The measurement of the near-bottom flow characteristics is crucial to correctly understand coastal processes. To overcome some of the limits of present state-of-the-art measuring instruments, we propose a novel approach to measure bottom shear stress under currents and waves based on the exploitation of magneto-rheological fluids, named ferrofluids. In particular, the deformation of a magnetically controlled ferrofluid drop O(0.01 ml) is transformed by a conditioning circuit into an output voltage which is proportional to the bottom shear stress. Calibration curves are presented for both steady-current and regular wave conditions, over fixed and weakly mobile beds, showing that the behaviour of the proposed measuring system can be assumed linear. In the range of the investigated parameters, it is shown that the working range is comprised between 0.08 N m-2 and an upper limit which is a function of the controlling magnetic field and the flow type.