A depletion layer played by aqueous organic liquids flowing in a platform of microfluidic integrated metamaterials is experimentally used to actively modulate terahertz (THz) waves. The polar configuration of water molecules in a depletion layer gives rise to a damping of THz waves. The parallel coupling of the damping effect induced by a depletion layer with the resonant response by metamaterials leads to an excellent modulation depth approaching 90% in intensity and a great difference over 210° in phase shift. Also, a tunability of slow-light effect is displayed. Joint time-frequency analysis performed by the continuous wavelet transforms reveals the consumed energy with varying water content, indicating a smaller moment of inertia related to a shortened relaxation time of the depletion layer. This work, as part of THz aqueous photonics, diametrically highlights the availability of water in THz devices, paving an alternative way of studying THz wave–liquid interactions and developing active THz photonics.