Commercial time of flight depth camera such as the Kinect v2 have been shown to perform underwater for 3D scene reconstruction of underwater objects. However, to incorporate the additional noise and incorporating effect of refraction due to the change in the imaging medium, a customized user implementation of the underlying scene reconstruction algorithms with the additional developed filters needs to be developed. This paper presents the details and performance of such a graphical user interface developed for Kinect v2. The GUI is a customized implementation of the Kinect Fusion framework, and incorporates underwater camera calibration, noise filtering, time of flight correction and refraction correction filters developed to adapt Kinect Fusion for 3D scene reconstruction in an underwater environment. Details of the user interface and the effect of various sub-functions and additional correction filters on the performance of Kinect Fusion reconstruction are discussed in detail. © 2017 IEEE.