Water resources are scarce in the Northeastern Loess Plateau, and water cellar water (WCW) is a vital water resource available in the vast rural areas of the region. The quality of WCW was assessed by principal component analysis (PCA) and Nemerow’s pollution index (NPI) for different rainfall catchment areas, depths, and storage times. Eleven indicators were measured, including pH, electrical conductivity (EC), F−, Cl−, NO3−, SO42−, Na+, NH4+, Ca2+, Mg2+, and K+. The results show that the tap water quality in the rural areas of the Northeastern Loess Plateau is above the second level and meets the drinking water standard (DWS), which is similar to the tap water quality in the region. The main component score of water quality from tile roof + cement ground (I) is 0.32, and the Nemero index is 0.41; the principal component score of water quality from cement ground (I) is 0.45, and the Nemero index is 0.29; the principal component score of water quality from trampled land (I) is 0.59, and the Nemero index is 0.44; the principal component score of water quality from tile roof + trampled land (II) is 1.87, and the Nemero index is 1.10. The rainwater harvesting catchment area of tile roof + cement ground (I) ensured the highest water quality, followed by cement ground (I), trampled ground (I), and tile roof + trampled ground (II). The water quality of the catchment area for artificially collected rainwater (roof tile surface, cement ground, etc.) was better than that of the original soil (trampled ground). The highest water quality was found at a storage time of 1 year (I), followed by 2.5 years (I), and 2 months (II). A depth of 4 m (I) contributed to the highest water quality, followed by 2 m (II), 3 m (II), and 1 m (II). Water quality improved with the increasing depth of WCW. The rainfall and WCW in the area were weakly alkaline, and the groundwater was contaminated with NO3−. PCA’s water quality assessment results were similar to the NPI method, indicating that both methods can be used in combination for unconventional water quality assessment.