Spatial-temporal variations of active sonar echo intensity can provide effective motion information for characterizing intruding small targets and play a key role in follow-up tracking, behavioral analysis, and recognition, etc. Inspired by the idea of optical flow, which can be used to calculate subtle spatial-temporal variations of each pixel in image sequences, a different motion acoustic flow field (MAFF) is proposed for estimating the motion of underwater small targets in successive active sonar echographs from harbor environments. This is because directly applying current calculation framework for optical flow presents two challenges in this case. The first challenge is that the echo intensity fluctuation breaks its potential assumption of brightness consistency in the pre-processing stage. The second challenge is that the small size of the blob targets could be smoothed out as outliers by its median filter-based post-processing. Hence starting from the classical optical flow equation, MAFF introduces a novel spatial-temporal connected component pre-processing and a novel blob shape segmentation refinement post-processing. Experiments on a set of real-world harbor datasets demonstrate the efficacy of our MAFF calculation framework.