Worldwide, it is common that the drinking water distribution systems (DWDSs) may be subjected to changes of supply water quality due to the needs of upgrading the treatment processes or switching the source water. However, the potential impacts of quality changed supply water on the stabilized ecological niches within DWDSs and the associated water quality deterioration risks were poorly documented. In the present study, such transition effects caused by changing the supply water quality that resulted from destabilization of biofilm and loose deposits in DWDS were investigated by analyzing the physiochemical and microbiological characteristics of suspended particles before (T0), during (T3-weeks) and after upgrading the treatments (T6-months) in an unchlorinated DWDS in the Netherlands. Our results demonstrated that after 6 months’ time the upgraded treatments significantly improved the water quality. Remarkably, water quality deterioration was observed at the initial stage when the quality-improved treated water distributed into the network at T3-weeks, observed as a spike of total suspended solids (TSS, 50–260%), active biomass (ATP, 95–230%) and inorganic elements (e.g. Mn, 130–250%). Furthermore, pyrosequencing results revealed sharp differences in microbial community composition and structure for the bacteria associated with suspended particles between T0 and T3-weeks, which re-stabilized after 6 months at T6-months. The successful capture of transition effects was especially confirmed by the domination of Nitrospira spp. and Polaromonas spp. in the distribution system at T3-weeks, which were detected at rather low relative abundance at treatment plant. Though the transitional effects were captured, this study shows that the introduction of softening and additional filtration did not have an effect on the water quality for the consumer which improved considerably after 6-months’ period. The methodology of monitoring suspended particles with MuPFiSs and additional analysis is capable of detecting transitional effects by monitoring the dynamics of suspended particles and its physiochemical and microbiological composition.