In this study, we consider the parameter estimation problem of a ship dynamics model. We consider two possible approaches to identify a continuous-time model from real data obtained on a river, where the presence of disturbances is a key issue. The first approach is identification through optimisation using a disturbance observer. The second approach corresponds to the refined instrumental variable method for linear parameter varying systems. In addition, we evaluate the accuracy of the parameter estimation through a sensitivity analysis. The obtained results show an improvement in the parameter estimates compared to identification procedures that do not consider the river disturbances. The application of the model for track-keeping control is also illustrated.