Underwater 3D reconstruction and appearance restoration remain challenging due to the complex optical properties of water, such as wavelength-dependent attenuation and scattering. Existing Neural Radiance Fields (NeRF)-based approaches often suffer from slow rendering and limited practicality, while vanilla 3D Gaussian Splatting (3DGS) lacks an effective mechanism to account for underwater degradation. To address this, we propose WaterClear-GS, a physics-informed reformulation of underwater Gaussian splatting that models degradation as intrinsic Gaussian attributes rather than external medium fields. Furthermore, we adopt a dual-branch optimization strategy that preserves underwater photometric consistency while encouraging a practical separation between restoration-oriented latent clean appearance and degradation. This strategy is enhanced by depth-guided geometry regularization and perception-driven image supervision, together with exposure constraints, spatially adaptive regularization, and physics-informed spectral regularization, which collectively promote spatial coherence and plausible visual appearance. Extensive experiments on standard benchmarks and our collected dataset demonstrate that WaterClear-GS achieves strong performance on both novel view synthesis (NVS) and underwater image restoration (UIR) tasks, while maintaining 160+ FPS real-time rendering. The code will be available at https://sherii888.github.io/WaterClear-GS/.

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