Transitions between atmosphere and soil, and between soil and roots, are two examples of small-scale boundaries across which the nutrient, water, and gas dynamics of ecosystems are modulated. Most atmospheric inputs to ecosystems have to pass through the soil; thus, the atmosphere–soil boundary influences the type and amount of materials and energy entering the soil. Belowground plant inputs occur through the rhizosphere, the zone of soil immediately adjacent to the root. This soil boundary layer affects root inputs to soil and root extraction of water and nutrients from soil. We discuss how water, carbon, nitrogen, and oxygen dynamics are affected by atmosphere–soil and soil–root boundaries and how light, soil pH, and dust are affected by the atmosphere–soil boundary. (We also examine pH with regard to the root–soil boundary, but not in a separate section.) We examine the linkages between these small-scale boundaries and landscape ecology and discuss how the understanding of small-scale boundaries can contribute to the emerging field of boundary theory.