A series of magnetoactive elastomer (MAE) coatings consisting of a silicone matrix and carbonyl iron particles (3–5 μm in diameter) have been synthesized and their hydrophobic properties have been investigated in various magnetic fields of disk-shaped permanent NdFeB magnets. Concentration of magnetic filler in MAEs has been varied in the range of 63–76 mass%. Both isotropic samples and structured samples synthesized in the magnetic field of 80 mT have been obtained. It has been shown that application of a magnetic field induces structuring of the filler on the surface of MAE coatings, resulting in formation of mountain-like microstructures. Microstructure relief on coating surfaces leads to an increase of a water contact angle which could be varied from 110° ± 10° at zero field up to 163° ± 2° at 600 mT. The contact angle at the maximum field increases with iron filler content and with softening of the polymer matrix.