This paper describes the modeling of a custom-made underwater glider capable of flexible maneuvers in constrained areas and proposes a control system. Due to the lack of external actuators, underwater gliders can be greatly influenced by environmental disturbance. In addition, the nonlinearity of the system affects the motions during the transition between each flight segment. Here, a data-driven parameter estimation experimental methodology is proposed to identify the nonlinear dynamics model for our underwater glider using an underwater motion capture system. Then, a nonlinear system controller is designed based on Lyapunov function to overcome environmental disturbance, potential modeling errors, and nonlinearity during flight state transitions. The capability of lowering the impact of environmental disturbance is validated in simulations. A hybrid control system applying PID controller to maintain steady state flights and the proposed controller to switch between states is also demonstrated by performing complex maneuvers in simulation. The proposed control system can be applied to gliders for reliable navigation in dynamic water areas such as fjords where the sea conditions may vary from calm to rough seasonally.