Collected water is filtered through the strata of soil or engineering growing soil, called substrate. After the soil reaches its saturation limit, excess water pools on the surface of the soil and eventually infiltrates the natural soil below. The bioretention soil mixture should typically contain 60% sand, 20% compost, and 20% topsoil. Soils with higher concentrations of compost have shown improved effects on filtering groundwater and rainwater. Non-permeable soil needs to be removed and replaced periodically to generate maximum performance and efficiency if used in the bioretention system. The sandy soil (bioretention mixture) cannot be combined with a surrounding soil that has a lower sand content because the clay particles will settle in between the sand particles and form a concrete-like substance that is not conducive to infiltration, according to a 1983 study. Compact lawn soil cannot harbor groundwater nearly as well as sandy soils, because the micropores within the soil are not sufficient for retaining substantial runoff levels.
When an area's soils are not permeable enough to allow water to drain and filter at an appropriate rate, the soil should be replaced and an underdrain installed. Sometimes a drywell with a series of gravel layers near the lowest spot in the rain garden will help facilitate percolation and avoid clogging at the sedimentation basin. However, a drywell placed at the lowest spot can become clogged with silt prematurely, turning the garden into an infiltration basin and defeating its purpose as a bioretention system. The more polluted the runoff water, the longer it must be retained in the soil for purification. Capacity for a longer purification period is often achieved by installing several smaller rain garden basins with soil deeper than the seasonal high water table. In some cases lined bioretention cells with subsurface drainage are used to retain smaller amounts of water and filter larger amounts without letting water percolate as quickly. A five-year study by the U.S. Geological Survey indicates that rain gardens in urban clay soils can be effective without the use of underdrains or replacement of native soils with the bioretention mix. Yet it also indicates that pre-installation infiltration rates should be at least .25 in/hour. Type D soils will require an underdrain paired with the sandy soil mix in order to drain properly.
Rain gardens are often located near a buildings roof drainpipe (with or without rainwater tanks). Most rain gardens are designed to be an endpoint of a buildings or urban site's drainage system with a capacity to percolate all incoming water through a series of soil or gravel layers beneath the surface plantings. A French drain may be used to direct a portion of the rainwater to an overflow location for heavier rain events. If the bioretention site has additional runoff directed from downspouts leading from the roof of a building, or if the existing soil has a filtration rate faster than 5 inches per hour, the substrate of the rain garden should include a layer of gravel or sand beneath the topsoil to meet that increased infiltration load. If not originally designed to include a rain garden onsite, downpipes from the roof can be disconnected and diverted to a rain garden for retrofit stormwater management. This reduces the amount of water load on the conventional drainage system, and instead directs water for infiltration and treatment through bioretention features. By reducing peak stormwater discharge, rain gardens extend hydraulic lag time and somewhat mimic the natural water cycle displaced by urban development and allow for groundwater recharge. While rain gardens always allow for restored groundwater recharge, and reduced stormwater volumes, they may not improve pollution unless remediation materials are included in the design of the filtration layers.