The study aimed to investigate the fecal contamination in shallow (depth <50 m) drinking water tube-wells (TWs) and household storage containers in the arsenic-affected area of rural Bihar. In this study, 365 TWs surveyed for As contamination, 164 TWs, and 68 storage containers for the presence/absence of fecal contamination. The results reveal that 32% (n = 111) of surveyed TWs (n =365) exceeded WHO guideline value for As of 10 µg L−1 and 11% (n = 40) of 50 µg L−1. Within 164 TWs and 68 storage containers, 25% (n = 40) and 43% (n = 29) respectively showed presence of fecal contamination. Arsenic contamination did not show significant relation to TWs depth, but deeper (18–50 m) TWs confirm the presence of fecal contamination. Results also depict that fecal contamination both in source and storage container influenced by socio-economic, sanitation practices, the presence of latrine, livestock close to source or containers.