Dynamic 3D Gaussian Splatting (3DGS) provides an efficient framework for dynamic scene reconstruction. Most existing approaches model scene dynamics with deterministic deformation fields, assuming each Gaussian follows a distinct geometric trajectory over time. This assumption breaks down underwater, where light scattering, refraction, marine snow and low visibility create substantial physical ambiguity in captured images. We present PUGS, a physics-guided uncertainty model for underwater dynamic 3DGS. PUGS learns inherent uncertainty induced by underwater image formation and leverages it as a physical signal for dynamic scene modeling. Rather than estimating a single deterministic displacement, it parameterizes each Gaussian's motion as a probability distribution with expected deformation and physical uncertainty. We adopt stochastic deformation optimization to sample Gaussian trajectories via local reparameterization, exploring multiple physically plausible solutions during training. We further propose uncertainty stochastic annealing and a dual-path self-consistency distillation objective, converting stochastic exploration to deterministic reconstruction while preserving temporal coherence. Extensive experiments on underwater dynamic datasets and physics-aware benchmarks demonstrate superior rendering quality, temporal consistency and reconstruction robustness. Our method achieves 1.16 dB PSNR gain over the strongest baseline on UVEB and 3.99 dB on DRUVA.

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