In this study, a novel microfluidic frequency reconfigurable and optically transparent water antenna is designed using three-dimensional (3D) printing technology. The proposed antenna consists of three distinct parts, including a circularly shaped distilled water ground, a sea water-based circular segmented radiator, and a circularly shaped distilled water-based load, all ingeniously constructed from transparent resin material. The presented antenna is excited by a disk-loaded probe. The frequency of the antenna can be easily tuned by filling and emptying/evacuating sea water from the multisegmented radiator. The radiator consists of three segments with different radii, and each segment has a different resonant frequency. When the radiator is filled, the antenna resonates at the frequency of the segment that is filled. When all the radiator segments are filled, the antenna operates at the resonant frequency of 2.4 GHz and possesses an impedance bandwidth of 1.05 GHz (40%) in the range of 2.10–3.15 GHz. By filling different radiator segments, the frequency could be tuned from 2.4 to 2.6 GHz. In addition to the frequency-switching characteristics, the proposed antenna exhibits high simulated radiation efficiency (with a peak performance reaching 95%) and attains a maximum realized gain of 3.8 dBi at 2.9 GHz. The proposed antenna integrates water as its predominant constituent, which is easily available, thereby achieving cost-effectiveness, compactness, and transparency characteristics; it also has the potential to be utilized in future applications, involving transparent and flexible electronics.