St. Louis City is largely served by combined sewers, which means that a single pipe carries stormwater and wastewater. Excess stormwater to the system can cause the system to surcharge, causing basement backups and, in some cases, overland flooding. The goal of the Cityshed Mitigation Program is to alleviate the effect of wet weather surcharging and overland flooding of the combined sewer system. MSD plans to spend $230 million in combined sewer area sub-watersheds over the life of MSD Project Clear.

In some areas of the Citysheds program, recurring system surcharges are nearly impossible to prevent: in these areas homes may have been built in low-lying areas or along original sewers that were once creek beds. The only way, in some cases, to help homeowners who experience chronic basement backups and sewer surcharges is to offer them the opportunity to participate in a voluntary buyout program. The Citysheds program began homeowner outreach for voluntary buyouts of this kind in 2013, estimating over 200 properties will be involved over the life of the program. These programs help homeowners through property purchase and relocation.

Other strategies for alleviating the effect of wet weather surcharging and overland flooding of the combined sewer system are relief sewers, control and detention of wet weather flows, and in some cases sewer separation.