Water and sanitary sewer services are provided to most Woodbury residents by the city's Utility Division. This division operates and maintains wells, water storage facilities, sanitary sewer lines, and lift stations; flushes and repairs city hydrants; and reads water meters.

The Utility Division also maintains sanitary sewer lines in Woodbury which discharge into the regional waste treatment system managed by the Metropolitan Council Environmental Services (MCES). Those properties not on sewer lines utilize private on-site septic systems. A separate building permit is required to install a septic system that conforms to state and city codes.