This paper discusses two methods for the rapid assessment of microorganisms in public recreational waters. Two different approaches have been selected: the first method was a fluorimetric measure of the ß-D- glucuronidase activity based on the hydrolysis of the substrate 4 methylumbelliferyl- ß-D-glucuronide; and, the second approach was a molecular test based on real-time Reverse Transcription - Polymerase Chain Reaction (quantitative RT-PCR) for specific quantification of E. coli 16S rRNA molecules. Special effort was made to standardize and automate the quantitative RT-PCR analysis, especially for the RNA extraction and purification steps. The objective of this study was to evaluate the capacity of both methods used for the rapid assessment of bathing water samples. A total of 549 samples and 252 samples collected from two different coastal sites (French Atlantic coast) and freshwater were respectively analyzed by the fluorimetric and RT-PCR assays. Results show that both methods are rapid: 1 hour for 6 samples analyzed by one fluorescence spectrophotometer; or, 3 hours for the simultaneous analysis of up to 15 samples by using a KingFisher mL (Thermo Fisher) robotic processor and real-time PCR apparatus (R.A.P.I.D. LT, Idaho Technology Inc.). With regard to the microbiological criteria of the current regulation, the results obtained with the fluorimetric and RT-PCR analysis compared with the standard method (ISO 9308-3) are congruent in more than 81% of analyzed samples. Because these methods provide a faster assessment of water quality, they have the potential to significantly reduce health risk resulting from exposure to recreational waters and also reduce errors in beach closings. The potential ability of these alternative methods to be more protective than the reference method is also discussed. Includes 17 references, tables, figures.