Enterococci are found in high abundance in the gastrointestinal tracts of many animals, including humans. Their presence in environmental waters can be an indicator of human or animal faecal pollution, and in the event of high rainfall their numbers are known to spike significantly. The rapid spread of resistance and virulence seen in clinical isolates raises concerns about the rate at which such virulence determinants are spread to commensals outside of hospital environments. The purpose of this study was to report on the distribution and survival of enterococci populations and the prevalence of virulence determinants among dominant clonal groups after an extreme flood event. Water samples were collected from 23 sites; four, six and eight weeks after flood waters subsided. In all, 482 enterococci were typed using a high resolution biochemical fingerprinting method and grouped into common or single biochemical phenotypes (C-BPT and S-BPT, respectively). Twenty-three C-BPTs (72.6%) were found, and clonal representatives were further assessed for their virulence. Virulence determinants screened included 7 virulence genes (VGs), biofilm formation and 14 antibiotics. Clones were also sequenced for species identification. Results indicated most round 1 and 2 sites were above acceptable levels, by round 3 all but one site were below national guidelines. Although there was a significant (P<0.05) decrease in the enterococci between round 2 and 3, 11 C-BPT (55.5%) persisted across the round 3 samples and all but one of these clones were multi-drug resistant and harboured one or more VG. Moreover, one of these clonal groups was found to persist across all samples; harbouring 4 VGs, strong biofilm activity at 25°C and multi-drug resistant. The prevalence and persistence of clonal groups across multiple sites and sampling rounds suggests naturalised populations. Although only speculative, the high presence of virulence determinants may be attributed to the effluent entering the river.