A bottle or jar filled halfway with a combination of substrate material will function as a passive hydroponic system. In this setup, a bottle garden can serve the purpose of a passive hydroponic system. Certain combinations of substrates (expanded clay pellets, growstones, soilless mix, parboiled rice hulls) will wick water above water-level while maintaining aeration. Too much water retaining material (such as rockwool, cloth, or a sponge) will promote root rot, while other materials (expanded clay rocks, parboiled rice hulls, synthetic fibers) alone may not wick water high enough. It is important that most of the roots stay above water-level, unless this plant is semi-aquatic. Paint (use nontoxic) the bottom half of the container to reduce light around the plant's root-zone.

For a passive hydroponic garden, a bottle works better as it allows water to condense, keeping roots moist. Porous aggregate and condensation are enough to water plants' roots, so no further wicking material is needed in a passive hydroponic bottle garden. Unless this is a glass container, a valve drain may help rid of excess salts. When necessary, drain the water, partially at a time, by placing this valve halfway between the substrate level and the bottom of the container.