This paper presents a novel method for measuring three-dimensional (3D) water surface dynamics in a partially filled pipe. The study on investigation of the 3D free surface dynamics in partially filled pipes is very limited. The method involves tinting the water white with titanium dioxide so that the water surface appears like a solid surface to image-based measuring systems. This method uses a high-resolution projector to project a stochastic pattern of light onto the water surface and uses two high-resolution cameras to capture the pattern on the deformed water surface. The 3D instantaneous water surface fluctuation can be computed from the images captured by the two cameras using a standard Digital Image Correlation algorithm. It is demonstrated that the surface dynamics parameters of turbulent flow in partially filled pipes, including surface fluctuations and surface velocity, can be measured using the projector, high-resolution cameras and DIC algorithm.