A large part of freshwater microorganism biodiversity is contained in the bromeliad ecosystem of the Neotropics, which form a multitude of small islands in a terrestrial matrix. While aquatic communities of bromeliads and their food-web organisation are relatively well documented, processes that shape diversity in such small water bodies remain largely understudied. Based on 217 bromeliad ecosystems from six sites located in French Guiana, we determined the factors that shape the diversity pattern of algal communities. We considered a broad range of environmental and ecological variables, including canopy openness, habitat characteristics, and invertebrate biomass, to identify the main drivers of algal community structure and biodiversity across bromeliads in a c. 25,000 km2 region. We found no evidence of random distribution or spatial structuring of algal communities. Algal biomass was mainly influenced by habitat size and complexity, particulate organic matter content, and light energy, while algal richness was primarily controlled by habitat size. Change in community structure as habitat size increases was driven by species turnover with increasing proportion of filamentous taxa. Our results indicate that, due to the large diversity of aquatic habitats they provide at a small spatial scale, bromeliads are critical ecosystems sustaining freshwater microorganism biodiversity.