The root microbiome has attracted increasing attention in both natural and agricultural systems due to its important role in plant health, however, hydroponic systems have been much less studied. Despite absence of soil, and the rigorous hygiene of the commercial glasshouse, we found that the hydroponic root microbiome contained similar species richness to the rhizosphere of plants grown in soil but was dominated by a small number of species. The microbial environment in a hydroponic rockwool slab is influenced by gradients of moisture, pH and ion concentration. These environmental factors result in the assembly of different microbial communities at distinct locations in the root zone, and the community composition at each location was consistent throughout a glasshouse. Community composition changed gradually and consistently over the life of the crop. We found that plant-associated Proteobacteria and Bacteroidota, many of which were likely to be motile, were significantly more abundant in the hydroponic system than the rhizosphere in soil, while filamentous Actinobacteria and spore-forming Bacilli and Pirellulaceae were significantly depleted. Understanding the ecological patterns of the hydroponic root microbial community microbiome may provide commercial growers an additional method for monitoring the health of the crop and enable detection of dysbiosis which can give early warning of plant stress or disease. Identification of microbial traits which are favoured in the hydroponic environment is useful for evaluating candidates for biocontrol and other microbiome manipulation in soilless cultivation systems.