Limited access to safe water enhances poverty, hunger and diseases. This study evaluated the drinking water quality stored in home-based systems, located in rural areas of Tunisia. Water management was also documented as an improvement of good practice as most of the water contamination could be related to behavioral patterns. Thirty-nine water samples from five different sources (rainwater, truck cistern, mix, etc.) were screened for enteric parasitic contamination with the modified Bailenger technique. This technique allowed the detection of three protozoa: Giardia spp.; Entamoeba histolytica/dispar/moshkovskii; Entamoeba coli and one helminth specie: Ascaris spp. The overall prevalence of these intestinal parasites was approximately 97% with a relatively high frequency of protozoa over helminths and more specifically E. histolytica/dispar/moshkovskii. This incidence could be correlated to the lack of hygiene practices, sanitation and education. This situation requires the need for frequent monitoring of the water quality and management in these areas.