In this paper, authors propose a new method of disturbance estimation that can be used for marine and air vehicles. As stability area for nonlinear systems is connected with performance of estimation, indirect measurement is proposed to estimate the error. The base for calculation is vehicle accelerations provided by navigation system. New algorithms were tested in simulation for which authors developed a block diagram of indirect adaptive control system that features independence of estimator from controller. Analysis of results showed that the error of the developed estimator in transient mode is 30-40% less than error of the linear estimator. In steady state mode, gain of the proposed estimator is equal to gain of the linear estimator and output noise is the same. Simulated system was implemented in mini motor boat, and showed good results in experiment. New estimator allowed to increase the accuracy of moving along the paths.