This manual provides general guidance for Department of Energy (DOE) officials for complying with Sect. 402 of the Clean Water Act (CWA) of 1977 and amendments. Section 402 authorizes the US Environmental Protection Agency (EPA) or states with EPA approved programs to issue National Pollutant Discharge Elimination System (NPDES) permits for the direct discharge of waste from a point source into waters of the United States. Although the nature of a project dictates the exact information requirements, every project has similar information requirements on the environmental setting, type of discharge(s), characterization of effluent, and description of operations and wastewater treatment. Additional information requirements for projects with ocean discharges, thermal discharges, and cooling water intakes are discussed. Guidance is provided in this manual on general methods for collecting, analyzing, and presenting information for an NPDES permit application. The NPDES program interacts with many sections of the CWA; therefore, background material on pertinent areas such as effluent limitations, water quality standards, toxic substances, and nonpoint source pollutants is included in this manual. Modifications, variances, and extensions applicable to NPDES permits are also discussed.