Habitat Conservation Planning BMPs

Experts from inside the U.S. Fish and Wildlife Service and the environmental consulting world discuss Habitat Conservation Plans (HCP)–what they are, what factors to consider when creating an HCP, and best management practices for doing so.

This topic was covered in the 20th episode of Ecobot’s webinar series, Convergence of Wetland Science and Technology. View recorded episodes here.


  • Habitat Conservation Planning (HCP) Best Management Practices (BMPs)
  • Procedures for Successful HCPs: Low Effect HCPs
  • Prediction Modeling for EO’s to Streamline HCPs

Moderator Jeremy Schewe, PWS, Chief Scientific Officer, Ecobot 

Presenters & Panelists Trish Adams, National HCP Coordinator, U.S. Fish and Wildlife Service
Colleen Reilly, Senior Manager, Environmental Consulting & Technology, Inc.
Dale Sparks, PhD, Principal Scientist, Environmental Solutions, Inc.
Victoria Foster, IPaC Program Manager, U.S. Fish and Wildlife Service

Introduction to Habitat Conservation Planning Habitat Conservation Plans (HCPs) arose from Section 10 of the Endangered Species Act (ESA), which regulates activities that affect endangered or threatened plants and animals. In order to understand the benefits and challenges of HCPs, says Trish Adams, National HCP Coordinator at the U.S. Fish and Wildlife Service (USFWS), it helps to first understand how Section 10 fits into the ESA.

The ESA, passed in 1973, forms the basis for endangered species protection in the United States. Intended to prevent endangerment and extinction of species due to human impacts on ecosystems, it protects species and their habitats. The USFWS and the National Marine Fisheries Service are joint authorities of the ESA. The sections of the ESA are as follows, with sections that primarily relate to HCPs bolded:

  • Preamble
  • Section 2: Findings and Purposes
  • Section 3: Definitions
  • Section 4: Listing, Critical Habitat Designation, Recovery Monitoring
  • Section 5: Land Acquisition
  • Section 6: Financial Assistance to States & Territories

  • Section 7: The Role of Federal Agencies

  • Section 8: International Cooperation
  • Section 8A: Convention Implementation
  • Section 9: Prohibited Acts

  • Section 10: Exceptions, including Permits

  • Section 11: Penalties and Enforcement

When the ESA was first authorized, only federal agencies could be exempted from Section 9 violations. Section 10 was added in 1988, providing a mechanism for non-federal entities to receive protections from violations under Section 9. This gave rise to the Incidental Take Permitting processes, which are described in Sections 10(a)(1)(A) and 10(a)(1)(B). Today’s discussion focuses on Section 10(a)(1)(B).

Incidental Take Permits Seeking an Incidental Take Permit (ITP) is a voluntary aspect of an HCP. Once an applicant begins to pursue an ITP, they are subject to the current regulations, and the USFWS will evaluate their HCP in accordance with the policy and guidance at the time of the application. Section 6 of the ESA incentivizes participation in this voluntary process, as there is federal funding available to develop the HCP when the applicant works with their State agency. Once the permit is acquired, there is a land acquisition grant available only to permittees that help to augment the HCP. The grant cannot be used for mitigation, only to augment the success of the HCP.


  • Take: harm, harass, pursue, hunt, shoot, wound, kill, trap, capture, collect, or attempt to engage in any such activity of a threatened and endangered species (defined under Section 9)
  • Harm: significant habitat modification which kills or injures a listed species through impairment of their essential behaviors, such as breeding, feeding, and sheltering
  • Incidental Take Permit: legal instrument through which incidental take of listed animal species is authorized
  • Habitat Conservation Plan: Demonstrates how the applicant will meet the permit issuance criteria. It is a requirement of the ITP and a legally binding agreement between the Secretary of the Interior and the permit holder.

The following criteria must be met to issue an ITP:

  • The taking will be incidental to an otherwise lawful activity;
  • Applicant will, to the maximum extent practicable, minimize and mitigate the impacts of the taking;
  • Ensures that adequate funding to fully implement the plan will be provided;
  • The taking will not appreciably reduce the likelihood of survival and recovery of listed species in the wild. 

An HCP can:

  • Reduce conflict between endangered species conservation and the economic activities such as development
  • Streamline permitting processes. 
  • Particularly if an HCP is programmatic and integrates other federal or state permitting, all permitting activities can be addressed under one plan, which can save years of time between permit applications and development
  • Provide a lawful mechanism for permitting non-Federal projects that will result in “incidental take” of federally-listed species
  • Describe anticipated impacts to protected wildlife, and how they can be minimized and mitigated
  • Reduce the risk of violation of the ESA and third-party lawsuits
  • Provide consistency for regulated activities and transparency for the permitting process
  • Streamline the permitting process
  • Support recovery implementation

In addition to the benefits listed above, HCPs support an adaptive management approach, such that changing circumstances can be  over the course of long-term HCPs. They enable long-term comprehensive planning, with concrete plans to follow, thereby reducing uncoordinated decision-making. They also provide consistency of minimization and mitigation requirements.

Common Criticisms of HCPs

  • HCPs can be difficult and time-consuming to negotiate, depending on the complexity of the HCP and the number of species involved. HCPs are designed to be nimble and allow applicants to formulate a plan that works for them, but that flexibility can sometimes lead applicants to create plans that need refining.
  • HCPs can be expensive, but these upfront costs frequently outweigh the funds saved by the streamlined permitting process and regulatory certainty HCPs provide
  • Some NGOs have asserted that HCPs (particularly older ones) are not effective conservation tools, and that they fall short of some biological goals and objectives of the plan.

Applicants can alleviate concerns about difficulties and time spent negotiating the process by doing comprehensive research in advance of submitting an HCP. Adams recommends the 2016 HCP handbook as a key resource, and suggests working with the USFWS to evaluate the biological side of things and come up with a reasonable plan. It’s helpful to identify key decision points and milestones, and consider who might need to be consulted as the plan is formulated, such as CEOs or other stakeholders, she says, and bringing solicitors and lawyers into the process early on can help identify and avoid potential pitfalls. 

“I’ve seen [the process] get to the very end, and the decision-makers up the chain had no idea what the consultants had agreed to in the plan, and it wasn’t acceptable to them, so we basically had to start over. It’s really important to keep everybody in tune,” Adams says. “And find your HCP champions…those champions can be stakeholders, they could be biologists, they could be consultants…sometimes it’s the people working in the county itself.” In those cases, applicants should take advantage of the short windows of opportunity between election cycles, since officials can turn over, and new officials may be unwilling to implement or approve what their predecessor had agreed to. Applicants can also utilize the resources provided by the National HCP Coalition, which has a mentoring program.

What’s on the Horizon For HCPs?

  • Expansion of Section 6 Planning Assistance grants, such that projects under Section 10, such as Candidate Conservation Agreements with Assurances (CCAAs) and Safe Harbor Agreements (SHAs) can qualify
  • Revisions to the Section 10 implementing regulations, which have not been revised in 20+ years, by simplifying the CCAA and SHA processes in order to increase flexibility in the HCP program
  • Implementation of ECOSphere,a cloud-based tool for tracking HCP applications, and an ePermitting tool for all USFWS permits, including ITPs
  • Updates to the 2016 HCP Handbook
  • Revision of HCP training course at the USFWS National Conservation Training Center in West Virginia

Procedures for Successful HCPs: Low-Effect HCPs Colleen Reilly, Senior Manager at Environmental Consulting & Technology, Inc. (ECT), is well-versed in HCPs from the consulting side. “The HCP program is a Conservation Planning Program for imperiled species,” Reilly says. “It was not really designed to be a permitting program. Now, here in Region 4 and Florida specifically, project proponents sometimes really do need to use Section 10 as more of a permitting program. Meaning we often need to approach the process with the ultimate goal of obtaining an individual ITP, and sometimes there’s no other avenue for obtaining it. There’s no programmatic option, there’s no umbrella HCP, or no federal nexus to go through Section 7…The low-effect HCP is one way the Section 10 process can be streamlined, and may therefore be considered more desirable by a project proponent. That’s when minor impacts are involved.”

What are Low-Effect HCPs? Low-effect HCPs are a special category of HCPs for those involving minor or negligible effects on federally listed, proposed, or candidate species and their habitats, and minor or negligible effects on other environmental values or resources. The goal is to expedite processing of HCPs with inherently low impacts. Low-effect HCPs must still meet the issuance criteria under Section 10(a)(2)(B) pursuant to 50 CFR 17.22(b) and 17.32(b), as overviewed earlier.

Low-effect HCPs are evaluated on a case-by-case basis. It’s important to note that the size of the permit area may not dictate the level of impact it has, so a small permit area could have a significant impact to an imperiled species, or a large permit area with minor impacts. The determination is based on the anticipated impacts prior to the implementation of a mitigation plan, but it does consider avoidance as part of the action. The biggest time savings with a low-effect HCP is that they do not have to undergo a complex National Environmental Policy Act (NEPA) process: because the impacts are minor or negligible, these HCPs are categorically excluded, pursuant to the department manual (516 DM 8.5(C)(2).) To determine whether a plan qualifies as a low-effect HCP or other categorical exclusion.

The average timeline for HCPs with minor impacts and categorical exclusion from NEPA can be approximately 14 months, dependant upon early planning, quality of information, available staff resources, and ongoing coordination and communication.

Like any other HCP, there are three main phases:

  • Phase 1: Planning (Pre-Application): This is the most critical phase, where the applicant is determining the extent and type of take they might anticipate as a result of their action. Ultimately, the applicant is determining if they must pursue an ITP. At this stage, the applicant coordinates with USFWS and confirms the requirements of the plan, and develops the draft HCP while the USFWS works concurrently on NEPA compliance, compliance with the National Historic Preservation Act, and the internal Section 7 process.

  • Phase 2: Public Review and Permit Decision: This phase is driven by the USFWS. The public review period for categorical exclusions is 30 days. In this phase, the applicant must resolve any outstanding issues, and once processed and approved, receives a permit decision and issuance.

  • Phase 3: Implementation: The applicant implements their conservation strategy from the HCP. They initiate covered activities, including implementation of avoidance and minimization measures, and provide monitoring and reporting.

Case Study: Low-Effect HCP for the Sand Skink Background

The sand skink is a threatened species of lizard endemic to the Sandy Ridges in Central Florida. It occurs primarily in native and degraded upland habitats that can include areas like agricultural areas and roadsides. Degraded habitats such as agricultural areas are frequently prioritized for development, since in many cases the land is lower,  there is less clearing involved, and there is less likely to be wetlands or other sensitive features present. These habitats may still harbor a low density or remnant population of skinks. Because these habitats are upland, they frequently don’t have an issue that would make it relevant for the Section 7 process. In this case, therefore, there is need for a Section 10 permit program, and it can typically qualify for a low-effect HCP. 

Project Overview and Challenges

  • 185 acres of proposed conversion of fallow and active citrus
  • Survey protocol for sand sinks is intensive and restricted seasionally
  • No federal nexus to facilitate Section 7 process
  • Short permitting timeline to hit deadline for large industrial development project, because species occurrence was initially overlooked


  • Phase One: Applicant selected a knowledgeable local consultant, involved internal legal counsel and senior management to expedite internal decision-making related to the HCP, and facilitated proactive communication with USFWS. The consultant developed an innovative survey protocol and determined the extent and type of take, and together they formulated avoidance and minimization measures and a low-risk mitigation strategy by purchasing credits from a species conservation bank. Under the same plan, the applicant was able to get authorization to cover other covered species: the bluetail mole skink, the gopher tortoise (a candidate species), and the Eastern Indigo Snake. The HCP included minimization measures to avoid the likelihood of take, and ensured compliance with other laws, including the National Historic Preservation Act. The applicant provided funding assurances, and was able to prepare a draft HCP in 10 days.

  • Phase Two: Because there were no outstanding issues during the permitting process and no public comments were received, the permit documents were finalized and the decision timeline from start to finish was 12 months. The applicant obtained a five-year renewable ITP.

  • Phase Three: The applicant was able to implement the conservation strategy immediately. They provided receipts for the mitigation credits to USFWS, and were able to proceed with their activities with legal protection and regulatory certainty. They were able to implement avoidance and minimization measures as part of the action that benefitted multiple species, and were able to implement a minimal monitoring program to ensure that the take was not exceeded.

Best Management Practices

“Remember that this is an applicant-driven process,” says Reilly. “The applicant needs to take control and use the tools available. They need to understand the regulations, know the species and the biology, and build a solid team that will get them through the process. Plan early and identify issues early.”

  • Applicant drives the process
  • Know the regulations and build a strong team of stakeholders
  • Identify and address important issues
  • Detail the covered activities, including avoidance and minimization measures 
  • Define impacts early, develop conservation strategy
  • Use good science, but get creative 
  • Covered species (BGEPA, MBTA, Candidate, State-listed T&E)
  • Consider compliance with other laws
  • Provide quality information
  • Coordinate and communicate frequently

Prediction Modeling for EOs to Streamline HCPs

What are models?

To demonstrate what a model is and why they’re useful, Dale Sparks, PhD, Principal Scientist at Environmental Solutions, Inc. (ESI), has a few illustrative quotes he likes to refer to. Steven L. Lima of Indiana State University calls them “the logical outcome of a series of assumptions.” This means, Sparks explains, that when putting together a model, one considers how things interact with one another, and capture that mathematically. The observations of how the model runs can inform the decision-making process in the regulatory environment.

Another authority on the subject, one of the most successful modelers and mathematicians of the 20th century, George E. P. Box, said, “Essentially all models are wrong, but some are useful.” 

“This gets to the idea that models are tools,” Sparks emphasizes. “That’s all they are. They are not an alternate reality. They’re not a replacement for reality.”

Models and HCPs

Models for HCPs can be used to:

  • Estimate species distribution or abundance
  • Estimate the number of individuals taken
  • Understand the impact of the taking
  • Estimate value of conservation practices

Modeling for distribution and abundance are most common. Oftentimes, there is incomplete information available about where species occur. To address this, scientists can use Species Distribution Models (SDMs) to estimate the range. Some examples of SDMs are expert-based, MaxEnt, MaxLike, and Binomial General Linear Models (BGLIMs). “There are lots of statistical tools,” Sparks says, “and academics spend an enormous amount of time fighting over which of them is appropriate.” Most tools will work, he said, with different strengths and weaknesses, so it’s important to figure out which is best for the case at hand.

One use of models is for estimating take. At its simplest: 

Take = Number of Animals Present x Proportional Risk

Take is usually closely related to the estimate of abundance, i.e. how many members of the species are present. The scientist can then extrapolate from the SDM and assume that the risk is related to habitat quality. Occupancy/encounter models can account for unoccupied areas. Some activities have well-defined risk profiles, such as wind energy.

Once there’s an understanding of how many individuals are being taken, it’s time to estimate the impact of the taking, which is what must be mitigated. Teams like Spark’s are often trying to estimate things like number of females, survivability, and reproductive success, since take of females is more impactful than loss of males in a polygamous species. Loss of juveniles is a minor concern for R-selected species. 

Habitat and Resource Equivalency Analyses (HEAS and REAs) are tools for estimating the impact of the taking, and they also estimate the value of the conservation measures. The biggest challenge there is finding a fair exchange rate. HEAs compare the value of different habitats, while REAS are useful when it’s necessary to change “currencies,” such as impacting individuals and mitigating habitat. In some cases, when an SDM reveals the presence of a population where it doesn’t seem suitable to support it, it means that either the model is wrong, or, if the model is correct, the population isn’t likely to survive without some kind of intervention. 

Modeling Best Practices

  • Use the right tool for the job. Even if there is no perfect tool, a model can still provide useful information. 
  • Be honest about the limitations. One possible approach is to use several approaches and average them. 
  • If there is already a standard, don’t change it unless there’s a good reason to.

Deliver the most defensible estimate. “You want to make sure that the tools you’re using capture the uncertainty and the reality that you’re uncertain,” Sparks says.

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