From a sequence of tracer satellite images, several methods (e.g. optical flow) exist to successfully estimate the main advecting current. Yet, this estimate is limited in resolution. To go beyond, we propose a new parametric estimation method to estimate second-order statistics of the residual small-scale velocity. We first express stochastic transport in a discrete setting to apply standard MLE techniques. Then we propose an efficient method to solve the MLE optimization problem through a fast log-likelihood gradient evaluation algorithm.