Previous research into microbial persistence on material surfaces following flooding has produced a wide range of results due to differing experimental conditions, including the temperature and humidity conditions of the experimental material and/or surrounding air. However, investigations to identify and quantify these factors and their links to the hygrothermal properties of building materials and the transient environmental conditions are rarely reported. This paper examines the viability of bacterial species on drying material surfaces that have been saturated with water or synthetic sewage. Escherichia coli and Enterococcus faecalis were inoculated on brick, wood, or plaster and allowed to dry at the conditions intended to mimic the remediation environments commonly found in domestic dwellings following a flood event. The inactivation rates were compared between environmental conditions, water type and the material properties of the surfaces. Significant differences were found in the declines in E. coli according to water type, the surface relative humidity and air relative humidity and between drying rates for sewage floods. Simulations using hygrothermal software were performed to illustrate the wide variation in material drying rates under different scenarios, taking into account material size, wall composition, and ventilation. The significantly differing rates of microbial death on flooded building materials under different drying regimes suggest that building simulation models can be useful tools for predicting the level and duration of microbial contamination in buildings following a flood event. A better understanding of microbial survival on drying surfaces can be used to assess the health risks to occupants in flood affected properties.