The influence of the geographical location and clone type on the contents of flavonols and organic acids of Sauvignon blanc grapes over the ripening process was investigated. The assay was carried out on three commercial clones of cv. Sauvignon blanc (Clone 242, Clone 107, and Clone 1-Davis) grown in two zones (referred to as low and high zones) in Casablanca Valley, Chile. The low zone is closer to the Pacific Ocean (i.e., 20 km away) than the high zone (which is 37 km away). Clear differences in the contents of total phenols, flavonols and organic acids of the grapes were observed during ripening. All the clones grown in the low zone exhibited a higher titratable acidity than those grown in the high zone. An analysis of the flavonol contents of the grape skins showed differences among clones associated with the geographical zone of cultivation. There was no difference in the tartaric acid concentration among clone types; however, a higher tartaric acid concentration was found in clones grown in the low zone than those grown in the high zone for all clone types. Similar results were found for the malic acid concentration. A discriminant analysis showed that the chemical analysis for the contents of total phenols, flavonols and organic acids influenced the classification based on the clone type. The results showed that grapes of different qualities can be grown in two geographical subunits into the larger area of Casablanca Valley.