We analyze long range wave propagation in three-dimensional random waveguides. The waves are trapped by top and bottom boundaries, but the medium is unbounded in the two remaining directions. We consider scalar waves, and motivated by applications in underwater acoustics, we take a pressure release boundary condition at the top surface and a rigid bottom boundary. The wave speed in the waveguide is known and smooth, but the top boundary has small random fluctuations that cause significant cumulative scattering of the waves over long distances of propagation. To quantify the scattering effects, we study the evolution of the random amplitudes of the waveguide modes. We obtain that in the long range limit they satisfy a system of paraxial equations driven by a Brownian field. We use this system to estimate three important mode-dependent scales: the scattering mean free path, the cross-range decoherence length and the decoherence frequency. Understanding these scales is important in imaging and communication problems, because they encode the cumulative scattering effects in the wave field measured by remote sensors. As an application of the theory, we analyze time reversal and coherent interferometric imaging in strong cumulative scattering regimes.