Abstraet--A new formulation of a pair of Boussinesq equations for three-dimensional nonlinear dispersive shallow-water waves is presented. This set of model equations permits spatial and temporal variations of the bottom topography and the presence of uniform currents. The newly derived equations are used to simulate the propagation of cnoidal waves and their interactions with a uniform current in a wave channel. The modified Euler's predictor-corrector algorithm for time advancing and a central difference representation for the space derivatives are applied to the computation of the basic equations. A set of open boundary conditions is developed to effectively transmit the cnoidal waves out of the computational domain. It is found that, as expected, the wave length decreases with an opposing current and increases with a following current. The wave height increases in magnitude with an opposing current and decreases with a following current. The Mach reflection due to oblique cnoidal waves propagating into an open channel with an opposing current is also investigated. Due to the opposing current, the wave patterns are compressed into smaller saddle-like regions in comparison with the Mach reflection without current effect.