The appropriateness of indicator organisms as surrogates for human pathogens in water quality modeling is dependent on similarities in both presence and transport behavior; however, very little data relating indicator and bacterial pathogen transport behavior in receiving waters is available. In this study observations of presence, partitioning behavior (i.e. association with settleable particles) and removal by upland detention basins were used to assess the suitability of six indicator organisms as surrogates for Salmonella spp. bacteria in an urban watershed. The fecal indicator bacteria (fecal coliforms, E. coli and enterococci) were most closely correlated with Salmonella in terms of presence and partitioning behavior (25–35% associated with settleable particles on average); however, further resolution of the variability associated with Salmonella partitioning is required. Higher removal of particle-associated microbes relative to the total microbial concentration by the detention ponds suggests that sedimentation may be an important removal mechanism. However, large fluctuations in pond performance between storm events and occasional net microbial exports in effluents indicate that these best management practices (BMPs), as currently implemented, will be unlikely to achieve water quality objectives.