Currently there are different approaches to filter algorithms based on the Kalman filter. One of the most used filter algorithms is the Ensemble Kalman Filter (EnKF). It uses a Monte Carlo approach to the filtering problem. Another approach is given by the Singular Evolutive Extended Kalman (SEEK) and Singular Evolutive Interpolated Kalman (SEIK) filters. These filters operate explicitly on a low-dimensional error space which is represented by an ensemble of model states. The EnKF and the SEIK filter have been implemented within a parallel data assimilation framework in the Finite Element Ocean Model FEOM. In order to compare the filter performances of the algorithms, several data assimilation experiments are performed. The filter algorithms have been applied with a model configuration of FEOM for the North Atlantic to assimilate the sea surface height in twin experiments. The dependence of the filter estimates on the represented error subspace is discussed. In the experiments the SEIK algorithm provides better estimates than the EnKF. Furthermore, the SEIK filter is much cheaper in terms of computing time.