(a) For purposes of this section, the following terms have the following meanings:

1. (1) “Permit” means any authorization issued by the department pursuant to this article to take a species listed by this chapter as candidate, threatened, or endangered. The term includes a consistency determination pursuant to Section 2080.1 and a concurrence determination pursuant to Section 2080.3 or 2080.4.
2. (2) “Permit application” means an application for a permit, an amendment to a permit, or a renewal of a permit. The term includes a consistency determination request pursuant to Section 2080.1 and a concurrence determination request pursuant to Section 2080.3 or 2080.4.
3. (3) “Permittee” includes any individual, firm, association, organization, partnership, business, trust, corporation, limited liability company, district, city, county, city and county, town, federal agency, and the state who applies for or who has received a permit pursuant to this article.
4. (4) “Project” has the same meaning as defined in Section 21065 of the Public Resources Code.
5. (5) “Project cost” means the total direct and indirect project expenses that include, but are not limited to, labor, equipment, permanent materials and supplies, subcontracts, overhead, and miscellaneous costs. The term shall not include permit or license expenses or mitigation costs. For purposes of this paragraph, the term “permit” includes, but is not limited to, a permit as defined in paragraph (1).

6. (6) “Voluntary habitat restoration project” means a project that meets both of the following requirements:

   1. (A) The project’s primary purpose is voluntary habitat restoration and the project may have other environmental benefits, and the project is not required as mitigation due to a regulatory action.
   2. (B) The project is not part of a regulatory settlement, a regulatory enforcement action, or a court order.

(b)

1. (1) The department shall collect a permit application fee for processing a permit application submitted pursuant to this article at the time the permit application is submitted to the department. Upon appropriation to the department from the Endangered Species Permitting Account, the department shall use the permit application fee to pay for all or a portion of the department’s cost of processing permit applications, permit development, and compliance monitoring pursuant to this article.

2. (2) This subdivision does not apply to any of the following:

   1. (A) Activities or costs associated with the review of projects, inspection and oversight of projects, and permits necessary to conduct timber operations, as defined in Section 4527 of the Public Resources Code, in accordance with Article 9.5 (commencing with Section 4629) of Chapter 8 of Part 2 of Division 4 of the Public Resources Code.
   2. (B) Permits or memoranda of understanding authorized by subdivision (a) of Section 2081.
   3. (C) Permits for voluntary habitat restoration projects.

(c) The department shall assess the permit application fee as follows, subject to subdivision (f):

1. (1) For a project, regardless of estimated project cost, that is subject only to Section 2080.1, 2080.3, or 2080.4, the department shall assess either of the following amounts:

   1. (A) Seven thousand five hundred dollars ($7,500).
   2. (B) Six thousand dollars ($6,000), if the project uses a department-approved conservation or mitigation bank to fulfill mitigation obligations pursuant to this article.

2. (2) For a project where the estimated project cost is less than one hundred thousand dollars ($100,000), the department shall assess either of the following amounts:

   1. (A) Seven thousand five hundred dollars ($7,500).
   2. (B) Six thousand dollars ($6,000), if the project uses a department-approved conservation or mitigation bank to fulfill mitigation obligations pursuant to this article.

3. (3) For a project where the estimated project cost is one hundred thousand dollars ($100,000) or more but less than five hundred thousand dollars ($500,000), the department shall assess either of the following amounts:

   1. (A) Fifteen thousand dollars ($15,000).
   2. (B) Twelve thousand dollars ($12,000), if the project uses a department-approved conservation or mitigation bank to fulfill mitigation obligations pursuant to this article.

4. (4) For a project where the estimated project cost is five hundred thousand dollars ($500,000) or more, the department shall assess either of the following amounts:

   1. (A) Thirty thousand dollars ($30,000).
   2. (B) Twenty-four thousand dollars ($24,000), if the project uses a department-approved conservation or mitigation bank to fulfill mitigation obligations pursuant to this article.
5. (5) The department shall collect a fee of seven thousand five hundred dollars ($7,500) for processing permit amendments that the department has determined are minor as defined in regulation or fifteen thousand dollars ($15,000) for processing permit amendments that the department has determined are major as defined in regulation.

(d)

1. (1) If the permit application fee paid pursuant to subdivision (c) is determined by the department to be insufficient to complete permitting work due to the complexity of a project or the potential effects of a project, the department shall collect an additional fee of up to ten thousand dollars ($10,000) from the permittee to pay for its estimated costs. Upon its determination, the department shall notify the permittee of the reasons why an additional fee is necessary and the estimated amount of the additional fee.
2. (2) The additional fee collected pursuant to paragraph (1) shall not exceed an amount that, when added to the fee paid pursuant to subdivision (c), equals thirty-five thousand dollars ($35,000). The department shall collect the additional fee before a final decision on the permit application by the department.

(e)

1. (1) For a permit application submitted to the department pursuant to this article on or after September 13, 2016, the department shall collect the permit application fee at the time the permit application is submitted. The department shall not deem the permit application complete until it has collected the permit application fee. A permit application submitted or deemed complete before September 13, 2016, shall not be subject to fees established pursuant to this section.
2. (2) If a permit application is withdrawn within 30 days after paying the permit application fee, the department shall refund any unused portion of the fee to the permittee.
3. (3) If a permit application is withdrawn after 30 days of paying the permit application fee, the department shall not refund any portion of the fee to the permittee.

(f)

1. (1) The department shall adjust the fees in this section pursuant to Section 713.
2. (2) The Legislature finds that all revenues generated under this section and used for the purposes for which they were imposed are not subject to Article XIII B of the California Constitution.
3. (3) The department, at least every five years, shall analyze permit application fees pursuant to Section 713 to ensure the appropriate fee amounts are charged.