Tropical floodplains are highly productive because of seasonal replenishment of water and nutrients, which substantially boost primary productivity. This study examined how the architecture of aquatic macrophytes affect the light and water quality and consequently the attachment and biomass of epiphytes on a floodplain in northern Australia. Results show that macrophyte structural complexity is not only important for water column light penetration but also for the development of epiphytes on macrophytes. Emergent grasses with simple vertical structure and high plant densities, limit light penetration and consequently the development and biomass of epiphytic algae. In contrast, submerged macrophytes growing just below the water surface, allow greater light penetration. The complex architecture of submerged macrophytes also provides a large surface area for the development of a dense covering of epiphytic algae. Other plant structural forms (e.g., plants with floating leaves) have a simple structure, variable light penetration and low epiphytic algae biomass. The emergent grass Pseudoraphis spinescens (R.Br.) Vickery also had low light penetration but the horizontal alignment of stems across the water surface allow greater exposure to sunlight of the stems and the consequent development of epiphytic algae. We conclude that (1) the complex structure of submerged plants effectively creates a “false bottom” in deeper waters so that they function similarly to the floodplain's littoral zone, and (2) that their extremely large surface area for attachment allows greater production of epiphytic algae than would occur on the sediment surface.