Swine can harbor Salmonella in their gastrointestinal tracts. It has been estimated that up to 48% of the U.S. swine herd may carry Salmonella. Housing sows in farrowing stalls has become controversial due to animal welfare-based criticisms. An alternative production system is to keep sows outdoors on pasture with access to individual farrowing huts. This study was designed to determine the effects of two production systems on indicator bacteria and Salmonella of sows housed indoors in farrowing stalls (n = 52) compared to sows housed outdoors (n = 52) in English style huts. Each farrowing radial contained one wallow, from which mud (n = 290) and water (n = 290) samples were collected weekly. All samples were analyzed for generic E. coli, coliforms and Salmonella. No differences (p > 0.05) were detected in Salmonella, generic E. coli and coliform populations between indoor farrowing stalls and outdoor farrowing huts. However, all 8 outdoor wallows contained Salmonella spp. at some point during the study (n = 49 Salmonella isolates). Salmonella genotypes persisted within some wallows for >5 months, and genetically indistinguishable Salmonella isolates were found in multiple wallows. Salmonella isolated from outdoor sow feces were genetically indistinguishable by PFGE from Salmonella isolated from wallows (n = 33) throughout the study, indicating that pathogenic bacteria were cycling between swine and their environment. In conclusion, the role of wallows in disseminating Salmonella within an outdoor swine herd appears to be significant.