Aquatic ecosystems are historically overlooked regarding the occurrence of Arbuscular Mycorrhizal Fungi (AMF). Tropical lakes in the southern hemisphere are generally impacted by human actions, such as those in Brazil, although they still preserve a great diversity of macrophyte species that can support AMF communities. Thus, the study aimed to test (i) whether AMF community structure (composition, richness, diversity, dominance, and evenness) differs between aquatic and terrestrial conditions, and (ii) between seasons—rainy and dry. A total of 60 AMF species, distributed in 10 families and 17 genera, were found, with a difference in AMF composition between conditions (terrestrial and aquatic) and seasons (dry and rainy). The absolute species richness differed between conditions, seasons, and interactions. The aquatic/rainy season, which retrieved the most significant number of species, had the highest absolute richness and number of glomerospores and differed significantly from the terrestrial/rainy season. The results suggest that a shallow oligotrophic lake harbors a high AMF richness. In addition, this environment has a distinct AMF community from the adjacent coastal sand plain vegetation and is affected by seasonality.