The hydrodynamics of a flagellated micro-organism is investigated when swimming close to a planar free-slip surface by means of numerical solutions of the Stokes equations obtained via a boundary element method. Depending on the initial conditions, the swimmer can either escape from the free-slip surface or collide with the boundary. Interestingly, the micro-organism does not exhibit a stable orbit. Independently of escape or attraction to the interface, close to a free-slip surface, the swimmer follows a counter-clockwise trajectory, in agreement with experimental findings (Di Leonardo et al., Phys. Rev. Lett., vol. 106 (3), 2011, 038101). The hydrodynamics is indeed modified by the free surface. In fact, when the same swimmer moves close to a no-slip wall, a set of initial conditions exists which result in stable orbits. Moreover, when moving close to a free-slip or a no-slip boundary, the swimmer assumes a different orientation with respect to its trajectory. Taken together, these results contribute to shed light on the hydrodynamical behaviour of micro-organisms close to liquid–air interfaces which are relevant for the formation of interfacial biofilms of aerobic bacteria.