The ecology of the most relevant Vibrio species for human health and their relation to water quality and biogeochemistry were studied in two estuaries in Argentinian Patagonia. Vibrio cholerae and Vibrio parahaemolyticus were reported in > 29% of cases at the Río Colorado and Río Negro estuaries. Neither the pandemic serogroups of Vibrio cholerae O1, Vibrio cholerae O139 nor the cholera toxin gene were detected in this study. However, several strains of V. cholerae (not O1 or O139) are able to cause human disease or acquire pathogenic genes by horizontal transfer. Vibrio vulnificus was detected only in three instances in the microplankton fraction of the Río Negro estuary. The higher salinity in the Río Colorado estuary and in marine stations at both estuaries favours an abundance of culturable Vibrio. The extreme peaks for ammonium, heterotrophic bacteria and faecal coliforms in the Río Negro estuary supported a marked impact on sewage discharge. Generally, the more pathogenic strains of Vibrio have a faecal origin. Salinity, pH, ammonium, chlorophyll a, silicate and carbon/nitrogen ratio of suspended organic particulates were the primary factors explaining the distribution of culturable bacteria after distance-based linear models. Several effects of dissolved organic carbon on bacterial distribution are inferred. Global change is expected to increase the trophic state and the salinisation of Patagonian estuaries. Consequently, the distribution and abundance of Vibrio species is projected to increase under future changing baselines. Adaptation strategies should contribute to sustaining good water quality to buffer climate- and anthropogenic- driven impacts.