Based on two decades of case law and state and tribal program experience, the Environmental Protection Agency has substantially updated its handbook on Clean Water Act (CWA) SC401 water quality certification and how states can use SC401 certification to protect wetlands and other aquatic resources. This new handbook, Clean Water Act Section 401 Water Quality Certification: A Water Quality Protection Tool For States and Tribes, describes CWA SC401 certification authorities, the way different state and tribal programs use certification, and how state and tribal certification programs leverage available resources to operate their certification programs. While this new handbook is not a rule and does not create any legal requirements or set policy, it provides a wide-ranging description of SC401 certification provisions and practices which may be helpful to states and tribes interested in using SC401 as an effective water resource protection tool. This document does not substitute for CWA section 401 itself, or the relevant EPA (and other federal or state/tribal) implementing regulations. States, tribes, and federal licensing/permitting agencies may consider other approaches consistent with the CWA and those regulations. EPA retains the discretion to revise this handbook in the future.