 

value. 

 Contiguous to or 

connects to other 

unprotected areas 

which have

minimal wildlife 

value. 

 Contiguous to or 

connects to other 

unprotected areas 

which have

wildlife value. 

 Contiguous to 

or connects to 

other protected 

areas which

have minimal

wildlife value. 

Contiguous to 

or connects to 

other protected 

areas which

have wildlife 

value. 

• Wildlife Use: Evaluate the use of the area by wildlife. Is wildlife observed in the area? 

Are there signs that the area is utilized by wildlife? Does the area contain a good food 

source, or provide other wildlife needs? Consider the different guilds of wildlife which 

may utilize the area; high use represents use by multiple guilds. 

0 3 5 7 10

No or very limited 

use of area at any 

time of year. 

Low seasonal 

use of area. 

Low year-round 

use of area. 

High seasonal 

use of area. 

High yearround use of 

area.
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• Uniqueness or Abundance: Examine the overall value of habitat to wildlife and its 

abundance or scarcity. Is the land especially unique or valuable to wildlife? Does it 

provide special habitat (i.e. production area, nesting habitat, critical winter range, 

etc.)? Is the habitat type common or unusual?

0 2 4 6 8 10

Exhibits 

common 

or 

abundant 

wildlife 

value 

Exhibits medium 

to low unique 

value for wildlife 

and is relatively 

abundant in the 

vicinity

Exhibits 

medium 

unique value 

for wildlife 

and is 

relatively 

abundant in 

the vicinity

Exhibits 

medium 

unique value 

for wildlife 

and is 

relatively 

scarce in the 

vicinity. 

Highly unique 

value for 

wildlife but is 

relatively 

scarce or 

becoming 

scare in the 

vicinity.

Highly 

unique value 

for wildlife 

and is very 

uncommon. 

• Water Supply: Examine the water supply for the area. Examine if the water is 

from a natural flowing stream or river, fed by ground water, or dependent on 

irrigation flows or delivery systems. Examine the nature of the water source. Is 

water present year-round or only seasonally? If the habitat is dependent on water

from non-natural sources to maintain its HQS, then what are the terms surrounding 

the water supply? Is an agreement in place to ensure a reliable source of water, or 

has a water budget been developed to ensure the sufficiency of the water?

0 2 4 6 8 10

No 

water 

supply 

Water 

supply is 

uncertain

Non-natural 

flows are 

seasonal, or yearround flows are 

uncertain

Non-natural 

seasonal flows are 

guaranteed; 

Seasonal natural 

flows are uncertain

Non-natural 

year-round flows 

are guaranteed or 

seasonal natural 

flows are certain

Perennial 

stream

• Alteration: Examine the habitat area and surrounding landscape for evidence of human

caused alteration, such as roads, mining, railroad tracks, urban and suburban encroachment. 

The more disturbance that has occurred on the land, the lower the score.

0 2 4 6 8 10

80% or more of 

land has been 

heavily 

developed or 

altered

70% has 

been 

developed or 

altered

50% has 

been 

developed or 

altered

30% has been 

developed or 

altered

10% or less of 

project or 

adjacent land

No 

alteration or 

development 

observed 
22 | Page

Examples of evaluation scoring and justification: 

Evaluation 

Criteria

Rationale Score

Stratification

Site is largely missing the mid-story and over-story canopy layers. 

The herbaceous layer is present and functioning. Interrupted stands 

of coyote willow and occasional tamarisk, Russian olive, young 

Siberian elms and very occasional Wood’s rose form the shrub layer. 

Shrubs overall poorly integrated into herbaceous layer. A tree layer is 

absent.

3 

Connectivity 

No connectivity with other wildlife habitat areas. Moderate 

connectivity with the Gunnison River via the downslope saline 

wetland. The river passes through public and private land, and only a 

small portion of the riparian corridor is vegetated in the project area. 

Connectivity exists to the west along the entire length of the canal, 

which ends in the adobes. To the east, the canal fringe is interrupted 

by tunnels. Excellent connectivity with upland habitat on public land 

that provides none of the habitat characteristics of the fringe wetland 

habitat evaluated. Public land is managed for multiple-use and 

provides moderate protections for wildlife. Private land at the west 

end is cultivated and not protected.

1 

C. Additional Considerations

Reclamation may consider other factors when determining appropriate scoring for habitat 

losses or habitat replacement projects. Any inclusion of additional considerations would need 

to be discussed on a project by project basis, in close coordination with Reclamation and FWS. 

Additional considerations which could potentially be used for scoring adjustments include but 

are not limited to:

• Operation and Maintenance Requirements: Does the habitat project have low 

maintenance needs and a high likelihood of becoming self-sustaining?

• Partnerships: Is there an opportunity for local partnerships to develop and/or manage the 

habitat area?

• Habitat for Sensitive or Special Value Species: Existing habitat and replacement habitat 

should be evaluated for federally or State listed species or their habitat (e.g., within 

proposed critical habitat for yellow-billed cuckoo). Also, species of special value such as 

raptors should be considered.

• Restoration of Missing Habitat Type: There is added value to replacement 

lands that create or restore a community or habitat type that is currently missing

or that provides a strategically important link between nearby riparian/wetland 

habitats (i.e. travel corridor). 
23 | Page

• Educational or Social Value: The site has value to the community as an 

environmental education site and will be managed to utilize this potential.

D. Land Acquisition as Habitat Replacement

Land acquisition may be considered as an option for habitat replacement by land purchase 

and/or protective mechanisms, such as conservation easements, for the benefit of wildlife. Land 

acquisition would be considered on a project by project basis. The land must include, or have 

the potential to include, suitable riparian and/or wetland habitat. Land acquisition may be 

permissible if: 

(1) the land contains degraded riparian and/or wetland habitat, a habitat replacement plan is 

provided, and an assurance of plan implementation is provided; or 

(2) the land is faced with an imminent threat that would notably reduce its habitat value. An 

imminent threat would include situations where the land is zoned for development or a 

development plan is in place. A habitat management plan would need to be prepared for 

the area in place of a habitat replacement plan. The habitat management plan should 

outline how the lands will be managed for the benefit of wildlife. 

Credits for land acquisition would be based on the value of the land using the evaluation 

criteria above. 

E. Stream Restoration Projects

For projects proposed to occur in and along degraded streams, habitat replacement plans could be 

developed which enhance streamside riparian/wetland habitat and/or instream functions. The 

habitat evaluation criteria listed above are not designed to evaluate instream restoration projects. 

Evaluations for instream restoration projects must be conducted by knowledgeable personnel with 

experience in recognizing visual indicators of stream function and demonstrated experience in 

stream restoration design and implementation. 

Reclamation is in the process of drafting stream restoration evaluation criteria, and will include 

those criteria in this document once finalized. In the meantime, contact your Reclamation Area 

Office for further guidance on evaluating stream restoration projects. 

F. Instream Flows as Habitat Replacement

Instream flows can help balance competing uses of water. Instream flows provide and enhance 

riparian vegetation and habitat for aquatic invertebrates, fishes, birds and other wildlife, and 

maintain the productivity, diversity, and resiliency of the biological resources which depend on 

riparian areas and adequate and reliable stream flows. Reclamation may consider the 

designation and protection of instream flows as habitat replacement if it can be shown that one 

or more of the following flow types may be enhanced:

• Subsistence Flows – The minimal stream flow needed during critical drought periods to 

maintain specified water quality conditions and to provide critical habitat space for the 

survival of aquatic organisms.
24 | Page

• Base Flow – The “normal” flow conditions found in a river in between storms; base 

flows provide adequate habitat for the support of diverse, native aquatic communities, 

and maintain groundwater levels to support riparian vegetation.

• High Flow Pulses – Short duration high flows within the stream channel that occur 

during or immediately following a storm event. They flush fine sediment deposits and 

waste products, restore normal water quality following prolonged low flows, and provide 

longitudinal connectivity for species movement along the river.

• Overbank Flow – An infrequent high flow event that breaches riverbanks. Overbank 

flows can restructure the channel and floodplain, recharge groundwater tables, deliver 

nutrients to riparian vegetation, trigger germination of riparian plants, and connect the 

channel with floodplain habitats that provide additional food for aquatic organisms.

Some considerations when proposing instream flows as habitat replacement:

• The instream flow must be protected. The water right must be transferred to an instream 

flow water right, and applicable state water laws would apply (i.e. in Colorado, only the 

Colorado Water Conservation Board may hold an instream flow water right for wildlife). 

• Seniority of the water right, and distance to the nearest downstream diversion.

• Identify the benefits of the instream flow to the affected stream segment.

• Determine the timing of instream flow availability. Would the instream flow be 

available at critical times to maximize seasonal benefits (i.e. available year-round, late 

season, low flows, etc.)? 

• What is the length of the stream reach (i.e. reference reach) which would benefit from 

the instream flow, and/or the increase in wetted perimeter? 

• Would the instream flow connect important reaches (e.g., provide water to a dewatered 

reach, thereby connecting two reaches of ecological importance)?

• Instream flows provided must be measured and monitored.

Instream flows may be considered for habitat replacement on a project by project basis, based 

on the overall value of the habitat lost as compared to the value of the proposed instream flows. 

An Instream Flow Assessment and Management Plan would need to be prepared, and should 

include the following:

• Clear goals which state the activities or functions that the instream flows are intended to 

support or achieve.

• Discussion of the considerations included above.

• The hydrology and flow regime of the stream system. To what degree has the natural 

flow regime been altered? 

• Documentation showing the protection or transfer of water rights for instream flows.

• Mechanism to measure and monitor the instream flows provided as habitat replacement

(i.e. construct bypass pipeline with a meter at the diversion and provide annual flow 

reports).

• Identify the wildlife species the instream flows will benefit, and describe these benefits.

Reclamation is in the process of drafting instream flow evaluation criteria, and will include 

those criteria in this document once finalized. In the meantime, contact your Reclamation Area 

Office for further guidance on evaluating instream flow projects.
25 | Page

VII. HABITAT REPLACEMENT PLANNING

Habitat replacement plans are developed with the intent to provide complete and concurrent 

replacement of habitat losses for the life of the salinity control project, typically 50 years, as stated in 

the FOA and in the application signed and submitted by the applicant. Habitat replacement activity 

will occur at the same time as project construction with the goal of having all initial habitat 

replacement development completed at the same time as the salinity control project. If habitat 

projects do not last the required 50 years, Reclamation operates under the expectation that a 

revitalized project or new projects will be implemented to complete the 50-year requirement, at the 

cost of the project applicant. 

A. Identifying a Habitat Replacement Project

The intent is to comply with the Salinity Control Act by developing replacement wetland and/or 

riparian habitat that is beneficial to wildlife, cost effective, viable and manageable for the life of 

the project.

An "Ideal" replacement property is one that:

1) Is near the salinity control project area so as to provide compensation, to the extent 

possible, for fish and wildlife that may be affected by the salinity control project.

2) Is an in-kind replacement of the particular habitat values lost.

3) Is contiguous to or connects other areas that have wildlife value, such as stream

corridors and wetland complexes.

4) Has a willing and able manager (e.g. state wildlife agency,volunteer conservation group, 

or a city or county agency).

5) Has the most characteristics that would assure viability for 50 years/life of the project

(e.g. location, ownership/easements, level of management/maintenance needs, fits within 

agency and public conservation plans and priorities, availability of managing partner)

Additional options and considerations for habitat replacement projects: 

• Are there partnerships with other agencies or entities which can be utilized to stretch funding 

and accomplish multiple objectives?

• Are there federal, state, county or local government properties with proposed habitat 

projects that need funding for implementation? Examples include: national wildlife refuges, 

national parks and conservation areas, wilderness study areas, state wildlife areas, state 

parks, county-designated open space areas, and lands with conservation easements. 

Agencies may agree to provide long-term operation and maintenance if habitat projects fit 

within their long-range plans and the anticipated O&M costs are limited.

• Are there properties (such as those listed above) that do not have planned habitat

enhancement projects but have potential for habitat development or enhancement?

• Are there lands under federal, state, or local jurisdictions adjacent to properties described 

above that could be developed and incorporated by the jurisdiction (i.e. adding adjoining 

land to a state wildlife area)?

• Does the applicant own or control lands with potential for habitat replacement? Ideal 
26 | Page

properties would include those along rivers or streams where sufficient groundwater and/or 

irrigation is available to support riparian and wetland species. Measures would need to be 

developed to assure that the habitat replacement is maintained for the life of the salinity 

control project implemented (normally 50 years).

Procedures for applicant's planning and designing habitat replacement projects:

1) Determine total habitat losses of lands impacted by the proposed action.

2) Identify opportunities for habitat projects closely resembling the Ideal property model 

described above.

3) Develop preliminary plan for habitat improvements that provide sufficient increase in total 

habitat value to offset losses.

4) Develop final plans in coordination with Reclamation and FWS. Include state wildlife 

agencies and landowners, as applicable.

5) Include monitoring, adaptive management, and reporting in the plan.

B. Preparation of Habitat Replacement Plans

Each applicant should contact the Reclamation Area Office overseeing their Cooperative 

Agreement for specific guidance or templates for preparing habitat replacement plans. The 

following items should be considered for inclusion in habitat replacement plans:

• Introduction (including the name of the salinity control project for which the habitat replacement 

plan is being prepared). 

• State the overall objectives of the habitat replacement project. 

• Describe the existing and desired ecological characteristics of the proposed site, including: 

- Habitat type and wildlife use

- Plant communities/vegetation

- Hydrology 

- Topography and soil conditions 

- Map showing the locations of the site 

- Site evaluation scoring and rationale.

• Provide detailed work descriptions and specifications for the project, including but not limited to: 

- Geographic boundaries of the project 

- Construction methods, timing, and sequence 

- Source(s), sufficiency and reliability of water availability and delivery 

- Methods for establishing the desired plant community 

- Methods to control invasive plant species 

- Proposed grading plan, including elevations and slopes (if applicable)

- Planting plan

- Soil management

- Erosion control measures
27 | Page

• Include a description and detailed schedule of all elements of implementation, including but not 

limited to grading and planting. 

• Present a description and schedule of maintenance and management requirements, including 

invasive species control, to ensure the continued viability of the resource once construction is 

completed. 

- “Before” photographs and a map indicating photo locations and direction. 

- Schedule should include monitoring visits once a year with Reclamation and FWS for the first 

five years of the project, and issuance of a yearly report to Reclamation (with photographs) for 

the remaining 45 years of the project. 

• Prepare a description of the ecologically-based standards that will be used to determine whether 

the habitat project is achieving its objectives.

• State the parameters to be monitored in order to determine if the habitat project is on track to 

meet performance standards and if adaptive management is needed. 

• Attach a copy of the recorded Conservation Easement or other site protection document. 

C. Review Procedures

The habitat replacement plan will be reviewed by Reclamation, as well as landowners and 

wildlife agencies, as appropriate. The plan will require acceptance by Reclamation prior to 

completion of NEPA or implementation of salinity control activities. Reclamation’s 

acceptance of the habitat replacement plan does not constitute technical approval of the design, 

which is the responsibility of the grant recipient. 

VIII. ROLES OF FISH AND WILDLIFE SERVICE AND

STATE & TRIBAL WILDLIFE AGENCIES

The FWS participates in the Salinity Control Program pursuant to authorities and 

responsibilities set forth in the Endangered Species Act, Fish and Wildlife Coordination Act, 

National Environmental Policy Act, and Migratory Bird Treaty Act. These authorities are not 

always applicable; however, Reclamation believes that coordination with the FWS on all 

program habitat replacement projects is appropriate and beneficial.

The FWS participates in the Salinity Control Program by providing technical assistance on fish 

and wildlife resource impact assessment, restoration, and management and acting as liaison 

with state wildlife management agencies. The FWS also provides independent review and 

oversight of program aspects dealing with fish and wildlife resources, including our 

assessment of the degree to which fish and wildlife have received due consideration in project 

planning and whether incidental fish and wildlife values foregone have been replaced.

Scope of work for FWS pertaining to the Salinity Control Program includes:
28 | Page

• Provide written evaluations or recommendations to Reclamation for the planning, 

design, and development of habitat replacement plans for Basinwide Program projects 

throughout the Upper Colorado River basin. Such evaluations or recommendations will 

be for the purpose of assisting Reclamation in assuring the habitat replacement 

commitments are met.

• Coordinate with Reclamation to conduct reviews and to review annual reports of existing 

habitat replacement projects.

Coordination with State and Tribal Wildlife Agencies (as applicable):

• If habitat replacement projects will be located on state or tribal lands, Reclamation will 

provide state or tribal wildlife agencies copies of all habitat replacement plans and/or 

wildlife agreements with a request for their review, comments and ultimate approval of 

the plan or agreement prior to implementation. The state and tribal wildlife agencies will 

be encouraged to contact the FWS Salinity Control Program coordinator to discuss the 

plan or agreements prior to final approval.

IX. MONITORING REQUIREMENTS 

Final payment for salinity control work should be made pending sufficient progress on habitat 

replacement work. Once a property has been developed for habitat replacement, the grant 

recipient is responsible for long-term maintenance and monitoring to ensure habitat 

replacement is successful. Habitat replacement plans should commit grantees to maintenance 

and monitoring for the life of the project. In addition, Reclamation and FWS (if available) will 

monitor each property at least once a year for the first five years after project completion to 

ensure that it is performing as intended and attaining habitat replacement plan objectives. After 

the first five years, if the project is meeting or progressing towards desired conditions, the 

frequency of monitoring can be adjusted to every three to five years for the remaining life of 

the project. Reclamation will direct grantees to repair any determined deficiencies.