Brazil is a biodiversity hotspot that encompasses six biomes over an extensive area in South America. However, freshwater biodiversity studies are heterogeneous between communities and regions and over time resulting in knowledge gaps. Thus, we assessed trends and knowledge gaps in the literature on freshwater communities in Brazil. We performed a literature review of fungi, phytoplankton, zooplankton, macroinvertebrate, meiofauna, and fish communities, and applied automatic text mining and topic modelling to the literature database of each group. The first studies on aquatic communities date from the early 1970s investigating zooplankton. From 2005, there was a rapid increase in community studies. Fish and macroinvertebrates were the most studied groups, while fungi were the least studied. Mapping the topic landscape, we found that most topics were community specific. For fish, the 'effect of dams' was the most frequent and hot topic. 'Fishery-management', 'habitat', 'functional diversity' were additional hot topics. For the macroinvertebrate community, ‘Benthic ecology’ and 'EPT biotic index' were frequent and a cold topic. Hot topics were 'riparian vegetation' and 'dispersal ecology and metacommunity’. For zooplankton, the most frequent topic was 'phytoplankton relationship', while 'beta diversity' was the hottest topic. For phytoplankton, frequent topics were 'floodplain', 'cyanobacteria-bloom', and 'temporal' and 'vertical abiotic variation'. For meiofauna, the most frequent and hot topic was 'Oligochaeta biodiversity'. Other hot topics were 'plant associated', 'lentic studies', 'temporary ecosystems', and 'hyporheic zone'. The most frequent and hot topic of fungi was 'macroinvertebrate relationship'. The only topic in publications of all communities was 'plant associated'. Most of the topics were on fundamental ecology. Applied ecology topics were limited to bioassessment and fishery-management. Topics approaching societal issues were related to land-use changes and fishery. Few studies used experimental approaches. Future research should focus on applied ecology, while fundamental studies need investigation on fungi and meiofauna aquatic communities.