Rapid analyses based on flow cytometry (FCM) and quantitative PCR (qPCR) were proposed and applied in a full-scale mobile water treatment plant (flow rate of 4.4 L/s) utilized as a civil protection module for drinking water production for quasi real-time monitoring. The rapid methods applied here are two cultivation-independent techniques (FCM and qPCR). The microbiological quality of water was monitored on the basis of alternative microbial parameters, detecting cells with an intact and permeabilised membrane (in 20 min), cells with beta-D-galactosidase activity (in 40 min) and Escherichia coil (E. coil, in less than 3 h). These rapid techniques were compared with some conventional culturable bacteria groups (aerobic mesophilic bacteria, total coliforms and E. coli). Although intact bacteria were two orders of magnitude higher than culturable aerobic mesophilic bacteria (due to a large fraction of viable-but-not-culturable cells, but also chemolithotrophic bacteria), they both showed not significant reduction in cells after filtration, 2-3 log of removal after ozonation and a regrowth of about 1 log after granular activated carbon. Cells with beta-D-galactosidase activity (belonging to the group of total coliforms) were higher than culturable total coliforms, due to a large presence of active-but-not-culturable cells, especially in ozone treated water. E. coli quantified by qPCR decreased through filtration and they were under the quantification limit after ozonation, analogously to culturable E. coil. Despite a higher quantification limit for FCM and qPCR, they appear sufficiently accurate and suitable as surrogate microbial parameters, considering their rapidity (about an half hour with FCM). In the case of strong stress conditions such as zonation, the surrogate microbial parameters, which include viable-but-not-culturable cells, might result more sensible in the evaluation of treatment efficiency. (C) 2014 Elsevier B.V. All rights reserved.