Recent studies have investigated the identification of governing equations of geophysical systems from data. Here, we investigate such identification issues for ocean surface dynamcis from ocean remote sensing data. From a methodological point of view, we address the learning of data-driven dynamical models when only provided with a noisy training dataset. We propose a novel architecture that relies on data assimilation schemes to learn the underlying dynamical model through the minimization of a reconstruction cost. We demonstrate the relevance of the proposed architecture with respect to the state-of-the-art approaches in the identification and forecasting of synthetic and real case-studies.