Water bodies might be sporadically contaminated by high faecal loads. To protect public health whilst bathing, the revised Bathing Water European Directive (2006/7/EC) requires to establish bathing water profiles to identify the source(s) of a faecal pollution upstream a targeted water body. Bacterial markers have been developed to trace for human, porcine or bovine pollution. The aim of this study was to examine the persistence of proposed human markers in seawater and freshwater microcosms. Human wastewater from a treatment plant was mixed with either seawater or freshwater (dilution 1/20) and microcosms were placed under constant mixing at 18°C in the dark during two months. The concentrations of each marker were followed weekly by specific quantitative PCR or culture. The general Bacteroidales marker (AllBac) was quantified until day 6 and day 20 in seawater and freshwater respectively. The human-specific Bacteroidales marker HF183 was quantified until day 6 in both types of water. A phylotype close to Bifidobacterium adolescentis was detected until day 13 in seawater and day 20 in freshwater. F-specific bacteriophages genotype II were detected for two days in seawater but survived for 13 days in freshwater. Culturable enteroccoci and E. coli were enumerated to less than 200 CFU/ 100 mL on day 13 and thereafter in both types of water which are limits for good quality water in Europe. Therefore all the human-associated markers may be detected in water classified as non satisfactory in terms of microbial quality for at least 6 days.