We present a portable, non-invasive, and low-cost three-dimensional tracking method to quantify in situ water-hopping kinematics of mudskippers. By combining dual-camera video recordings with tracking fish path, Gaussian Splatting terrain reconstruction and epipolar geometric analysis, we capture detailed 3D trajectories of mudskippers in their natural tidal-flat habitats. Our proposed method resolves complex hopping motions, including both straight and curved escape paths, and reveals that horizontal distance, hopping height, and speed are strongly influenced by fish size and local terrain features. These results highlight both the biomechanical and ecological significance of water-hopping in mudskippers, demonstrating how a simple, deployable 3D approach can resolve complex amphibious movements in challenging field environments.