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). 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 multiscale 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.