Various types of permits are issued by the federal, state, and local governments to protect the quality of Idaho’s surface and ground waters. Idaho’s Pollutant Discharge Elimination System (IPDES) permits are issued by the state, and dredge and fill permits and hydroelectric power licenses are issued by the federal government. DEQ also issues permits regulating land application of wastewater and operation of swine facilities, while local governments handle wastewater pretreatment and septage tank pumper permits.

The IPDES E-Permitting system is a web interface for IPDES applicants and permittees to complete and submit permit applications and notices of intent, submit compliance reporting documents, and track invoices and payments.