This paper deals with the problem of marine vessels trajectory tracking control in presence of environmental disturbances. In order to achieve this objective, a previously published methodology for controllers design was improved. A new model error estimation based scheme is proposed to reduce the effect of the perturbations in the tracking error. The approach is effective and low complexity thanks to uncertainty estimation based on numerical method theory. This modification ensures the tracking error convergence to zero, even in presence of polynomial uncertainties (demonstration available). Different tests are presents and a performance comparison with the previous controller is shown to highlight improvements of up to 29%. The control methodology is developed in discrete time, however, is validated by numerical simulations using a continuous time model. •The trajectory tracking control in marine vessel under uncertainties is addressed.•The controller design for trajectory tracking is based on linear algebra.•The approach is applied in a nonlinear system with additive uncertainty.•Zero convergence of tracking error under polynomial uncertainties is demonstrated.•Simulations under modeling errors and disturbance in control actions are performed.