Aims: To compare decay profiles of ruminant-and cattle-associated molecular markers for faecal contamination and Escherichia coli, facilitating their correct application in water quality studies. Methods and Results: We generated decay profiles for cultivable E. coli, a general Bacteroidales genetic marker (GenBac3), ruminant markers (CF128, Rum2Bac) and cattle markers (CowM2, CowM3) using faeces-seeded mesocosms, and selected best fitting models for each decay profile. Global model fitting tested for differences between decay profiles. After normalizing for initial concentration, decay curves differed significantly between E. coli and all genetic markers except CowM3. Decay curves for CF128 differed from GenBac3 and Rum2Bac, but Rum2Bac and GenBac3 decay profiles did not differ. Despite similar survival profiles for some markers, highly varied initial concentrations affected time to nondetection. Conclusions: Decay curves and time until nondetection differed among markers from the same host. However, the Rum2Bac and GenBac3 markers had similar decay profiles and could potentially be investigated further for source allocation using the ratio method. Significance and Impact of the Study: As the use of genetic markers for microbial source tracking becomes increasingly common, caution is necessary. Both the shape of decay curves and time to nondetect may differ depending on the marker selected, resulting in possible misinterpretation of results and precluding application of a 'ratio method' of source allocation.