Anoxygenic phototrophic bacteria have recently been recognized as a ubiquitous component of microbial communities in lakes and marine environments, but studies of the ecological factors that control their significance are scarce. We conducted a manipulative field experiment using natural freshwater microcosms, the tank bromeliad ecosystem, to test the response of anoxygenic and oxygenic phototrophic microorganisms to an environmental gradient across the forest edge. We assessed the biomass of these photosynthetic communities by their pigment content and used structural equation modeling to evaluate the importance of different habitat variables as ecological drivers. We show that anoxygenic phototrophic bacteria are primarily driven by small detrital organic particles rather than directly by light. In contrast, light and habitat size were the main factors controlling the biomass of oxygenic phototrophic microorganisms. Anoxygenic phototrophic bacteria inhabiting the bromeliad ecosystem represent huge concentrations of bacteriochlorophyll a relative to large pelagic environments and form an essential and dominant part of photosynthetic biomass across a wide range of ecological conditions. These freshwater photoheterotrophs are likely to play a pivotal and unsuspected role in energy flow and nutrient cycling in neotropical forests.