The objective of this study is to determine and compare the heavy metal (Zn, Cu, Cd, Pb) and bacterial (E. coli, coliform and Salmonella spp.) contamination between swine farms utilizing biogas and non-biogas systems in the central part of Thailand. Results showed that average levels of E. coli, coliform, BOD, COD, Zn, Cu and Pb in sludge from the post-biogas pond were higher than the standard limits. Moreover, the levels of E. coli, coliform, Cd and Pb were also higher than the standard limits for dry manure. The levels of E. coli, coliform and BOD on biogas farms were lower than on non-biogas farms. Following isolation of Salmonella spp., it was found that Salmonella serovars Rissen was the most abundant at 18.46% (12/65), followed by Anatum 12.31% (8/65), and Kedougou 9.23% (6/65). The pathogenic strains of Salmonella serovars Paratyphi B var. java and Typhimurium were present in equal amounts at 4.62% (3/65) in samples from all swine farms. This study revealed that significant reduction in E. coli and coliform levels in sludge from covered lagoon biogas systems on swine farms. The presence of Salmonella as well as Cd and Pb, in significant amount in dry manure, suggests that there is a high probability of environmental contamination if it is used for agricultural purposes. Thus, careful waste and manure disposal from swine farms and the regular monitoring of wastewater is strongly recommended to ensure the safety of humans, other animals and the environment.