The use of porous micro-and nanostructured materials within microfluidic devices results in unique fluid transport characteristics. In this paper, we investigate the microfluidic behavior of hybrid alumina nanotube-based pathways within the hydrophobic carbon nanotube (CNT) barriers. These hybrid systems provide unique benefits for potential liquid transport control in porous structures with real-time sensing of fluids. In particular, we examine how the alignment of the alumina nanostructures with high internal porosity enables increased capillary action and sensitivity of detection. Based on the Lucas and Washburn model (LW) and the modified LW models, the microfluidic behavior of these systems is detailed. The time exponent prediction from the models for capillary transport in porous media is determined to be ≤0.5. The experimental results demonstrate that the average capillary rise in the nanostructured media driven by a capillary force follows t0.7. The hydrophilic/electrically insulating and hydrophobic/electrically conductive patterned structures of the device are used for electronic measurements within the microfluidic channels. The device structure enables the detection of fluid samples of very low analyte concentrations (1 μM) that can be achieved due to the very high surface area of the hybrid structure combined with the electrical conductivity of the CNT support structure.