In the present paper, molecular dynamics simulations were performed to study the influence of two temperature control strategies on water flow behaviour inside planar nanochannel. In the simulations, the flow was induced by the force acting on each water molecule in the channel. Two temperature control strategies were considered: (a) frozen wall simulations, in which the dynamics of confining wall atoms was not solved and the thermostat was applied to the water, and (b) dynamic wall simulations, in which the dynamics of confining wall atoms was solved, and the thermostat was applied to walls while water was simulated in the microcanonical ensemble. The simulation results show that the considered temperature control strategies has no effect on the shape of the water flow profile, and flow behaviour in the channel is well described by the Navier–Stokes equation solution with added slip velocity. Meanwhile, the slip velocity occurring at the boundaries of the channel is linearly dependent on the magnitude of the flow inducing force in both frozen wall and dynamic wall simulations. However, the slip velocity is considerably greater in simulations when the wall dynamics are solved in contrast to the frozen wall simulations.