This paper presents an integrated adaptive estimator-controller scheme for a class of systems with only partially measured states. To estimate the non-measured states, a fast adaptive estimator is applied. The estimation is used in the L1 adaptive controller, which adapts to time-varying unknown parameters and time-varying bounded disturbances in the system without restricting their rate of variation. The results demonstrate that the L1 adaptive controller has guaranteed performance bounds for system's both input and output, while using the estimation of the regulated outputs. The approach is used to control the bottom hole pressure of a well drilling system, in which the measurement of the pressure is updated at a low rate. Simulations verify the theoretical findings.