The development of cost-effective methods for estimating hydraulic conductivity profiles has been an ongoing effort in the field of engineering practice, which can be used to increase availability to clarify the hydrogeological complexity of fractured rock aquifers for the aid of solving groundwater-related problems. A methodology is presented, which combines electrical well logs, fluid conductivity logs, double packer hydraulic tests, Archie’s law, and the Kozeny-Carman-Bear equation to investigate relations between formation factor and hydraulic conductivity. This method was applied to develop hydraulic conductivity profiles based on the data collected from 88 boreholes in Taiwan's mountainous areas. The investigation results include: (1) Well logging signals were suggested to be categorized by rock types to establish effective relationships with hydraulic conductivity. (2) Removing the mud-bearing section data with two proposed data clustering techniques could effectively enhance the correlation between the formation factor and hydraulic conductivity. (3) The predictive models for estimating hydraulic conductivity have been developed for sandstone, schist, and slate. (4) The prevalence of clay content in most of Taiwan's mountainous rock formations has been found, which implies that careful consideration of clay-related issues in complex geologic formations is essential while applying Archie's law theory.