From the US Army Corps:
The “Clean Water Act (CWA) Section 401 Certification Rule” (85 Fed. Reg. 42,210) became effective September 11, 2020. Codified at 40 C.F.R. Part 12, the Rule promulgated by the U.S Environmental Protection Agency (USEPA) establishes new procedures intended to promote consistent implementation of CWA Section 401 and regulatory certainty in the federal permitting process. CWA 401 requires that, for any federally licensed or permitted project that may result in a discharge into waters of the United States, a water quality certification be issued to ensure that the discharge complies with applicable water quality requirements. The Rule sets forth several new procedures including requesting pre-filing meetings and establishing a reasonable period of time. More information on the Rule is available at: https://www.epa.gov/CWA-401. Stakeholders and prospective permit applicants are encouraged to carefully read and be familiar with the requirements of the new rule.
1. Pre-Filing Meeting Request: Before submitting a request for an individual CWA 401 water quality certification (WQC) to the certifying authority, a project proponent must request a pre‑filing meeting with the certifying authority at least 30 days prior to submitting the WQC request. The certifying authority will determine whether the meeting will be held, but submittal of the request for a pre-filing meeting is required.
2. WQC Request: Applicants submitting a request for WQC for an activity which require a DA permit must submit the request to the Sacramento District concurrently. When possible, the Sacramento District encourages applicants and permittees to obtain WQC before submitting a DA permit application. It would be beneficial to have the DA permit application materials include a statement about the 401 pre-filing meeting request, including the date and outcome of the request. Synchronizing the submittal of the WQC with the submittal of a DA permit application, permit verification request, or request for permit modification may reduce potential conflicts, improve coordination, and result in sooner decisions.
3. Reasonable Period of Time: The Rule requires the certifying authority act on a WQC request within a reasonable period of time, not to exceed one year after receipt of a WQC request. The Sacramento District will establish the reasonable period of time on either a categorical or case-by-case basis, according to criteria prescribed by the Rule. In general, for DA permit applications and requests for permit modifications, the Sacramento District will communicate to the certifying authority the reasonable period of time to act on certification requests will be 60 days. On a case-by-case basis, the Sacramento District may determine a longer timeframe is necessary. In addition, at the request of the certifying authority or project proponent, the reasonable period of time may be extended. In accordance with the Rule, within 15 days of receipt of a request for WQC, the Sacramento District will notify the certifying authority of the following information: (1) the date of receipt; (2) the applicable reasonable period of time to act on the certification request; and, (3) the date upon which waiver will occur if the certifying authority fails or refuses to act on the certification request.
The procedures outlined in this public notice are for the Sacramento District only. If you have any questions, please contact Kara Hellige (firstname.lastname@example.org, (970) 259-1604; ext. 1007).
 Projects qualifying for an existing general WQC are not required to go through the new Section 401 WQC process. Examples of existing general WQC include applicable 2017 NWPs in California, Utah, and Nevada.