This guidance discusses the circumstances under which EPA, when it is the National Pollutant Discharge Elimination System (NPDES) permitting authority, may, in its discretion, specify mixing zones in NPDES permits. Specifically, this guidance addresses the ability to include mixing zones in EPA-issued permits in the absence of a permit-specific authorization from the state through the Clean Water Act (CWA) $401 certification process. The guidance is divided into five sections. The first section provides an overview of the importance of mixing zones in establishing water quality-based effluent limits and the role of EPA and states in setting mixing zone policy. The second section discusses the types of mixing zone provisions commonly found in state water quality standards. Section three discusses the legal authority for EPA to establish a mixing zone in a permit based upon such provisions. Section four provides guidance regarding when to include a mixing zone in an NPDES permit where an EPA Region is the permitting authority. The final section discusses implications of this guidance on inclusion of schedules of compliance in EPA-issued permits.