Many coastal lagoons in the tropics harbor mangrove formations settled in intertidal zones, which exhibit high diversity and complexity. However, these ecosystems are under severe threat due to increasing anthropogenic pressures. Microorganisms are among the most efficient organisms involved in mangrove ecosystem processes. On solid substrates, they are organized into biofilms consisting mainly of heterotrophic bacteria and autotrophic eukaryotes. Changes in trophic conditions are known to modify the functioning and diversity of these communities. The present study investigated the relationship between changes in nutrient concentrations and changes in microbial communities in a tropical mangrove located in Chirongui Bay (Mayotte Island, France). One site, which was exposed to pre-treated wastewater and considered as impacted, was compared to a pristine control site. Microbial communities sampled from sediments, water and biofilms (colonized on roots or on artificial substrates) were subjected to functional, structural, and diversity measurements. At the impacted site, cell densities (flow cytometry) were significantly higher in the bacterial community, whereas neither the biomass values, nor the photosynthetic performance of the phototrophic community (PhytoPAM) revealed any difference between the 2 sites. The diversity of the phototrophic community (PhytoPAM) showed that the contribution of green algae and diatoms was higher at the impacted site. Molecular fingerprinting (DGGE) of eukaryotic and prokaryotic communities highlighted the presence of contrasting diversity patterns, depending on whether they originated from an impacted site or not. Pre-treated effluents impacted both the structure and the diversity of the microbial communities. Insight into functional diversity of these communities is required in order to improve our understanding of their ability to tolerate effluent discharges, and to assess their biological capacity to remove anthropogenic nutrients.