Water quality of some traditionally protected water bodies (Obi Pond, Abua Lake, Usede Lake, Atochi Stream and River Ethiope (Source) and unprotected water bodies (Ame-Oghene Pond, Oguta Lake, Omoku Pond, Tenmako Lake and Ikarama Lake) that commonly serve for domestic and drinking purposes in the Niger Delta area of Nigeria have been studied. The purpose of this study was to compare the water quality of traditionally protected water bodies with unprotected water bodies. Water samples collected from the identified sources was experimentally determined using various laboratory methods. Study was carried out within the early rainy season (May to June) of 2013. The water quality of each of the water bodies was assessed using Malaysian water quality index (WQI) and results show that, the water quality of the traditionally protected Obi Pond, Abua Lake, Usede Lake, Atochi Stream and River Ethiope (Source) are 76.73, 76.13, 76.65, 77.04 and 81.25, respectively and belong to class II. Empirically, the water quality can be described as good. The WQI of unprotected Ame-Oghene Pond, Oguta Lake, Tenmako Lake, Ikarama Lake and Omoku Pond are 65.64, 67.46, 37.60, 43.38 and 65.81, respectively. Water quality of Ame-Oghene Pond, Oguta Lake and Omoku Pond belong to Class III and can empirically be described as medium or average while the water quality of Tenmako Lake and Ikarama Lake belong to Class IV and can be empirically described as fair. Using the two-tailed T-test formula to evaluate the null hypotheses, results showed that the calculated t-value was 123.98 while that obtained from the t-Tables at 95% confidence level was 2.31 and hence the null hypotheses was rejected. This means that there is significant difference between the water quality of traditionally protected water bodies and the unprotected water bodies. We are of the view that by incorporating natural sacred sites into the existing protected area networks will improve natural resource conservation.