A theoretical approach is applied to describe the diffraction of water waves by a structure in a channel of arbitrary configuration. The solution was achieved by applying the three-dimensional (3D) boundary element method and is valid for a structure of arbitrary shape. The derived model was applied to analyze the effect of the structure geometry and the configuration of the channel on diffracted wave field and on generalized wave-load components. The results show that the wave field in the channel and wave loads on a structure strongly depend on wavelength and the geometry of the structure. The far-field wave amplitudes and wave load components oscillate with increasing wave number, and for selected wave frequencies, the incoming waves are fully transmitted and forces on the structure simultaneously vanish. This result is of practical importance. The oscillations depend primarily on the length of the structure and are associated with the formation of partially standing waves in the subdomain along the structure, which affect wave reflection in the main channel and wave loads on the structure. The effect of the draft and width of the structure on the oscillations is very limited. However, the draft and width of a structure has a substantial effect on the magnitude of wave reflection and transmission, especially for narrow channels. Moreover, the draft and width of a structure has a substantial effect on wave-load components. The analysis of the results indicates that it is difficult to simplify a theoretical description because, even for a channel of a constant depth and ideal vertical walls, once a structure is present in the channel, the problem needs to be described by 3D formulation, which complicates the solution. Theoretical results are in reasonable agreement with experimental data.