This paper proposes a flexible and reconfigurable water-based frequency-selective absorber (WFSA), comprising a water-filled, 3D printed flexible thermoplastic urethane (TPU) multilayer absorption layer and a bandpass frequency-selective surface (FSS) transmission layer with vertical gaps. The proposed WFSA absorbs 90% of radiation across the 4.21 to 15.93 GHz band. This gives it a relative bandwidth of 116%. Its transmission bandwidth is 44.9%, with insertion loss less than 3 dB. The minimum insertion loss is 0.75 dB at 0.47 GHz. The device is stable up to an incident angle of 60°. It works equally well for both TE and TM polarization. Finally, it achieves a 10 dB reduction in radar cross-section (RCS) in both flat and curved forms. Moreover, the WFSA can be reconfigured by adjusting parameters such as the water temperature, water content, and internal liquid type to modify the absorption and transmission bands. This feature makes it a cost-effective and environmentally friendly solution for achieving electromagnetic stealth-transmission synergy to protect valuable ground targets.