Citygarden includes six separate rain gardens. Four small rain gardens along 9th Street filter site runoff, as well as runoff from 9th Street itself. Each individual block within the garden also contains a rain garden, which gathers site runoff through both surface flow and a series of underground pipes. These pipes are called a subsurface drainage system, which collects water from all over Citygarden and empties it into the rain gardens.

These six rain gardens, covering more than 5,000 square feet, collect and infiltrate stormwater from two-thirds of the site's surfaces.

A rain garden is a planted depression in the ground that forms a "bioretention area" by collecting water runoff from impervious areas and storing it, which allows it to be filtered and slowly absorbed by the soil, rather than flowing into storm drains. This helps prevent erosion, water pollution, and flooding.

Rain gardens also improve water quality through a nutrient removal, or "filtering" process, which takes place as the water comes in contact with the soil and roots of the surrounding trees, shrubs, and vegetation.