Over the last 30 years, the frequency and occurrence of intense rainfall, and thus extreme hydrological events –flooding- has steadily increased. Drainage infrastructure in the UK was not designed for a changing climate, and many sewer systems in densely populated urban areas, are unable to cope. Sewage overflow and surface run off in urban areas can act as vectors for the dissemination of pathogens, known to cause disease among human populations. Most of the previous studies in this field have focused on using faecal indicators such as E.coli when assessing the public health risk of floodwater [1]. However, traditional indicators do not accurately reflect the true risk that urban flooding poses [2]. Little is understood in regards to the survivability and behaviour of pathogens in different urban settings, which are fundamental to determine potential risks to public health. Previous investigations in UK waterlogged soils have shown a clear response of microbial communities to water table variation, temperature, and nutrient availability in soil profiles [3]. This research aims to investigate, using advanced molecular methods, the dynamics of pathogens (i.e. movement through soil and survival rates), and microbial interactions at the soil/water interface- collecting information from field work studies and laboratory-controlled experiments. The outcomes from this research will inform future management strategies of flooded sites that will aid to protect public health.