Chronic Kidney Disease of uncertain etiology (CKDu) is a fatal disease that causes death from kidney failure due to unknown risk factors and has already affected more than 400,000 people in the rural agricultural landscape (dry zone) of Sri Lanka. The major drinking source in Sri Lanka is groundwater and it is suspected that the pollution of groundwater sources due to agricultural means has a major impact on CKDu. The primary objective of this study is to determine whether rainwater can be used as an alternative safe drinking water source in Girandurukotte area, Sri Lanka, which is known to be an area endemic for CKDu. The physical, chemical, and biological analyses were performed to compare the water quality parameters of three water sources (groundwater, surface water, and rainwater) for Girandurukotte area. The most common storage tanks in polyethylene (PE) and ferrocement (FC) were compared to assess the influence of the material of rainwater tank on water quality. The results showed that there is a significant difference in rainwater in terms of water quality compared to groundwater and surface water. Rainwater in FC and PE tanks showed significant differences (p < 0.05) for some parameters however, they were still within accepted potable drinking water standards.