Microbes process a significant fraction of organic material in marine systems, and the composition and activity of their communities are strongly modulated by fluctuations in nutrient availability. To investigate the distribution and dynamics of microbial communities in tropical lagoon ecosystems, bacteria and archaea were quantified from water column samples collected in lagoons around Moorea, French Polynesia during May 2021, April 2022, and April 2023 using eDNA sequencing. Environmental DNA was extracted and sequenced to assess microbial community composition, with data processed using the QIIME 2 platform (version 2023.7). Microbial communities in fringing reef habitats differed from those in mid-lagoon and back reef sites. These differences in microbial communities were related to patterns of water column nutrients and fluorescent dissolved organic matter, providing a baseline for understanding how lagoon microbial communities respond to spatial and temporal variability in reef environments.