Magnetic nanogels (MNG) -soft colloids made of polymer matrix with embedded in it magnetic nanoparticles (MNPs)are promising magneto-controllable drug carriers. In order to develop this potential, one needs to clearly understand the relationship between nanogel magnetic properties and its behaviour in a hydrodynamic flow. Considering the size of the MNG and typical time and velocity scales involved in their nanofluidics, experimental characterisation of the system is challenging. In this work, we perform molecular dynamics (MD) simulations combined with the Lattice-Boltzmann (LB) scheme aiming at describing the impact of the shear rate ( γ) on the shape, magnetic structure and motion of an MNG. We find that in a shear flow the centre of mass of a MNG tends to be in the centre of a channel and to move preserving the distance to both walls. The MNG monomers along with translation are involved in two more types of motion, they rotate around the centre of mass and oscillate with respect to the latter. It results in synchronised tumbling and wobbling of the whole MNG accompanied by its volume oscillates. The fact the a MNG is a highly compressible and permeable for the carrier liquid object makes its behaviour different from that predicted by classical Taylor-type models. We show that the frequency of volume oscillations and rotations are identical and are growing function of the shear rate. We find that the stronger magnetic interactions in the MNG are, the higher is the frequency of this complex oscillatory motion, and the lower is its amplitude. Finally, we show that the oscillations of the volume lead to the periodic changes in MNG magnetic energy.