This manual addresses many water quality standards issues that facilities may encounter, including existing uses, use attainability analyses (UAAs) to revise designated uses, fish consumption advisories, whole effluent toxicity (WET) criteria, and sediment criteria. The manual will provide guidance on a number of listing issues, including listings due to violations of narrative criteria and fish consumption advisories, delisting, listing waters that are impaired but do not need a TMDL because they are expected to meet standards through other means, and challenging an erroneous listing determination. The second part of this manual will discuss permitting discharges to impaired waters during the interim period before TMDLs are developed. The manual will describe the development of water quality-based effluent limitations on impaired waters, and will also discuss a number of issues for affected facilities to consider during the permitting process, including timing (when the permit should be issued), watershed permitting, verifying the impairment determination before the permit is issued, other controls available to bring the water into attainment, reasonable potential calculations, voluntary reduction measures, non-numeric effluent limitations, and calculating numeric effluent limitations.