This paper is concerned with three-dimensional water wave motion over undulated seabed. For the wave motion problem in seawater of finite depth, the fluid domain is usually unbounded horizontally but bounded vertically by free water surface and seabed which have their own boundary conditions. To study local wave motion over undulated region only, a novel Dirichlet-to-Neumann (DtN) boundary condition is suggested on an artificial circular cylindrical surface by which the fluid domain is divided into an interior region with finite volume and an exterior region. A unique solution of wave motion in the interior region is guaranteed by the novel boundary condition on the artificial cylindrical surface and the other boundary conditions on mean free water surface and undulated seabed. The solution is obtained by using Boundary Integral Equation (BIE) with all boundary conditions including the novel artificial boundary condition. Upon verification for a submerged square cylinder, the present model is extended to the case of an array of rounded-rectangular cylinders or circular paraboloidal shoals.