MR velocimetry of liquid flow in opaque porous filters may play an important role in better understanding the mechanisms of deep bed filtration. With this knowledge, the efficiency of separating the suspended solid particles from the vertically flowing liquid can be improved, and thus a wide range of industrial applications such as wastewater treatment and desalination can be optimized. However, MR velocimetry is challenging for such studies due to the low velocities, the severe B₀ inhomogeneity in porous structures, and the demand for high spatial resolution and an appropriate total measurement time during which the particle deposition will change velocities only marginally. In this work, a modified RARE-based MR velocimetry method is proposed to address these issues for velocity mapping on a deep bed filtration cell. A dedicated RF coil with a high filling factor is constructed considering the limited space available for the vertical cell in a horizontal MR magnet. Several means are applied to optimize the phase contrast RARE MRI pulse sequence for accurately measuring the phase contrast in a long echo train, even in the case of a low B₁ homogeneity. Two means are of particular importance. One uses data acquired with zero flow to correct the phase contrast offsets from gradient imperfections, and the other combines the phase contrast from signals of both odd and even echoes. Results obtained on a 7T preclinical MR scanner indicate that the low velocities in the heterogeneous system can be correctly quantified with high spatial resolution and an adequate total measurement time, enabling future studies on flow during the filtration process.