Anthropic impacts and climatic factors act jointly on ecosystems as forcing agents of change, often leading to their deterioration. The effect of these agents depends on geographic location, climate and vegetation, among other natural and anthropogenic factors that characterize the studied environment. In order to understand the impact of these factors over aquatic and terrestrial ecosystems it is important to have continuous, standardized and extended information over time. Within aquatic ecosystems, microbial assemblages play a fundamental role in the cycles of matter and energy, and also have the potential to be robust indicators of the ecological and sanitary status of the ecosystem, due to their sensitivity and rapid response to environmental changes. In this sense, long term monitoring of microbial assemblages could provide valuable information on the characteristics of water bodies and the changes they undergo. Considering these premises, in the framework of the first meeting of the collaborative network on microbial aquatic ecology in Latin America (µSudAqua), held in La Paloma (Rocha, Uruguay) in December 2017, the creation of a set of observatories was decided, whose main objective is to evaluate how anthropogenic impact and climatic factors, in a latitudinal gradient, influence the structure and dynamics of the microbial community at the continental level in the diversity of aquatic environments in the region. Thus, the Latin American Microbial Observatory Network was born. Microbial observatories are valuable tools that have been established around the world in order to have access to systemized information on microscopic communities. However, they are scarce in Latin America. In this Observatory Network, observatory sites corresponding to different aquatic environments (freshwater, marine, lentic, lotic, with different types of anthropic impact) were selected based on their accessibility in order to achieve continuous sampling. Likewise, the observatory sites chosen contemplate a minimum bimonthly (preferably monthly) and simultaneous frequency, in the surface layer of the water column (euphotic), and the measurement of simple parameters, using protocols agreed upon by its members, which facilitate long-term continuity and the possibility of making comparative analyses between the different sites. This book aims to list the established and standardized protocols for sampling physicochemical parameters and biological communities in water, and subsequent analyses in the laboratory, taking into account the different water bodies. The main objective of this network is to strengthen the collaborative links between research laboratories from different Latin American countries in order to enhance the capabilities and knowledge of each group. In this way, we intend to promote the exchange of knowledge to find collective answers to questions that concern us as a region.