Swine manure has a high load of pathogens, which can pose a risk to human and environmental health. In Brazil, studies evaluating the survival of pathogens in soil are scarce. Therefore, this study aimed to evaluate the survival, percolation, and leaching of enterobacteria in clayey soil after fertilization with swine manure. For this purpose, soil columns were fertilized with manure spiked with enterobacteria. The microorganisms’ behavior was monitored in terms of survival, percolation, and leaching with and without rain. Soil samples were collected, and Escherichia coli and Salmonella enterica serovar Senftemberg were quantified. The results indicated that E. coli survived for a longer period (43 days) than S. senftemberg (14 days). E. coli percolated quickly through the soil, leaching 60 cm in less than 5 min during rainy events and remaining viable for up to 24 h after the rain. The results show the importance of treating manure effectively before being added to the soil. An efficient treatment could be anaerobic digestion, followed by a pond system. Considering the characteristics of swine-producing regions, the load of effluents applied to the soil may percolate, leach, or run off and consequently contaminate water bodies with pathogens.