The survival and multiplication of human pathogenic and antibiotic-resistant bacteria in ecosystems is of increasing concern but has been little explored. Wetlands can be contaminated by water fluxes from rivers and may present environmental conditions leading to bacterial survival and multiplication. To test this hypothesis, we sampled 16 wetlands located along three rivers of the Jura Massif, France. The bacterial contamination of the wetland and river waters was measured monthly over a one-year cycle together with the water physico-chemical characteristics. We assessed the abundance of three pathogenic species: Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa. The concentrations of E. coli producing extended-spectrum beta-lactamase (ESBL E. coli) or belonging to the phylogenetic group B2 (E. coli B2-more pathogenic) were also measured. We found that rivers carried total E. coli, ESBL E. coli, and K. pneumoniae to wetlands. ESBL E. coli poorly survived in wetlands, whereas total E. coli and K. pneumoniae possibly met favourable physico-chemical conditions for survival and multiplication in these habitats. K. pneumoniae peaked in summer in warm and shallow wetlands. Total E. coli and E. coli B2 potentially reached wetlands through sources other than rivers (hillslope groundwater or leaching from contaminated fields).