Microorganisms in indoor settings, where we spend ~90% of our time, impact human health and well-being. Deeper understanding of the built environment microbiome is needed to be able to efficiently manage these microorganisms. Indoor microbial communities are known to vary in abundance, composition and diversity depending on material type, moisture levels and occupants. Here, we used as combination of epiflourescent microscopy and fluorescence- activated cell sorting (FACS) we expanded upon existing knowledge of the built environment to allow broader characterization of microbial abundances in fiberboard and drywall material in high moisture conditions. Using epifluorescence and differential contrast microscopy we estimated viral, bacterial and fungal abundance in the two material types. Fungi were almost exclusively observed on drywall coupons. We visually identified the fungal genera Alternaria, Ulocladium and Chaetomium on drywall coupons. These are known secondary and tertiary colonizers of building materials with high water activity. Fungal spores and hyphae length were estimated separately for the two material types. We observed a decline in the number of spores at a later timepoint and concurrent emergence of hyphae. Overall, these results demonstrated that drywall was more susceptible to water damage and microbial succession. Furthermore, we extended our analysis of the dynamics of microbial growth and metabolism on building materials by using flow cytometry-based methods to differentiate between viable and non-viable cells. We also used FACS to collect viable and non-viable cells fractions separately. Overall, this study has important implications for buildings with leaks, in flood-prone regions, spaces with prolonged damp conditions like bathrooms and their impact on human health.