Legionella pneumophila (Lp) is responsible for Legionnaires' disease. This bacterium grows in water systems and is transmitted to human upon aerosolization. Cooling towers are one of the main sources of large outbreak. To better understand the growth of Lp in cooling towers and its interaction with the resident microbiome, we built a lab-scale cooling tower pilot to study the dynamics of Lp colonization in relationship to resident microbiota and spatial distribution. This pilot consists of cold and warm water pipe sections connected to an aerated cooling vessel, simulating a typical open evaporative cooling tower. It was filled with water from an operating cooling tower. The objective of the study was to characterize the microbial community in the pilot cooling tower residing in the biofilm and in the water and relate it with the dynamics of Lp colonization and local temperature. The microbial communities were characterized by 16S rRNA gene and 18S rRNA gene amplicon sequencing.