As studies increasingly support the presence of health risks associated with mold and moisture, understanding fungal concentrations and physical measurements as they relate to the microenvironment becomes more important. We conducted a cross-sectional study in the homes of 64 subjects. The primary objective of this study was to use trained inspectors' list of indicators in rooms (bathroom, bedroom, and basement) and determine whether these indicators are associated with higher fungal levels or physical measurements. A new category for combining the concentrations of fungal species, referred to as moisture indicator fungi (MIF), is used in the analysis. Our results show that basements with a musty odor, efflorescence, water sources, or mold have a two- to threefold increase in fungal concentrations over basements without these indicators. The regression model for the basement was highly predictive of indoor MIF concentrations (r2 = .446, p = .017). Basement water sources are substantial predictors of indoor total fungi, MIF, and Aspergillus/Penicillium spp. MIF concentrations are higher in homes with basement water sources, and most notably, the increase in MIF concentrations is significant in other living spaces (bathroom and bedroom) of the dwelling. Basement water sources are important moisture/mold indicators for epidemiologists to use in exposure assessments performed in residential dwellings.