The purpose of this study was to investigate the removal of pathogenic and indicator micro-organisms in integrated constructed wetland (ICW) systems treating agricultural wastewater. Nine ICW's treating piggery (3) or dairy (6) wastewaters were sampled and indicator micro-organisms were enumerated in the influent as well as the effluent from the first, mid- and final cells. The presence/absence of Salmonella was also determined and any Salmonella isolates recovered were characterized. Mean counts of coliform, E. coli and Enterococcus across all nine ICW systems were lower in the final effluent than in the effluent from cell 1 (P < 0.001). An antibiotic susceptible isolate of Salmonella Dublin, a bovine-adapted serotype, was isolated from the influent to one dairy ICW but was not detected in any of the ICW cells. An antibiotic sensitive Salmonella Dublin isolate with the same molecular fingerprint was also recovered from the cell 1 effluent of another dairy ICW but was absent from the influent and the mid-cell and final effluents. Salmonella Typhimurium DT104b was detected in the liquid fraction of anaerobically digested pig manure as well as in the effluent from the first cell and mid-cell of an ICW treating this material, but was absent in the final effluent. Molecular fingerprinting by pulsed field gel electrophoresis demonstrated that the recovered isolates were highly related. However, they had different antimicrobial resistance profiles, with some highly resistant isolates recovered. In conclusion, counts of indicator micro-organisms were reduced significantly within ICW, with E. coli and Enterococcus non-detectable in the final effluent. Moreover, Salmonella, when present in the influent, appears to have been removed.