This study aims to apply fecal sterols as a chemical indicator to track feces contamination sources in the canals in Bangkok. The sewage and canal sediments were examined during the dry season. Fecal sterols in the canals were evaluated over a one-year period (2011–2012) for the selected sterol compounds. Several factors including season, canal water levels, rainfall data, and sewage were correlated to fecal contamination. The highest concentrations of cholesterol (CHR) (8.321 μg/L), coprostanol (CPN) (6.490 μg/L), and cholestanol (CHN) (1.205 μg/L) in discharged sewage were found from the community near Samata Amonmak bridge. Maximum yearly average fecal sterol contents observed in the canal sediments were: CHR (12.478 μg/g), CHN (10.782 μg/g), and CPN (16.903 μg/g). They indicate high fecal pollution both from human and warm-blooded animals such as dogs' and birds' feces. The water level in canals and rainfall intensity influenced changes in fecal sterol contents. Suspended solids in the canal water during summer were correlated with the sterol contents. Overall, it can be summarized that the studied canals were highly polluted with organic matter and enteric bacteria. Human feces from the discharged sewage were the major source of fecal contamination in Ong-Ang and Bang-Lumphu canals.