Biofilm formation, loose deposit accumulation and water quality deterioration in drinking water distribution systems have been widely reported. However, the accumulation and distribution of harbored elements and microbes in the different niches (loose deposits, PVC-U biofilm, and HDPE biofilm) and their corresponding potential contribution to water quality deterioration remain unknown. This precludes an in-depth understanding of water quality deterioration and the development of proactive management strategies. The present study quantitatively evaluated the distribution of elements, ATP, Aeromonas spp., and bacterial communities in distribution pipes (PVC-U, D = 110 mm, loose deposit and biofilm niches) and household connection pipes (HDPE, D = 32 mm, HDPE biofilm niches) at ten locations in an unchlorinated distribution system. The results show that loose deposits in PVC-U pipes, acting as sinks, constitute a hotspot (highest total amount per meter pipe) for elements, ATP, and target bacteria groups (e.g., Aeromonas spp., Mycobacterium spp., and Legionella spp.). When drinking water distribution system niches with harbored elements and microbes become sources in the event of disturbances, the highest quality deterioration potential (QDP) is that of HDPE biofilm; this can be attributed to its high surface-to-volume ratio. 16s rRNA analysis demonstrates that, at the genus level, the bacterial communities in the water, loose deposits, PVC-U biofilm, and HDPE biofilm were dominated, respectively, by Polaromonas spp. (2–23%), Nitrosipra spp. (1–47%), Flavobacterium spp. (1–36%), and Flavobacterium spp. (5–67%). The combined results of elemental composition and bacterial community analyses indicate that different dominant bio-chemical processes might occur within the different niches—for example, iron-arsenic oxidizing in loose deposits, bio-calumniation in PVC-U biofilm, and methane oxidizing in HDPE biofilm. The release of 20% loose deposits, 20% PVC-U biofilm and 10% HDPE biofilm will cause significant changes of water bacterial community.