Despite the fact that a system created in relativistic heavy ion collisions is an isolated quantum system, which cannot increase its entropy in the course of unitary quantum evolution, hydrodynamical analysis of experimental data seems to indicate that the matter formed in the collisions is thermalized very quickly. Based on common consideration of hydrodynamics as an effective theory in the domain of slow- and long-length modes, we discuss the physical mechanisms responsible for the decoherence and emergence of the hydrodynamic behavior in such collisions, and demonstrate how such physical mechanisms work in the case of the scalar field model. We obtain the evolution equation for the Wigner function of a long-wavelength subsystem that describes its decoherence, isotropization, and approach to thermal equilibrium induced by interaction with short-wavelength modes. Our analysis supports the idea that decoherence, quantum-to-classical transition and thermalization in isolated quantum systems are attributed to the experimental context, and are related to a particular procedure of decomposition of the whole quantum system into relevant and irrelevant from an observational viewpoint subsystems.