Legionella spp. and NTM are waterborne opportunistic pathogens that cause sporadic respiratory disease, following the inhalation of contaminated aerosols. Sources are rarely found but it is has been suggested that domestic water systems, in particular showers, may be reservoirs of infection. This study analysed water and aerosol samples from UK domestic showers to determine the presence and prevalence of Legionella spp. and NTM. Legionella spp. and NTM, including clinically relevant strains, were detected in 48% and 78% of showers respectively. Aerosol sampling of positive showers using Andersen and cyclone samplers revealed high concentrations of viable NTM in the air but viable Legionella spp. could not be recovered and was only detected by quantitative polymerase chain reaction (qPCR). Household shower systems may represent a risk of infection to susceptible individuals. Further studies are required to determine this risk and possible mitigation strategies in light of an increasing elderly and immunocompromised population.