The snake robot can be used to monitor and maintain underwater structures and environments. The motion of a snake robot is achieved by lateral undulation which is called the gait pattern of the snake robot. The parameters of a gait pattern need to be adjusted for compensating environmental uncertainties. In this work, 3D motion dynamics of a snake robot for the underwater environment is proposed with vertical motion using the buoyancy variation technique and horizontal motion using lateral undulation. “The neutral buoyant snake robot motion in hypothetical plane and added mass effect is negligible”, these previous assumptions are removed in this work. Two different control algorithms are designed for horizontal and vertical motions. The existing super twisting sliding mode control (STSMC) is used for the horizontal serpentine motion of the snake robot. The control law is designed on a reduced-ordered dynamic system based on virtual holonomic constraints. The vertical motion is achieved by controlling the mass variation using a pump. The water pumps are controlled using the event-based controller or Proportional Derivative (PD) controller. The results of the proposed control technique are verified with various external environmental disturbances and uncertainties to check the robustness of the control approach for various path following cases. Moreover, the results of STSMC scheme are compared with SMC scheme to check the effectiveness of STSMC. The practical implementation of the work is also performed using Simscape Multibody environment where the designed control algorithm is deployed on the virtual snake robot.