This study evaluated the effect of different storage vessels on the microbiological and physicochemical properties of rainwater harvested from different rooftops in Owerri. Different storage vessels were assembled and used to stored rainwater delivered by using different catchments. The catchments used were corrugated iron sheet roof, asbestos roof, stone coated roof, aluminum roof, and thatched roof. Rainwater was also collected directly from rainfall, in the open environment and stored in the vessels. The storage vessels were plastic contain, metal tank, earthen ware pot, and block/cemented tank. The study was designed in such a way that each of the storage vessels received water from each of the catchments for storage. In all, a total of 24 storage vessels were used. Each of the catchment delivered rainwater to a peculiar plastic container, metal samples were allowed to stay in the vessels for some days before they were taken to the laboratory for analysis using standard methods. From the results observed, the storage vessels made more microbial impact on the stored rainwater samples that physicochemical impact. Six bacterial and mould organisms were isolated from the stored rainwater samples. However, the molecular identification study for the bacterial organisms revealed plasmid possessed E. coli, P. aeruginosa, and Enterobacter sp., which made them resistant to the antibacterial drugs. From the observation of the present study, storage vessels may impact more on bacterial contamination than physicochemical or metal contamination. This study has shown the effect of different storage vessels on the microbiological and physicochemical properties of rainwater harvested from different rooftops in Owerri, Nigeria.