Microbial communities associated to plants are greatly influenced by water availability in soil. In flooded crops, such as rice, the impact of water management on microbial dynamics is not fully understood. Here, we present a comprehensive study of the rice microbiota investigated in an experimental field located in one of the most productive area of North Italy. The microbiota associated to paddy soil and root was investigated using 454 pyrosequencing of 16S, ITS and 18S rRNA gene amplicons under two different water managements, upland (non-flooded, aerobic) and lowland (traditional flooding, anaerobic) at three plant development stages. Results highlighted a major role of the soil water status in shaping microbial communities, while phenological stage had low impacts. Compositional shifts in prokaryotic and fungal communities upon water management consisted in significant abundances changes of Firmicutes, Methanobacteria, Chloroflexi, Sordaryomycetes, Dothideomycetes and Glomeromycotina. A vicariance in plant beneficial microbes and between saprotrophs/pathotrophs was observed between lowland and upland. Moreover, through network analysis we demonstrated different co-abundances dynamics between lowland and upland conditions with a major impact on microbial HUBs (strongly interconnected microbes) which fully shifted to aerobic microbes in the absence of flooding.