The impact of surface reflection upon transmission through and energy distributions within random media has generally been described in terms of the boundary extrapolation lengths zb,zb′ at the input and output end of an open sample, which are the distance beyond the sample surfaces at which the energy density within the sample extrapolates to zero [1, 2, 3, 4]. The importance of reflection at the sample boundaries plays a key role in the scaling of transmission [5, 6]. Here we consider the impact of surface reflection on the propagation of diffusive waves [7, 8] in terms of the modification of the distribution of transmission eigenvalues (DTE) [9, 10, 11, 12, 13, 14, 15, 16]. We review our finding of a transition in the analytical form of the DTE at the point that the sample length equals |zb − zb′|. The highest transmission eigenvalue for stronger asymmetry in boundary reflection is strictly smaller than unity. The average transmission and profiles of energy density inside the sample can still be described in terms of the sample length, L, and the boundary extrapolation lengths on both sides of the sample, zb,zb′. For localized waves, we find the energy density profile within the sample is a segment of the distribution that would be found in a longer sample with length L + zb + zb′. These results suggest new ways of controlling wave interference in both diffusive and localized systems by varying boundary reflectivity.