Buenos Aires city and surroundings is one of the largest 20 urban agglomerations in the World. It is crossed by the Reconquista River, a lowland course directly associated with millions of people. The present study deals with an assessment of microbial populations from surface wateralong the main course and its tributaries over a period of three years. These watercourses showed high levels of total bacteria and coliform densities. The following seventeen bacterial species were identified: Acinetobacter baumannii, Aeromonas hydrophila, Burkholderia cepacia, Chromobacterium violaceum, Citrobacter freundii, Cronobacter sakazakii, Erwinia carotovora, Escherichia coli, Photobacterium damselae, Providencia rettgeri, Pseudomonas aeruginosa, P. luteola, P. oryzihabitans, Serratia fonticola, S. marcescens, S. odorifera and Vibrio fluvialis These include pathogens related with nosocomial infections. Their implications for human health as well as for the aquatic ecosystems are analyzed.