The Wastewater Treatment Department is composed of the Wastewater Treatment Superintendent and eight employees, and is responsible for the treatment of wastewater prior to discharge to Corpening Creek. The department also maintains wastewater pump stations.

The City maintains the Corpening Creek Wastewater Treatment Plant, located on NC 226 South in Marion. At present, the Corpening Creek Plant can treat up to 3,000,000 gallons per day (3 mgd). However, the Plant is currently operating at less than one-third of its permitted capacity, with an average daily flow of 900,000 gallons per day (0.9 mgd). The Plant provides wastewater treatment service within the City, and in some areas outside the City and has sufficient capacity to handle future industrial, commercial and residential growth.

In 2011, the City completed a $6.6 million Wastewater Improvements Project that involved repairs to wastewater lines to reduce inflow and infiltration of stormwater and surface water into watsewater lines, eliminated the City's Catawba River Wastewater Treatment Plant and pumped wastewater flow from that facility to the Corpening Creek Wastewater Treatment Plant, and also involved upgrades to the Corpening Creek Plant to make that facility a true 3 million gallon per day wastewater plant capable of meeting all current and future State and Federal regulations.

As of May 27, 2010, the City of Marion no longer discharges treated wastewater into the Catawba River upstream of Lake James.

The Department maintains 22 wastewater pump stations, and performs all treatment operations, testing, and reports, as required by State and Federal law. The Department also schedules the cleaning of sewer lines on a regular basis, and makes needed repairs to sewer lines.