Leptospirosis is a zoonosis of global distribution that affects tropical and temperate areas. Under suitable conditions, Leptospira can survive in water and soil and contribute to human and animal infections. The objective of this study was to describe the presence of pathogenic Leptospira in peri-domestic water samples from rural households in southern Chile. Water samples, including puddles, containers, animal troughs, rivers, canals, and drinking water were collected from 236 households and tested for Leptospira using a PCR assay targeting the lipL32 gene. Evidence of Leptospira presence was detected in all sample types; overall, 13.5% (77/570) samples tested positive. A total of 10/22 (45.5%) open containers, 12/83 (14.5%) animal drinking sources, 9/47 (19.1%) human drinking sources, and 36/306 (19.3%) puddles tested positive. Lower income (OR = 4.35, p = 0.003), increased temperature (OR = 1.23, p < 0.001), and presence of dogs (OR = 15.9, p = 0.022) were positively associated with positive puddles. Increased number of rodent signs was associated with positive puddles in the household (OR = 3.22); however, only in the lower income households. There was no association between PCR positive rodents and puddles at the household level. Results revealed the ubiquity of Leptospira in the household environment and highlight the need to develop formal approaches for systematic monitoring.