We investigate the dynamics of bosonic atoms in elongated Josephson junctions. We find that these systems are characterized by an intrinsic coupling between the Josephson mode of macroscopic quantum tunneling and the sound modes. This coupling of Josephson and sound modes gives rise to a damped and stochastic Langevin dynamics for the Josephson degree of freedom. From a microscopic Lagrangian, we deduce and investigate the damping coefficient and the stochastic noise, which includes thermal and quantum fluctuations. Finally, we study the time evolution of relative-phase and population-imbalance fluctuations of the Josephson mode and their oscillating thermalization to equilibrium.
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