Oswaldo Cruz Foundation and Secretariat of Health Surveillance, Brazilian Ministry of Health, the National Institutes of Health (grant numbers R01 AI052473, U01 AI088752, R01 TW009504, R25 TW009338, and R01 AI121207) and from the Wellcome Trust (102330/Z/13/Z).Leptospirosis, a zoonosis caused by pathogenic Leptospira, primarily a ects tropical, developing regions, especially communities without adequate sanitation. Outbreaks of leptospirosis have been linked with the presence of pathogenic Leptospira in water. In this study, we measured the physicochemical characteristics (temperature, pH, salinity, turbidity, electrical conductivity, and total dissolved solids (TDS)) of surface waters from an urban slum in Salvador, Brazil, and analyzed their associations with the presence and concentration of pathogenic Leptospira reported previously. We built logistic and linear regression models to determine the strength of association between physicochemical parameters and the presence and concentration of Leptospira. We found that salinity, TDS, pH, and type of water were strongly associated with the presence of Leptospira. In contrast, onlypHwas associated with the concentration of the pathogen in water. The study of physico-chemical markers can contribute to a better understanding of the occurrence of Leptospira in water and to the identification of sources of risk in urban slum environments.