Rainwater has been found to be a valuable source of drinking water in Europe, especially in such crisis situations as those caused by contamination of water uptake into water supply systems, large-scale floods or terrorist attacks (e.g., biological weapons). The microbiological quality of water plays a significant role, which is directly related to the potential health risks associated with harvested rainwater (including rainwater stored in the tanks). Microbial contamination is commonly found in rainwater. However, in the literature, detailed results of qualitative and quantitative microbiological assessments are sparse and remain unexplored. Therefore, the aim of this study was to investigate and analyze changes in the microbiological quality of roof-harvested rainwater stored in the tanks, depending on the collection conditions (type of roof surface), storage duration and season. Authors elucidate that conditions such as storage duration, the season in which rainwater is collected, the roof-like surface types and morphology of the catchment area highly affect rainwater quality. This study showed that rainwater harvested from a galvanized steel sheet roof had the best microbial quality, regarding the lowest number of bacteria, while rainwater from a flat roof covered with epoxy resin was the worst. Further, it was detected that rainwater collected in autumn and spring obtained the best microbiological quality. Moreover, a decrease in the number of bacteria was observed in correlation to storage duration. The water became sanitary safe after six weeks of storage at 12 °C. Its use for purposes requiring drinking water quality before six weeks of storage required disinfection.