In this study, modelling and control of a two-link robot manipulator whose first link is rigid and the second one is flexible is considered for both land and underwater conditions. Governing equations of the systems are derived from Hamilton's Principle and differential eigenvalue problem. A computer program is developed to solve non-linear ordinary differential equations defining the system dynamics by using Runge-Kutta algorithm. The response of the system is evaluated and compared by applying classical control methods; proportional control and proportional + derivative (PD) control and an intelligent technique; integral augmented fuzzy control method. Modelling of drag torques applied to the manipulators moving horizontally under the water is presented. The study confirmed the success of the proposed integral augmented fuzzy control laws as well as classical control methods to drive flexible robots in a wide range of working envelope without overshoot compared to the classical controls.