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Freshwater environments and coastal marine areas provide key ecosystem services to society and serve as habitats for biodiversity. However, they face major challenges from human activities and climate factors, leading to global degradation. The effect of these agents depends on geographic location and climate, among other factors. To comprehensively understand the effect of these factors, continuous, standardized and long-term information is crucial. In particular, the aquatic microbiome plays a fundamental role in the cycling of matter and has been shown to act as a robust indicator of ecological status. Long-term monitoring of microbial assemblages can provide valuable insights into the characteristics and the changes water bodies undergo, delivering early warnings of critical impacts. Thus, the Latin American Aquatic Microbial Observatory Network (AMOLat) was set up during the inaugural meeting of the Latin American Collaborative Network on Microbial Aquatic Ecology (μSudAqua) in 2017. Observatory sites were carefully chosen, considering their accessibility and local relevance to each research group, ensuring the ongoing consistency of sampling efforts. This work aims to provide a historical overview of the network’s formation, highlighting key debates and definitions that took place during 2017-2023. Furthermore, it includes an initial characterization of the observatory sites and explores the possibilities that they offer to understand the structure and function of aquatic ecosystems in Latin America. The network presently encompasses 13 observatories, spanning a broad latitudinal range, numerous ecoregions and diverse aquatic ecosystems, displaying different environmental and anthropic impacts. Participating groups enhanced interactions, created a Protocol Book and showcased initial results through various communication efforts. Ultimately, establishing a regional network of aquatic observatories becomes mandatory for providing essential reference points to assess the response of microorganisms to global change in both the short and long term within Latin America.