Scour monitoring is crucial for providing early warning of bridge safety and extending the knowledge of scour process. Traditional methods that rely on underwater instruments encounter difficulties in installation and operation in harsh fluvial environment. Time domain reflectometry (TDR)-based scour sensing wire was recently introduced as a promising technique to improve field deployment and durability. This study focused on further improving the concept of TDR sensing wire for better sensor package and performance. An innovative bundled bottom-up sensing cable was proposed to improve sensor durability and avoid the adverse effect of sensor fouling. The sensor durability is enhanced by twisting two sets of steel strands (as two opposing electrodes for the waveguide) around a coaxial cable into a composite sensing cable. The inner coaxial cable is introduced and armored by the sensing steel strands to direct TDR pulse to the bottom end before connecting to the sensing waveguide formed by steel strands for bottom-up sensing. Furthermore, taking advantage of a new data reduction method by using time-lapse differential waveform, robustness of system calibration and scour estimation is further enhanced. Experimental results revealed the optimal design of bundled TDR sensing cable, effectiveness of the bottom-up sensing approach, and better performance of the differential waveform method.