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Biology Monitoring Guidance
Post-Construction Biology Monitoring  
The Geo-Environmental (GE) Section provides standards and procedures for ODOT to streamline environmental compliance procedures. This includes biological monitoring, which is typically required as a condition of biological permits, such as federal and state Endangered Species Act (ESA) incidental take permits and state fish passage permits. Resources have been developed to support biological monitoring efforts, including a database, template reports, field checklist, GIS files, GPS/field mapping applications. Check this website periodically for the latest information and guidance. 
The symbol indicates requirements for ODOT Environmental employees and consultants on ODOT projects (as per ODOT Tech Bulletin GE09-04(b)).  Implementation procedures follow each requirement.

This web site contains resources for ODOT Environmental employees, consultants on ODOT projects and local agency employees who utilize permits held by ODOT or FHWA Oregon Office (includes local agency Federal-Aid Highway Program projects) to complete the most common biological monitoring requirements. The monitoring guidelines described here do not apply to wetland monitoring, mitigation banks or mitigation for 4(f) resources.

Annual, post-construction monitoring following these standards is required for all FAHP projects that involve restoration of ESA resources, mitigation, or habitat enhancements (particularly fish passage or installation of fish habitat improvements), regardless of proponent agency.  At this time, ODOT does not manage mitigation monitoring for other local-agency projects or Corps/DSL permits held by the local agency, even if the project used Federal-Aid funding.   ​
Types of Biological Monitoring
The following types of permits require post-construction or annual biological monitoring:
Annual Monitoring Report – a  requirement of most ESA Section 7 Biological Opinions to evaluate how well the site or project is meeting performance standards or success criteria required of the relevant regulations (e.g., Fish Passage), habitat restoration plan, or the permit (see Biology Monitoring Reports). The monitoring period is indicated in the Biological Opinion (typically 5 years, but may be longer performance standards not been met within that period). Annual, post-construction monitoring begins the calendar year after project completion. The Year 1 annual monitoring report is typically due by the end of the first calendar year (December 31) after construction has been completed, although it may be extended to the next year if the Project Completion report was completed in the fall.

Mitigation Feature - a component of the mitigation site that is being tracked for success according to ESA Section 7 commitments. It may be an area with riparian plantings, a section of stream with root wads, a patch of noxious weeds, etc. 

Mitigation Site - the location of restoration and compensatory mitigation associated with a permit. The mitigation site typically includes the entire area of direct impact associated with an action (temporary and permanent disturbances within the construction limits) and possibly also the area where off-site mitigation was performed.


Project Completion Report – a report that is required in most ESA Section 7 Biological Opinions. The project completion (or sometimes called post-construction) report describes how a project met terms and conditions of the Biological Opinion during construction, such as work area isolation, erosion control, and vegetation removal (see Biology Monitoring Reports). The due date for the Project Completion report is specified in the Biological Opinion (typically 60-days after completion of construction).


Resource Protection Area (RPA) – an area on ODOT property with sensitive environmental resources protected under state or federal law that do not require unique or modified maintenance activities to ensure resource protection.


Special Management Area (SMA) - an area on ODOT right-of-way with sensitive environmental resources that are protected under state or federal law, and require unique or modified maintenance actions to ensure continued viability of the resource.  State and federal regulations do not differentiate SMA and RPAs; resource protections are equally required. However ODOT manages the sites differently due to proximity to routine maintenance activities.


SMA Monitoring Report – for compliance with state laws that require tracking the status of listed plant populations on state lands, ODOT has negotiated with the Oregon Department of Agriculture to complete and submit Site Check and Population Monitoring reports for all SMA and RPAs with routine maintenance work or other construction activities (see Biology Monitoring Reports). 

Biological Monitoring Data

The GIS Unit and GE Section cooperatively maintain statewide Biology Mitigation Monitoring and SMA GIS databases to map and track mitigation compliance for all projects with ODOT biology mitigation and site monitoring requirements.

  • The GE Section uses information in the databases to forecast and justify the ODOT post-construction monitoring budget to insure that monitoring funds are continually available.
  • GE also uses the databases to track budgets, track regulatory compliance, track success of statewide mitigation efforts, determine if and when mitigation banking is justified, and provide continuous improvement of ODOT mitigation or monitoring efforts.

Environmental employees and Region environmental manager may use the databases for work scheduling and project tracking. Most of the site and project information are in the Project Point and Project Boundary layers. 

·          ​​​​​​For Biology Mitigation monitoring, project and permit information is tracked in a Project Point layer, while objectives and performance are tracked in a Project Boundary layer. 

o        The Project Point corresponds to a unique permitted action typically associated with a distinct project and key number. The point will be mapped at the approximate site center or nearest roadway and tenth-mile marker.  Each project is assigned a unique identifying number, the Environmental Site_ID, used to distinguish environmental resources (i.e., different numbering system for Biology Mitigation, Wetland Mitigation, SMA, etc.). 

o        The Project Boundary is a polygon layer that corresponds to a restoration or mitigation area.  A project may have multiple boundaries with the same Site_ID if a permitted action has multiple and geographically distinct restoration or mitigation areas.

·          For SMA and RPA monitoring, site, performance, and population information are managed in a Project Boundary layer only.  A distinct site typically has one boundary, so a separate data layer is not needed.  A site corresponds to not only a unique geographic area but also unique management conditions. 

There are separate GIS layers for mapping finer scale management and mitigation features, such as re-vegetation areas, weed patches, or stream features.

At this time, the GE Section utilizes the GIS layers as the primary biology monitoring database, to update annual performance information based on annual monitoring reports.

The GIS layers are managed as enterprise geodatabases in the statewide GIS server, and require versioning and check-out as described below. Access to the GIS layers is restricted to ODOT Environmental employees and ODOT-contracted consultants. However, local agency projects with ODOT-managed permits that require mitigation and post-construction monitoring will also need to add to the databases (see procedures, below).

Before heading out for field monitoring, you may complete the Biology Monitoring Checklist to ensure that you are well prepared to gather the appropriate data.

ODOT Environmental employees are required to update the Biology Mitigation Monitoring Database for each ODOT project with biology mitigation obligations, and shall ensure that all active mitigation sites are mapped in the Biology Mitigation Site Point GIS file.

Procedures for adding new Biology Mitigation, SMA or RPA sites to GIS layers (in-house ODOT or local agency projects managed by ODOT, e.g., Federal-Aid STIP projects that use FAHP for ESA consultation):

·         There’s a good chance that the GE biologists will already have created a Project Point using information provided in various FAHP project reports. 

·         At least one month prior to the first annual monitoring site visit, coordinate with the ODOT GIS Unit or the FAHP Program Manager to check that the Project Point has been added to the Biology mitigation monitoring GIS layer(s) and to create the Project Boundary(ies) on your behalf.  If the Project Point hasn’t been created, ask that both point and boundary be created. To create the point or boundary, provide the following information:

o         A map clearly that clearly depicts, or a generic GIS polygon layer, the site restoration and/or mitigation boundary(ies).

o         Project key number, name, primary project type.  A key number is needed for file management. If a project has no key number (e.g., maintenance projects), request that GE assigned one, via email to GeoAdminWorkOrders@odot.state.or.us.

o        Monitoring biologist’s name, employer, and phone number.

o        For biology monitoring, for each boundary, identify if site restoration has been performed, such as bank stabilization, native plantings, etc. Site restoration is defined as returning temporarily disturbed areas to natural conditions. 

o         Also for each biology monitoring boundary, provide the main categories of relevant mitigation or restoration objectives, such as fish passage, in-stream habitat), wildlife habitat, wildlife passage, riparian improvements (larger area or enhancements to pre-construction conditions. Mitigation for stormwater management is only tracked via annual biology monitoring if it was a habitat enhancement, not things like treatment swales or detention basins.

o         For SMA or RPA sites, also provide the protected species, date the population was first observed, and any baseline population data you have.    

Procedures for editing Biology Mitigation, SMA or RPA sites to GIS databases (ODOT sites):


     The GIS layers need to be edited each monitoring site visit to update the performance and status of the mitigation or restoration activities or population being tracked. To edit the GIS data:

o         Determine if you will be editing during a field visit using GPS, or desktop GIS.

o         Request a check-out of type of project (biology or SMA monitoring) you wish to edit using the GIS Unit’s GPS checkout form by noting in the request form that it is a new site visit (same process for checking out data to be edited using desktop GIS). You may also request reference layers such as roads or aerial imagery with this check-out, which will help navigate to site. When the data request is submitted, the GIS Unit will assign an Environmental Site_ID.

o         The GIS Unit will direct you to a folder that can be directly copied onto a handheld GPS device for field work, or the GIS layer(s) can be added to your desktop GIS project map document (e.g., ArcMap). 

o         Using the ArcPad or ArcGIS editing tools, edit relevant layers, geometry and/or attribute information. Try to complete as much of the attribute data as relevant to the project, particularly date last observed and performance at that time. ODOT’s GIS staff or GE biologists can assist with editing. GE recommends that Environmental employees also map important mitigation features using GPS (ArcPad forms for biology mitigation features are also available), although this is not mandatory.  The Arcpad forms are excellent tools for tracking changes over time, creating maps for monitoring reports, or developing site plans for maintenance contracts. However, you should maintain rough sketches or As-Built Plans of site boundary and mitigation features as back-up (in case of technical difficulties with the GPS technology). More information on using the Biology Mitigation Monitoring ArcPad forms can be found in GPS Application User's Guide.

o        When finished, save edits, close the project, and copy/paste the edited file folder to the check-in folder as directed by the GIS Unit when you check-out the data.


Field Monitoring Protocols
Before heading out for field monitoring, you may complete the Biology Monitoring Checklist to ensure that you are well prepared to gather the appropriate data.  
ODOT’s Transportation Data Section (Transportation Development Division) maintains the statewide Biology Mitigation Geographic Information System (GIS) files.   

ODOT Environmental employees shall ensure that the boundary/extent of all active mitigation sites are mapped in the Biology Mitigation GIS Database.
  • At least one week prior to your first monitoring site visit, or even towards the end of the construction monitoring period, contact ODOT’s GIS unit via ODOT GPS Data@odot.state.or.us, to check-out the GIS files.
  • Request to check-out, at a minimum, the existing site point layer (that you should have already created), and a “blank” boundary layer.  If you do not know what is needed for the check-out process, contact the GIS Unit for assistance.  If you are heading out to do your field monitoring with GPS, also check-out the feature layers.  
  • Map the boundary, either:
    • In the field using GPS,
    • Or, create the record via hand-digitizing in a desktop GIS environment.
    • NOTE: GPS field mapping is more accurate, and ODOT’s GIS Unit has ArcPad/GPS software specifically for ODOT Biology monitoring.
    • The boundary is the geographic extent of the mitigation features associated with a permitted project.  More than one boundary may be applicable if the mitigation includes geographically discontinuous features.  It is up to the discretion of the lead Environmental employee what constitutes separate boundaries.  The combination of all boundaries per site will be used as the total area of mitigation for that project.
  1. Environmental employees may seek assistance from the GIS Unit employees to hand-digitize boundaries.
  2. ODOT’s Biology Monitoring ArcPad applications, ArcPad equipment, and software are required if GPS mapping is used.
  3. ODOT’s GIS Unit provides support and training on use of the Biology Mitigation GIS and GPS applications.
  4. A quick reference guide for using the GeoXT and ArcPad is available at: http://intranet.odot.state.or.us/gis/PDF/docs/BioApp_One_Page_PLS.pdf 
  5. A more complete user-guide is available for the ODOT Biology Mitigation GPS applications.
         GPS Application User's Guide 

GE recommends that Environmental employees also map important mitigation features using GPS (ArcPad applications for biology mitigation features are also available), although this is not mandatory.   
The GPS applications are excellent tools for tracking changes over time, creating maps for monitoring reports, or developing site plans for maintenance contracts.  However, you should maintain rough sketches or As-Built Plans of site boundary and mitigation features as back-up (in case of technical glitches with the electronic applications). 

Biological Monitoring Reports


To improve consistency and success tracking, all ODOT biology mitigation monitoring reports shall be prepared with template reports (see definitions):


Project Completion Report Used to describe permit compliance during and at the end of project construction.


Annual Monitoring Report - Used to document the performance and progress of relevant permit requirements or regulations, such as habitat restoration, fish passage, bank stabilization.  

·         For biological monitoring for DSL permits, add the DSL cover sheet , and attach Vegetation Sampling Data forms completed in the field or other field data sheets.

·         For individual ESA consultations or DSL and Corps permits, the annual monitoring report should include the exact permit requirements relevant to mitigation and monitoring.

o    The easiest way to do this is to cut/paste the relevant conditions and attach them to the report.

o    Do not simply reference the permit document because it is too difficult to track down the permit each time one wants to review the monitoring report.

SMA/Botanical Monitoring Form – Used to document population monitoring completed at SMA and RPA sites with ongoing maintenance or other activities.

SMA/Botanical Inspection Form
 – Used to document yearly inspections of SMA and RPA sites with ongoing maintenance or other activities, between population monitoring years.

Report Distribution Guidelines

All mitigation monitoring reports shall be sent directly to the permitting authority from the Region Tech Centers (except GE-managed Mitigation Management Contract, in which Consultant transmits reports), regardless of action agency (ODOT, FHWA, or Corps). 
      1.      Combine monitoring report, figures & attachments into one Adobe Acrobat                 document (cover letter not needed with template reports). Use GE file                       naming convention (e.g. 11522_BMR2010_Kitson_Ridge)

2.     For individual ESA consultations, Corps and DSL permits, mail a hard copy of the original, complete document directly to the appropriate regulatory authority (see addresses below).  For ESA consultations, mail a hard copy to the Corps only if: (1) they were the federal nexus and permittee (e.g., SLOPES), or (2) they required monitoring for non-wetland compensatory mitigation, aquatic or riparian impacts. If applicable, indicate in the cover letter that you have already submitted the report to NMFS.

3.     For FAHP projects, follow report distribution guidelines in the most updated User’s Guide

4.     For SLOPES projects, email the complete document directly to NMFS, using the SLOPES IV email box (slopes.nwr@noaa.gov)). Only Action Completion and Final Monitoring reports are required to be submitted to regulators, but GE standards require completion of annual monitoring and reporting to NRU-Trans for all active mitigation sites.

5.      For OTIA III projects, upload to appropriate monitoring folder in EDMS, and send email notification to ODOT (as per #6 below) and the NMFS liaison.

6.   Except for FAHP projects, for statewide asset management and regulatory coordination, email copies of monitoring reports to NRU-Trans@odot.state.or.us. Note, we no longer send FHWA copies of monitoring reports; instead GE will provide an annual summary to FHWA.

  Mailing Addresses:

Mr. Kim Kratz or Mr. Mike Tehan
National Marine Fisheries Service
Habitat Conservation Division, Oregon State Office
1201 Lloyd Blvd., Suite 1100
Portland, OR 97232-2737

(currently, Mr. Kratz for Regions 1-3, Mr. Tehan for Regions 4-5)
Compliance Section
U. S. Army Corps of Engineers
333 SW First Ave.
Portland, OR 97204-3495
  Joe Zisa, Division Chief
Division of Energy, Infrastructure and Ecosystems Services
2600 SE 89th Ave., Suite 100
Portland, OR 97266 
Russ Klassen
Department of State Lands
775 Summer Street NE
Salem, OR 97301

Monitoring Budgets


GE provides budgets for post-construction site management (monitoring and site maintenance). Expenditure accounts and sub jobs are assigned per Region and Program, with a loaded budget that was developed based on site-specific projections from Environmental employees. The environmental monitoring expenditure accounts are based on the biennium budget cycle.

Mitigation sites that require remediation or corrective work, or maintenance costs greater than $5,000 (or as indicated by GE) for post-construction site management must use project-specific a Corrective Action expenditure account rather than the Region/Program accounts. More information can be found in the Monitoring Budgets Advisory.
Corrective Action (CA) budget requests must be submitted to the Monitoring Program Coordinator (see Contacts in the Biology website), with a completed Corrective Action Plan.

Mitigation Capitol Improvement Plan

The CA Plan budget request should encompass all monitoring, maintenance and       corrective work anticipated to bring the project into compliance and to final               close-out.  

CA budgets are not limited to the biennium budget cycle, but remain active until the budget Is spent or the project is completed (close-out).

Site Management

ODOT Region Environmental employees and local agencies using ODOT/Federal-Aid Highway funding are responsible for maintaining and managing mitigation and restoration sites even after construction, until final permit requirements have been met. ODOT Region Environmental employees are also responsible for maintaining and managing SMA and RPA sites to ensure protection of the listed species.  
  • Management activities may be conducted by the agency’s Maintenance employees or a Contractor using appropriate charge accounts (See Monitoring Budgets section above), but the monitoring biologist will typically have to coordinate directly with them to plan and schedule the work. 
  • For ODOT, biology mitigation, SMA and RPA sites are managed by the Region environmental units. Regions may coordinate with the local maintenance office, or hire contractors (“Small Procurements” may be applicable for work under $5,000). 
  • Typically, regular coordination with the Maintenance Supervisor or Contractor is needed to ensure the work takes place as agreed-upon.
  • When using a Contractor, the hiring manager is responsible for inspecting the work. An Inspection Checklist may be used to assist with inspecting work performed by Contractors, and can also be used to inspect work performed by OYCC and agency maintenance crews.
Site management will cease after related permit obligations have been met. On a case-by-case basis, site management may be allowed to continue after permit obligations are met but this will require written approval from GE and the Region Environmental Unit manager.



Contact the following staff to report problems or suggest changes:
Beth Sandver - Editor / John Raasch - Content Owner