Hydroponic production systems are challenged by root diseases, but can be made less susceptible to infection. While the systems are mostly unchallenged by nematodes, pathogens that can live and spread though water still cause loss of yield. Common diseases would be Phytophthora, Pythium, Fusarium and bacteria such as Erwinias and Pseudomonads. Since horticulture cannot be performed in a sterile environment on a commercial scale, insight in population dynamics of pathogens in aquatic systems as well as plants' resilience need to be understood to lower the risk of infection. This paper addresses a number of biological principles in aquatic ecology that could be used in improving system design processes as well as providing the first data on the population dynamics in chrysanthemum production on deep flow systems in The Netherlands using next generation sequencing (NGS). It was observed that free colonisation of the water leads to highly diverse bacterial populations, while inoculation with water from an established deep flow pond leads to more uniform populations in the long run. Temperature can strongly influence bacterial populations. Addition of benefical micro-organisms leads to increase plant resilience against diseases. It is yet unclear whether such reduced infection is due to direct antagonistic effect, through a plant-endophyte symbiotic relationship or through competition for nutrients (sugars) or physical space. Fungal populations could not be studied since the similarity of DNA-database was too low to draw conclusions.