This paper presents an improved borehole prospecting methodology based on a combination of techniques in the hydrogeological characterization of fractured rock aquifers. The approach is demonstrated by on-site tests carried out in the Hoshe Experimental Forest site and the Tailuge National Park, Taiwan. Borehole televiewer logs are used to obtain fracture location and distribution along boreholes. The heat-pulse flow meter log is used to measure vertical velocity flow profiles which can be analyzed to estimate fracture transmissivity and to indicate hydraulic connectivity between fractures. Double-packer hydraulic tests are performed to determine the rock mass transmissivity. The computer program FLASH is used to analyze the data from the flowmeter logs. The FLASH program is confirmed as a useful tool which quantitatively predicts the fracture transmissivity in comparison to the hydraulic properties obtained from packer tests. The location of conductive fractures and their transmissivity is identified, after which the preferential flow paths through the fracture network are precisely delineated from a cross-borehole test. The results provide robust confirmation of the use of combined flowmeter and packer methods in the characterization of fractured-rock aquifers, particularly in reference to the investigation of groundwater resource and contaminant transport dynamics.