This paper proposes a novel multi-scale fluid flow data assimilation approach, which integrates and complements the advantages of a Bayesian sequential assimilation technique, the Weighted Ensemble Kalman filter (WEnKF) [27]. The data assimilation proposed in this work incorporates measurement brought by an efficient multiscale stochastic formulation of the well-known Lucas-Kanade (LK) estimator. This estimator has the great advantage to provide uncertainties associated to the motion measurements at different scales. The proposed assimilation scheme benefits from this multi-scale uncertainty information and enables to enforce a physically plausible dynamical consistency of the estimated motion fields along the image sequence. Experimental evaluations are presented on synthetic and real fluid flow sequences.