OBJECTIVE To better understand and manage the fate and transport of Salmonella in agricultural watersheds, we developed a culture-based, five tube-four dilution most probable number (MPN) method for enumerating dilute densities of Salmonella in environmental waters. RESULTS The MPN method was a combination of a filtration technique for large sample volumes of environmental water, standard selective media for Salmonella and a TaqMan confirmation step. This method has determined the density of Salmonella in 20-l samples of pond inflow and outflow streams as low as 0.1 MPN l(-1) and a low 95% confidence level 0.015 MPN l(-1). Salmonella densities ranged from not detectable to 0.55 MPN l(-1) for pond inflow samples and from not detectable to 3.4 MPN l(-1) for pond outflow samples. Salmonella densities of pond inflow samples were associated with densities of Escherichia coli and faecal enterococci that indicated stream contamination with faeces and with nondetectable pond outflow densities of the faecal indicator bacteria. The MPN methodology was extended to flux determinations by integrating with volumetric measurements of pond inflow (mean flux of 2.5 l s(-1)) and outflow (mean flux of 5.6 l s(-1)). Fluxes of Salmonella ranged from 100 to greater than 10(4) MPN h(-1). CONCLUSIONS This is a culture-based method that can detect small numbers of Salmonella in environmental waters of watersheds containing animal husbandry and wildlife. CONCLUSIONS Applying this method to environmental waters will improve our understanding of the transport and fate of Salmonella in agricultural watersheds, and can be the basis of valuable collections of environmental Salmonella.